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HEADER SERINE HYDROLASE 11-JUL-97 1JFR
TITLE CRYSTAL STRUCTURE OF THE STREPTOMYCES EXFOLIATUS LIPASE AT
TITLE 2 1.9A RESOLUTION: A MODEL FOR A FAMILY OF PLATELET-
TITLE 3 ACTIVATING FACTOR ACETYLHYDROLASES
COMPND MOL_ID: 1;
COMPND 2 MOLECULE: LIPASE;
COMPND 3 CHAIN: A, B;
COMPND 4 ENGINEERED: YES
SOURCE MOL_ID: 1;
SOURCE 2 ORGANISM_SCIENTIFIC: STREPTOMYCES EXFOLIATUS;
SOURCE 3 EXPRESSION_SYSTEM: ESCHERICHIA COLI;
SOURCE 4 EXPRESSION_SYSTEM_GENE: STREPTOMYCES EXFOLIATUS
KEYWDS SERINE HYDROLASE, LIPASE
EXPDTA X-RAY DIFFRACTION
AUTHOR Y.WEI,Z.S.DEREWENDA
REVDAT 1 15-JUL-98 1JFR 0
JRNL AUTH Y.WEI,L.SWENSON,C.CASTRO,U.DEREWENDA,W.MINOR,
JRNL AUTH 2 H.ARAI,J.AOKI,K.INOUE,L.SERVIN-GONZALEZ,
JRNL AUTH 3 Z.S.DEREWENDA
JRNL TITL STRUCTURE OF A MICROBIAL HOMOLOGUE OF MAMMALIAN
JRNL TITL 2 PLATELET-ACTIVATING FACTOR ACETYLHYDROLASES:
JRNL TITL 3 STREPTOMYCES EXFOLIATUS LIPASE AT 1.9 A RESOLUTION
JRNL REF STRUCTURE (LONDON) V. 6 511 1998
JRNL REFN ASTM STRUE6 UK ISSN 0969-2126 2005
REMARK 1
REMARK 2
REMARK 2 RESOLUTION. 1.9 ANGSTROMS.
REMARK 3
REMARK 3 REFINEMENT.
REMARK 3 PROGRAM : REFMAC
REMARK 3 AUTHORS : MURSHUDOV,VAGIN,DODSON
REMARK 3
REMARK 3 DATA USED IN REFINEMENT.
REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.9
REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 8.0
REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.0
REMARK 3 COMPLETENESS FOR RANGE (%) : NULL
REMARK 3 NUMBER OF REFLECTIONS : 48642
REMARK 3
REMARK 3 FIT TO DATA USED IN REFINEMENT.
REMARK 3 CROSS-VALIDATION METHOD : NULL
REMARK 3 FREE R VALUE TEST SET SELECTION : NULL
REMARK 3 R VALUE (WORKING + TEST SET) : NULL
REMARK 3 R VALUE (WORKING SET) : 0.140
REMARK 3 FREE R VALUE : 0.186
REMARK 3 FREE R VALUE TEST SET SIZE (%) : NULL
REMARK 3 FREE R VALUE TEST SET COUNT : NULL
REMARK 3
REMARK 3 FIT/AGREEMENT OF MODEL WITH ALL DATA.
REMARK 3 R VALUE (WORKING + TEST SET, NO CUTOFF) : NULL
REMARK 3 R VALUE (WORKING SET, NO CUTOFF) : 0.140
REMARK 3 FREE R VALUE (NO CUTOFF) : 0.186
REMARK 3 FREE R VALUE TEST SET SIZE (%, NO CUTOFF) : NULL
REMARK 3 FREE R VALUE TEST SET COUNT (NO CUTOFF) : NULL
REMARK 3 TOTAL NUMBER OF REFLECTIONS (NO CUTOFF) : NULL
REMARK 3
REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT.
REMARK 3 PROTEIN ATOMS : 3924
REMARK 3 NUCLEIC ACID ATOMS : 0
REMARK 3 HETEROGEN ATOMS : 0
REMARK 3 SOLVENT ATOMS : 607
REMARK 3
REMARK 3 B VALUES.
REMARK 3 FROM WILSON PLOT (A**2) : NULL
REMARK 3 MEAN B VALUE (OVERALL, A**2) : NULL
REMARK 3 OVERALL ANISOTROPIC B VALUE.
REMARK 3 B11 (A**2) : NULL
REMARK 3 B22 (A**2) : NULL
REMARK 3 B33 (A**2) : NULL
REMARK 3 B12 (A**2) : NULL
REMARK 3 B13 (A**2) : NULL
REMARK 3 B23 (A**2) : NULL
REMARK 3
REMARK 3 ESTIMATED COORDINATE ERROR.
