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HEADER HYDROLASE 05-JUL-01 1JJF
TITLE STRUCTURAL BASIS FOR THE SUBSTRATE SPECIFICITY OF THE
TITLE 2 FERULOYL ESTERASE DOMAIN OF THE CELLULOSOMAL XYLANASE Z OF
TITLE 3 CLOSTRIDIUM THERMOCELLUM
COMPND MOL_ID: 1;
COMPND 2 MOLECULE: ENDO-1,4-BETA-XYLANASE Z;
COMPND 3 CHAIN: A;
COMPND 4 FRAGMENT: RESIDUES 20-287;
COMPND 5 SYNONYM: FERULOYL ESTERASE; XYLANASE Z; 1,4-BETA-D-XYLAN
COMPND 6 XYLANOHYDROLASE Z;
COMPND 7 EC: 3.2.1.8;
COMPND 8 ENGINEERED: YES
SOURCE MOL_ID: 1;
SOURCE 2 ORGANISM_SCIENTIFIC: CLOSTRIDIUM THERMOCELLUM;
SOURCE 3 ORGANISM_COMMON: BACTERIA;
SOURCE 4 GENE: XYNZ;
SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI;
SOURCE 6 EXPRESSION_SYSTEM_COMMON: BACTERIA;
SOURCE 7 EXPRESSION_SYSTEM_STRAIN: BL21;
SOURCE 8 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID;
SOURCE 9 EXPRESSION_SYSTEM_PLASMID: PET21B
KEYWDS FERULOYL ESTERASE, FERULIC ACID ESTERASE, FAE_XYNZ, XYNZ
EXPDTA X-RAY DIFFRACTION
AUTHOR F.D.SCHUBOT,I.A.KATAEVA,D.L.BLUM,A.K.SHAH,L.G.LJUNGDAHL,
AUTHOR 2 J.P.ROSE,B.-C.WANG
REVDAT 1 31-OCT-01 1JJF 0
JRNL AUTH F.D.SCHUBOT,I.A.KATAEVA,D.L.BLUM,A.K.SHAH,
JRNL AUTH 2 L.G.LJUNGDAHL,J.P.ROSE,B.-C.WANG
JRNL TITL STRUCTURAL BASIS FOR THE SUBSTRATE SPECIFICITY OF
JRNL TITL 2 THE FERULOYL ESTERASE DOMAIN OF THE CELLULOSOMAL
JRNL TITL 3 XYLANASE Z FROM CLOSTRIDIUM THERMOCELLUM
JRNL REF BIOCHEMISTRY V. 40 12524 2001
JRNL REFN ASTM BICHAW US ISSN 0006-2960
REMARK 1
REMARK 2
REMARK 2 RESOLUTION. 1.75 ANGSTROMS.
REMARK 3
REMARK 3 REFINEMENT.
REMARK 3 PROGRAM : CNS 1.0
REMARK 3 AUTHORS : BRUNGER,ADAMS,CLORE,DELANO,GROS,GROSSE-
REMARK 3 : KUNSTLEVE,JIANG,KUSZEWSKI,NILGES, PANNU,
REMARK 3 : READ,RICE,SIMONSON,WARREN
REMARK 3
REMARK 3 REFINEMENT TARGET : ENGH & HUBER
REMARK 3
REMARK 3 DATA USED IN REFINEMENT.
REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.75
REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 19.03
REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000
REMARK 3 OUTLIER CUTOFF HIGH (RMS(ABS(F))) : NULL
REMARK 3 COMPLETENESS (WORKING+TEST) (%) : 95.8
REMARK 3 NUMBER OF REFLECTIONS : 21940
REMARK 3
REMARK 3
REMARK 3 FIT TO DATA USED IN REFINEMENT.
REMARK 3 CROSS-VALIDATION METHOD : THROUGHOUT
REMARK 3 FREE R VALUE TEST SET SELECTION : RANDOM
REMARK 3 R VALUE (WORKING SET) : 0.189
REMARK 3 FREE R VALUE : 0.206
REMARK 3 FREE R VALUE TEST SET SIZE (%) : 10.000
REMARK 3 FREE R VALUE TEST SET COUNT : 2186
REMARK 3 ESTIMATED ERROR OF FREE R VALUE : 0.004
REMARK 3
REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN.
REMARK 3 TOTAL NUMBER OF BINS USED : 6
REMARK 3 BIN RESOLUTION RANGE HIGH (A) : 1.75
REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.86
REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 87.80
REMARK 3 REFLECTIONS IN BIN (WORKING SET) : 2951
REMARK 3 BIN R VALUE (WORKING SET) : 0.2510
REMARK 3 BIN FREE R VALUE : 0.2650
REMARK 3 BIN FREE R VALUE TEST SET SIZE (%) : 10.40
REMARK 3 BIN FREE R VALUE TEST SET COUNT : 341
REMARK 3 ESTIMATED ERROR OF BIN FREE R VALUE : 0.014
REMARK 3
REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT.
REMARK 3 PROTEIN ATOMS : 1968
REMARK 3 NUCLEIC ACID ATOMS : 0
REMARK 3 HETEROGEN ATOMS : 1
REMARK 3 SOLVENT ATOMS : 281
REMARK 3
REMARK 3 B VALUES.
REMARK 3 FROM WILSON PLOT (A**2) : 14.10
REMARK 3 MEAN B VALUE (OVERALL, A**2) : 18.60
REMARK 3 OVERALL ANISOTROPIC B VALUE.
REMARK 3 B11 (A**2) : -0.06000
REMARK 3 B22 (A**2) : 1.87000
REMARK 3 B33 (A**2) : -1.81000
REMARK 3 B12 (A**2) : 0.00000
REMARK 3 B13 (A**2) : 0.00000
REMARK 3 B23 (A**2) : 0.00000
REMARK 3
REMARK 3 ESTIMATED COORDINATE ERROR.
REMARK 3 ESD FROM LUZZATI PLOT (A) : 0.18
REMARK 3 ESD FROM SIGMAA (A) : 0.16
REMARK 3 LOW RESOLUTION CUTOFF (A) : 5.00
REMARK 3
REMARK 3 CROSS-VALIDATED ESTIMATED COORDINATE ERROR.
REMARK 3 ESD FROM C-V LUZZATI PLOT (A) : 0.20
REMARK 3 ESD FROM C-V SIGMAA (A) : 0.16
REMARK 3
REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES.
REMARK 3 BOND LENGTHS (A) : 0.005
REMARK 3 BOND ANGLES (DEGREES) : 1.20
REMARK 3 DIHEDRAL ANGLES (DEGREES) : 24.30
REMARK 3 IMPROPER ANGLES (DEGREES) : 0.86
REMARK 3
REMARK 3 ISOTROPIC THERMAL MODEL : RESTRAINED
REMARK 3
REMARK 3 ISOTROPIC THERMAL FACTOR RESTRAINTS. RMS SIGMA
REMARK 3 MAIN-CHAIN BOND (A**2) : 1.67 ; 1.500
REMARK 3 MAIN-CHAIN ANGLE (A**2) : 2.35 ; 2.000
REMARK 3 SIDE-CHAIN BOND (A**2) : 2.56 ; 2.000
REMARK 3 SIDE-CHAIN ANGLE (A**2) : 3.46 ; 2.500
REMARK 3
REMARK 3
REMARK 3 BULK SOLVENT MODELING.
REMARK 3 METHOD USED : FLAT MODEL
REMARK 3 KSOL : 0.42
REMARK 3 BSOL : 79.68
REMARK 3
REMARK 3 NCS MODEL : NULL
REMARK 3
REMARK 3 NCS RESTRAINTS. RMS SIGMA/WEIGHT
REMARK 3 GROUP 1 POSITIONAL (A) : NULL ; NULL
REMARK 3 GROUP 1 B-FACTOR (A**2) : NULL ; NULL
REMARK 3
REMARK 3 PARAMETER FILE 1 : PROTEIN_REP.PARAM
REMARK 3 PARAMETER FILE 2 : ION.PARAM
REMARK 3 PARAMETER FILE 3 : WATER_REP.PARAM
REMARK 3 TOPOLOGY FILE 1 : PROTEIN.TOP
REMARK 3 TOPOLOGY FILE 2 : ION.TOP
REMARK 3 TOPOLOGY FILE 3 : WATER_REP.TOP
REMARK 3
REMARK 3 OTHER REFINEMENT REMARKS: NULL
REMARK 4
REMARK 4 1JJF COMPLIES WITH FORMAT V. 2.3, 09-JULY-1998
REMARK 100
REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 19-JUL-2001.
REMARK 100 THE RCSB ID CODE IS RCSB013842.