REMARK 3 ESD FROM LUZZATI PLOT (A) : 0.0159
REMARK 3 ESD FROM SIGMAA (A) : NULL
REMARK 3 LOW RESOLUTION CUTOFF (A) : NULL
REMARK 3
REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES.
REMARK 3 DISTANCE RESTRAINTS. RMS SIGMA
REMARK 3 BOND LENGTH (A) : 0.016 ; 0.020
REMARK 3 ANGLE DISTANCE (A) : 0.028 ; 0.040
REMARK 3 INTRAPLANAR 1-4 DISTANCE (A) : 0.052 ; 0.050
REMARK 3 H-BOND OR METAL COORDINATION (A) : NULL ; NULL
REMARK 3
REMARK 3 PLANE RESTRAINT (A) : NULL ; NULL
REMARK 3 CHIRAL-CENTER RESTRAINT (A**3) : NULL ; NULL
REMARK 3
REMARK 3 NON-BONDED CONTACT RESTRAINTS.
REMARK 3 SINGLE TORSION (A) : NULL ; NULL
REMARK 3 MULTIPLE TORSION (A) : NULL ; NULL
REMARK 3 H-BOND (X...Y) (A) : NULL ; NULL
REMARK 3 H-BOND (X-H...Y) (A) : NULL ; NULL
REMARK 3
REMARK 3 CONFORMATIONAL TORSION ANGLE RESTRAINTS.
REMARK 3 SPECIFIED (DEGREES) : NULL ; NULL
REMARK 3 PLANAR (DEGREES) : 9.2 ; 37.0
REMARK 3 STAGGERED (DEGREES) : 21.0 ; 15.0
REMARK 3 TRANSVERSE (DEGREES) : 18.0 ; 15.0
REMARK 3
REMARK 3 ISOTROPIC THERMAL FACTOR RESTRAINTS. RMS SIGMA
REMARK 3 MAIN-CHAIN BOND (A**2) : 2.301 ; 2.000
REMARK 3 MAIN-CHAIN ANGLE (A**2) : 3.390 ; 3.000
REMARK 3 SIDE-CHAIN BOND (A**2) : 2.846 ; 2.000
REMARK 3 SIDE-CHAIN ANGLE (A**2) : 4.216 ; 3.000
REMARK 3
REMARK 3 OTHER REFINEMENT REMARKS:
REMARK 3 X-PLOR ALSO WAS USED.
REMARK 3 FINAL RMS COORD. SHIFT 0.0114 ANGSTROMS
REMARK 3 MEAN B VALUE (MAIN-CHAIN, A**2) : 18.1
REMARK 3 MEAN B VALUE (SIDE-CHAIN, A**2) : 23.4
REMARK 4
REMARK 4 1JFR COMPLIES WITH FORMAT V. 2.2, 16-DEC-1996
REMARK 6
REMARK 6 RESIDUES 1 - 2 WERE NOT SEEN IN THE ELECTRON DENSITY.
REMARK 200
REMARK 200 EXPERIMENTAL DETAILS
REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION
REMARK 200 DATE OF DATA COLLECTION : 08-JUL-1996
REMARK 200 TEMPERATURE (KELVIN) : 293
REMARK 200 PH : 7.75
REMARK 200 NUMBER OF CRYSTALS USED : 8
REMARK 200
REMARK 200 SYNCHROTRON (Y/N) : N
REMARK 200 RADIATION SOURCE : NULL
REMARK 200 BEAMLINE : NULL
REMARK 200 X-RAY GENERATOR MODEL : NONIUS F591
REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M
REMARK 200 WAVELENGTH OR RANGE (A) : 1.54
REMARK 200 MONOCHROMATOR : NONE
REMARK 200 OPTICS : MIRRORS
REMARK 200
REMARK 200 DETECTOR TYPE : DIP2000
REMARK 200 DETECTOR MANUFACTURER : MACSCIENCE
REMARK 200 INTENSITY-INTEGRATION SOFTWARE : DENZO AND SCALEPACK
REMARK 200 DATA SCALING SOFTWARE : CCP4
REMARK 200
REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 49042
REMARK 200 RESOLUTION RANGE HIGH (A) : 1.9
REMARK 200 RESOLUTION RANGE LOW (A) : 20.
REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 0.
REMARK 200
REMARK 200 OVERALL.
REMARK 200 COMPLETENESS FOR RANGE (%) : 95.4
REMARK 200 DATA REDUNDANCY : 4.8
REMARK 200 R MERGE (I) : 0.045
REMARK 200 R SYM (I) : 0.045
REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 14.75
REMARK 200
REMARK 200 IN THE HIGHEST RESOLUTION SHELL.
REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : NULL
REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : NULL
REMARK 200 COMPLETENESS FOR SHELL (%) : NULL
REMARK 200 DATA REDUNDANCY IN SHELL : NULL
REMARK 200 R MERGE FOR SHELL (I) : NULL
REMARK 200 R SYM FOR SHELL (I) : NULL
REMARK 200 <I/SIGMA(I)> FOR SHELL : NULL
REMARK 200
REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MIR
REMARK 200 SOFTWARE USED: SHELX90, MLPHARE, CCP4
REMARK 200 STARTING MODEL: NULL
REMARK 200
REMARK 200 REMARK: NULL
REMARK 280
REMARK 280 CRYSTAL
REMARK 280 SOLVENT CONTENT, VS (%): 54.
REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.65
REMARK 280
REMARK 280 CRYSTALLIZATION CONDITIONS: NULL
REMARK 290
REMARK 290 CRYSTALLOGRAPHIC SYMMETRY
REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 1 21 1
REMARK 290
REMARK 290 SYMOP SYMMETRY
REMARK 290 NNNMMM OPERATOR
REMARK 290 1555 X,Y,Z
REMARK 290 2555 -X,Y+1/2,-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 0.00000
REMARK 290 SMTRY2 2 0.000000 1.000000 0.000000 26.49989
REMARK 290 SMTRY3 2 0.000000 0.000000 -1.000000 0.00000
REMARK 290
REMARK 290 REMARK: NULL
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 4*RMSD AND BY MORE THAN 0.150 ANGSTROMS (M=MODEL
REMARK 500 NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE
REMARK 500 NUMBER; I=INSERTION CODE).
REMARK 500
REMARK 500 STANDARD TABLE:
REMARK 500 FORMAT: (10X,I3,1X,A3,1X,A1,I4,A1,1X,2(A4,A1,3X),12X,F5.3)
REMARK 500
REMARK 500 EXPECTED VALUES: ENGH AND HUBER, 1991
REMARK 500
REMARK 500 M RES CSSEQI ATM1 RES CSSEQI ATM2 DEVIATION
REMARK 500 0 ARG A 20 CD ARG A 20 NE 0.194
REMARK 500 0 LEU A 170 CB LEU A 170 CA 0.177
REMARK 500 0 LEU A 170 CG LEU A 170 CD1 0.155
REMARK 500 0 SER A 262 CA SER A 262 C 0.351
REMARK 500 0 SER B 262 CA SER B 262 C 0.285
REMARK 850
REMARK 850 CORRECTION BEFORE RELEASE
REMARK 850 ORIGINAL DEPOSITION REVISED PRIOR TO RELEASE
REMARK 850 DATE REVISED: 25-AUG-1997 TRACKING NUMBER: T12178
REMARK 999
REMARK 999 SEQUENCE
REMARK 999 1JFR A GB 153517 1 - 50 NOT IN ATOMS LIST
REMARK 999 1JFR B GB 153517 1 - 50 NOT IN ATOMS LIST
DBREF 1JFR A 3 262 GB 153517 M86351 51 310
DBREF 1JFR B 3 262 GB 153517 M86351 51 310
SEQRES 1 A 262 ALA ALA ASN PRO TYR GLU ARG GLY PRO ALA PRO THR ASN
SEQRES 2 A 262 ALA SER ILE GLU ALA SER ARG GLY PRO TYR ALA THR SER
SEQRES 3 A 262 GLN THR SER VAL SER SER LEU VAL ALA SER GLY PHE GLY
SEQRES 4 A 262 GLY GLY THR ILE TYR TYR PRO THR SER THR ALA ASP GLY
SEQRES 5 A 262 THR PHE GLY ALA VAL VAL ILE SER PRO GLY PHE THR ALA
SEQRES 6 A 262 TYR GLN SER SER ILE ALA TRP LEU GLY PRO ARG LEU ALA
SEQRES 7 A 262 SER GLN GLY PHE VAL VAL PHE THR ILE ASP THR ASN THR
SEQRES 8 A 262 THR LEU ASP GLN PRO ASP SER ARG GLY ARG GLN LEU LEU
SEQRES 9 A 262 SER ALA LEU ASP TYR LEU THR GLN ARG SER SER VAL ARG
SEQRES 10 A 262 THR ARG VAL ASP ALA THR ARG LEU GLY VAL MET GLY HIS
SEQRES 11 A 262 SER MET GLY GLY GLY GLY SER LEU GLU ALA ALA LYS SER