REMARK 200
REMARK 200 EXPERIMENTAL DETAILS
REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION
REMARK 200 DATE OF DATA COLLECTION : 21-NOV-1999
REMARK 200 TEMPERATURE (KELVIN) : 100.0
REMARK 200 PH : 4.60
REMARK 200 NUMBER OF CRYSTALS USED : 1
REMARK 200
REMARK 200 SYNCHROTRON (Y/N) : Y
REMARK 200 RADIATION SOURCE : APS
REMARK 200 BEAMLINE : 17ID
REMARK 200 X-RAY GENERATOR MODEL : NULL
REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M
REMARK 200 WAVELENGTH OR RANGE (A) : 1.0
REMARK 200 MONOCHROMATOR : SI 111 CHANNEL
REMARK 200 OPTICS : NULL
REMARK 200
REMARK 200 DETECTOR TYPE : CCD
REMARK 200 DETECTOR MANUFACTURER : MARRESEARCH
REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL2000
REMARK 200 DATA SCALING SOFTWARE : SCALEPACK
REMARK 200
REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 21940
REMARK 200 RESOLUTION RANGE HIGH (A) : 1.750
REMARK 200 RESOLUTION RANGE LOW (A) : 20.000
REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 0.000
REMARK 200
REMARK 200 OVERALL.
REMARK 200 COMPLETENESS FOR RANGE (%) : 95.3
REMARK 200 DATA REDUNDANCY : 5.000
REMARK 200 R MERGE (I) : 0.07000
REMARK 200 R SYM (I) : 0.07000
REMARK 200 FOR THE DATA SET : 23.3000
REMARK 200
REMARK 200 IN THE HIGHEST RESOLUTION SHELL.
REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.75
REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.80
REMARK 200 COMPLETENESS FOR SHELL (%) : 83.4
REMARK 200 DATA REDUNDANCY IN SHELL : 3.20
REMARK 200 R MERGE FOR SHELL (I) : 0.33000
REMARK 200 R SYM FOR SHELL (I) : 0.33000
REMARK 200 FOR SHELL : 2.500
REMARK 200
REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH
REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MIRAS
REMARK 200 SOFTWARE USED: SOLOMON
REMARK 200 STARTING MODEL: NULL
REMARK 200
REMARK 200 REMARK: NULL
REMARK 280
REMARK 280 CRYSTAL
REMARK 280 SOLVENT CONTENT, VS (%): 35.0
REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 1.90
REMARK 280
REMARK 280 CRYSTALLIZATION CONDITIONS: PEGMME2000, AMMONIUM SULFATE,
REMARK 280 SODIUM ACETATE, GLYCEROL
REMARK 290
REMARK 290 CRYSTALLOGRAPHIC SYMMETRY
REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 21 21 21
REMARK 290
REMARK 290 SYMOP SYMMETRY
REMARK 290 NNNMMM OPERATOR
REMARK 290 1555 X,Y,Z
REMARK 290 2555 1/2-X,-Y,1/2+Z
REMARK 290 3555 -X,1/2+Y,1/2-Z
REMARK 290 4555 1/2+X,1/2-Y,-Z
REMARK 290
REMARK 290 WHERE NNN -> OPERATOR NUMBER
REMARK 290 MMM -> TRANSLATION VECTOR
REMARK 290
REMARK 290 CRYSTALLOGRAPHIC SYMMETRY TRANSFORMATIONS
REMARK 290 THE FOLLOWING TRANSFORMATIONS OPERATE ON THE ATOM/HETATM
REMARK 290 RECORDS IN THIS ENTRY TO PRODUCE CRYSTALLOGRAPHICALLY
REMARK 290 RELATED MOLECULES.
REMARK 290 SMTRY1 1 1.000000 0.000000 0.000000 0.00000
REMARK 290 SMTRY2 1 0.000000 1.000000 0.000000 0.00000
REMARK 290 SMTRY3 1 0.000000 0.000000 1.000000 0.00000
REMARK 290 SMTRY1 2 -1.000000 0.000000 0.000000 21.64650
REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000
REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 39.88850
REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000
REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 31.82600
REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 39.88850
REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 21.64650
REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 31.82600
REMARK 290 SMTRY3 4 0.000000 0.000000 -1.000000 0.00000
REMARK 290
REMARK 290 REMARK: NULL
REMARK 300
REMARK 300 BIOMOLECULE: 1
REMARK 300 THIS ENTRY CONTAINS THE CRYSTALLOGRAPHIC ASYMMETRIC UNIT
REMARK 300 WHICH CONSISTS OF 1 CHAIN(S). SEE REMARK 350 FOR
REMARK 300 INFORMATION ON GENERATING THE BIOLOGICAL MOLECULE(S).
REMARK 350
REMARK 350 GENERATING THE BIOMOLECULE
REMARK 350 COORDINATES FOR A COMPLETE MULTIMER REPRESENTING THE KNOWN
REMARK 350 BIOLOGICALLY SIGNIFICANT OLIGOMERIZATION STATE OF THE
REMARK 350 MOLECULE CAN BE GENERATED BY APPLYING BIOMT TRANSFORMATIONS
REMARK 350 GIVEN BELOW. BOTH NON-CRYSTALLOGRAPHIC AND
REMARK 350 CRYSTALLOGRAPHIC OPERATIONS ARE GIVEN.
REMARK 350
REMARK 350 BIOMOLECULE: 1
REMARK 350 APPLY THE FOLLOWING TO CHAINS: A
REMARK 350 BIOMT1 1 1.000000 0.000000 0.000000 0.00000
REMARK 350 BIOMT2 1 0.000000 1.000000 0.000000 0.00000
REMARK 350 BIOMT3 1 0.000000 0.000000 1.000000 0.00000
REMARK 465
REMARK 465 MISSING RESIDUES
REMARK 465 THE FOLLOWING RESIDUES WERE NOT LOCATED IN THE
REMARK 465 EXPERIMENT. (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN
REMARK 465 IDENTIFIER; SSSEQ=SEQUENCE NUMBER; I=INSERTION CODE.)
REMARK 465
REMARK 465 M RES C SSSEQI
REMARK 465 LEU A 20
REMARK 465 VAL A 21
REMARK 465 THR A 22
REMARK 465 ILE A 23
REMARK 465 SER A 24
REMARK 465 SER A 25
REMARK 465 THR A 26
REMARK 465 SER A 27
REMARK 465 ALA A 28
REMARK 465 ALA A 29
REMARK 465 GLY A 285
REMARK 465 ASN A 286
REMARK 465 THR A 287
REMARK 500
REMARK 500 GEOMETRY AND STEREOCHEMISTRY
REMARK 500 SUBTOPIC: COVALENT BOND LENGTHS
REMARK 500
REMARK 500 THE STEREOCHEMICAL PARAMETERS OF THE FOLLOWING RESIDUES
REMARK 500 HAVE VALUES WHICH DEVIATE FROM EXPECTED VALUES BY MORE
REMARK 500 THAN 6*RMSD (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN
REMARK 500 IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE).
REMARK 500
REMARK 500 STANDARD TABLE:
REMARK 500 FORMAT: (10X,I3,1X,2(A3,1X,A1,I4,A1,1X,A4,3X),F6.3)
REMARK 500
REMARK 500 EXPECTED VALUES: ENGH AND HUBER, 1991
REMARK 500
REMARK 500 M RES CSSEQI ATM1 RES CSSEQI ATM2 DEVIATION
REMARK 500 PRO A 125 CG PRO A 125 CB 0.038
REMARK 500 PRO A 194 CG PRO A 194 CB 0.032
REMARK 500 MET A 275 CE MET A 275 SD -0.042
REMARK 500
REMARK 500 GEOMETRY AND STEREOCHEMISTRY
REMARK 500 SUBTOPIC: COVALENT BOND ANGLES
REMARK 500
REMARK 500 THE STEREOCHEMICAL PARAMETERS OF THE FOLLOWING RESIDUES
REMARK 500 HAVE VALUES WHICH DEVIATE FROM EXPECTED VALUES BY MORE
REMARK 500 THAN 6*RMSD (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN
REMARK 500 IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE).
REMARK 500
REMARK 500 STANDARD TABLE:
REMARK 500 FORMAT: (10X,I3,1X,A3,1X,A1,I4,A1,3(1X,A4,2X),12X,F5.1)
REMARK 500
REMARK 500 EXPECTED VALUES: ENGH AND HUBER, 1991
REMARK 500
REMARK 500 M RES CSSEQI ATM1 ATM2 ATM3
REMARK 500 SER A 82 N - CA - C ANGL. DEV. = -7.5 DEGREES
REMARK 500 TYR A 85 N - CA - C ANGL. DEV. = -7.7 DEGREES
REMARK 500 ASN A 126 N - CA - C ANGL. DEV. =-11.8 DEGREES
REMARK 500 THR A 127 N - CA - C ANGL. DEV. = 8.6 DEGREES
REMARK 500 TYR A 160 N - CA - C ANGL. DEV. = -7.2 DEGREES
REMARK 500 LEU A 222 N - CA - C ANGL. DEV. = -9.8 DEGREES
DBREF 1JJF A 20 287 SWS P10478 XYNZ_CLOTM 20 287
SEQRES 1 A 268 LEU VAL THR ILE SER SER THR SER ALA ALA SER LEU PRO
SEQRES 2 A 268 THR MET PRO PRO SER GLY TYR ASP GLN VAL ARG ASN GLY
SEQRES 3 A 268 VAL PRO ARG GLY GLN VAL VAL ASN ILE SER TYR PHE SER
SEQRES 4 A 268 THR ALA THR ASN SER THR ARG PRO ALA ARG VAL TYR LEU
SEQRES 5 A 268 PRO PRO GLY TYR SER LYS ASP LYS LYS TYR SER VAL LEU
SEQRES 6 A 268 TYR LEU LEU HIS GLY ILE GLY GLY SER GLU ASN ASP TRP
SEQRES 7 A 268 PHE GLU GLY GLY GLY ARG ALA ASN VAL ILE ALA ASP ASN
SEQRES 8 A 268 LEU ILE ALA GLU GLY LYS ILE LYS PRO LEU ILE ILE VAL
SEQRES 9 A 268 THR PRO ASN THR ASN ALA ALA GLY PRO GLY ILE ALA ASP
SEQRES 10 A 268 GLY TYR GLU ASN PHE THR LYS ASP LEU LEU ASN SER LEU
SEQRES 11 A 268 ILE PRO TYR ILE GLU SER ASN TYR SER VAL TYR THR ASP
SEQRES 12 A 268 ARG GLU HIS ARG ALA ILE ALA GLY LEU SER MET GLY GLY
SEQRES 13 A 268 GLY GLN SER PHE ASN ILE GLY LEU THR ASN LEU ASP LYS
SEQRES 14 A 268 PHE ALA TYR ILE GLY PRO ILE SER ALA ALA PRO ASN THR
SEQRES 15 A 268 TYR PRO ASN GLU ARG LEU PHE PRO ASP GLY GLY LYS ALA
SEQRES 16 A 268 ALA ARG GLU LYS LEU LYS LEU LEU PHE ILE ALA CYS GLY
SEQRES 17 A 268 THR ASN ASP SER LEU ILE GLY PHE GLY GLN ARG VAL HIS
SEQRES 18 A 268 GLU TYR CYS VAL ALA ASN ASN ILE ASN HIS VAL TYR TRP
SEQRES 19 A 268 LEU ILE GLN GLY GLY GLY HIS ASP PHE ASN VAL TRP LYS
SEQRES 20 A 268 PRO GLY LEU TRP ASN PHE LEU GLN MET ALA ASP GLU ALA
SEQRES 21 A 268 GLY LEU THR ARG ASP GLY ASN THR
HET PT 285 1
HETNAM PT PLATINUM (II) ION
FORMUL 2 PT PT1 2+
FORMUL 3 HOH *281(H2 O1)
HELIX 1 1 ARG A 103 GLU A 114 1 12
HELIX 2 2 ASP A 136 SER A 148 1 13
HELIX 3 3 SER A 148 TYR A 157 1 10
HELIX 4 4 ASP A 162 GLU A 164 5 3
HELIX 5 5 SER A 172 THR A 184 1 13
HELIX 6 6 PRO A 203 PHE A 208 1 6
HELIX 7 7 GLY A 212 LEU A 219 1 8
HELIX 8 8 LEU A 232 ASN A 246 1 15
HELIX 9 9 ASP A 261 GLY A 280 1 20
SHEET 1 A 8 GLN A 50 SER A 58 0
SHEET 2 A 8 SER A 63 LEU A 71 -1 O SER A 63 N SER A 58
SHEET 3 A 8 ILE A 121 PRO A 125 -1 O ILE A 122 N TYR A 70
SHEET 4 A 8 VAL A 83 LEU A 87 1 O LEU A 84 N VAL A 123
SHEET 5 A 8 ARG A 166 LEU A 171 1 O ALA A 167 N TYR A 85
SHEET 6 A 8 TYR A 191 ILE A 195 1 O TYR A 191 N ILE A 168
SHEET 7 A 8 LEU A 221 GLY A 227 1 O LEU A 221 N ILE A 192
SHEET 8 A 8 VAL A 251 ILE A 255 1 O VAL A 251 N ILE A 224
CISPEP 1 LEU A 31 PRO A 32 0 0.07
CRYST1 43.293 63.652 79.777 90.00 90.00 90.00 P 21 21 21 4
ORIGX1 1.000000 0.000000 0.000000 0.00000
ORIGX2 0.000000 1.000000 0.000000 0.00000
ORIGX3 0.000000 0.000000 1.000000 0.00000
SCALE1 0.023098 0.000000 0.000000 0.00000
SCALE2 0.000000 0.015710 0.000000 0.00000
SCALE3 0.000000 0.000000 0.012535 0.00000
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