SEQRES 12 A 262 ARG THR SER LEU LYS ALA ALA ILE PRO LEU THR GLY TRP
SEQRES 13 A 262 ASN THR ASP LYS THR TRP PRO GLU LEU ARG THR PRO THR
SEQRES 14 A 262 LEU VAL VAL GLY ALA ASP GLY ASP THR VAL ALA PRO VAL
SEQRES 15 A 262 ALA THR HIS SER LYS PRO PHE TYR GLU SER LEU PRO GLY
SEQRES 16 A 262 SER LEU ASP LYS ALA TYR LEU GLU LEU ARG GLY ALA SER
SEQRES 17 A 262 HIS PHE THR PRO ASN THR SER ASP THR THR ILE ALA LYS
SEQRES 18 A 262 TYR SER ILE SER TRP LEU LYS ARG PHE ILE ASP SER ASP
SEQRES 19 A 262 THR ARG TYR GLU GLN PHE LEU CYS PRO ILE PRO ARG PRO
SEQRES 20 A 262 SER LEU THR ILE ALA GLU TYR ARG GLY THR CYS PRO HIS
SEQRES 21 A 262 THR SER
SEQRES 1 B 262 ALA ALA ASN PRO TYR GLU ARG GLY PRO ALA PRO THR ASN
SEQRES 2 B 262 ALA SER ILE GLU ALA SER ARG GLY PRO TYR ALA THR SER
SEQRES 3 B 262 GLN THR SER VAL SER SER LEU VAL ALA SER GLY PHE GLY
SEQRES 4 B 262 GLY GLY THR ILE TYR TYR PRO THR SER THR ALA ASP GLY
SEQRES 5 B 262 THR PHE GLY ALA VAL VAL ILE SER PRO GLY PHE THR ALA
SEQRES 6 B 262 TYR GLN SER SER ILE ALA TRP LEU GLY PRO ARG LEU ALA
SEQRES 7 B 262 SER GLN GLY PHE VAL VAL PHE THR ILE ASP THR ASN THR
SEQRES 8 B 262 THR LEU ASP GLN PRO ASP SER ARG GLY ARG GLN LEU LEU
SEQRES 9 B 262 SER ALA LEU ASP TYR LEU THR GLN ARG SER SER VAL ARG
SEQRES 10 B 262 THR ARG VAL ASP ALA THR ARG LEU GLY VAL MET GLY HIS
SEQRES 11 B 262 SER MET GLY GLY GLY GLY SER LEU GLU ALA ALA LYS SER
SEQRES 12 B 262 ARG THR SER LEU LYS ALA ALA ILE PRO LEU THR GLY TRP
SEQRES 13 B 262 ASN THR ASP LYS THR TRP PRO GLU LEU ARG THR PRO THR
SEQRES 14 B 262 LEU VAL VAL GLY ALA ASP GLY ASP THR VAL ALA PRO VAL
SEQRES 15 B 262 ALA THR HIS SER LYS PRO PHE TYR GLU SER LEU PRO GLY
SEQRES 16 B 262 SER LEU ASP LYS ALA TYR LEU GLU LEU ARG GLY ALA SER
SEQRES 17 B 262 HIS PHE THR PRO ASN THR SER ASP THR THR ILE ALA LYS
SEQRES 18 B 262 TYR SER ILE SER TRP LEU LYS ARG PHE ILE ASP SER ASP
SEQRES 19 B 262 THR ARG TYR GLU GLN PHE LEU CYS PRO ILE PRO ARG PRO
SEQRES 20 B 262 SER LEU THR ILE ALA GLU TYR ARG GLY THR CYS PRO HIS
SEQRES 21 B 262 THR SER
FORMUL 3 HOH *612(H2 O1)
HELIX 1 1 ASN A 13 GLU A 17 1 5
HELIX 2 2 GLN A 67 SER A 69 5 3
HELIX 3 3 ALA A 71 GLN A 80 5 10
HELIX 4 4 PRO A 96 GLN A 112 1 17
HELIX 5 5 ARG A 117 ARG A 119 5 3
HELIX 6 6 SER A 131 SER A 143 5 13
HELIX 7 7 SER A 186 SER A 192 1 7
HELIX 8 8 THR A 211 ASN A 213 5 3
HELIX 9 9 THR A 217 ILE A 231 1 15
HELIX 10 10 THR A 235 PHE A 240 5 6
HELIX 11 11 ASN B 13 GLU B 17 1 5
HELIX 12 12 GLN B 67 SER B 69 5 3
HELIX 13 13 ALA B 71 GLN B 80 5 10
HELIX 14 14 PRO B 96 GLN B 112 1 17
HELIX 15 15 ARG B 117 ARG B 119 5 3
HELIX 16 16 SER B 131 SER B 143 5 13
HELIX 17 17 SER B 186 SER B 192 1 7
HELIX 18 18 THR B 211 ASN B 213 5 3
HELIX 19 19 THR B 217 ILE B 231 1 15
HELIX 20 20 THR B 235 LEU B 241 5 7
SHEET 1 A 6 THR A 25 VAL A 30 0
SHEET 2 A 6 GLY A 41 PRO A 46 -1 N TYR A 45 O SER A 26
SHEET 3 A 6 VAL A 83 ILE A 87 -1 N THR A 86 O THR A 42
SHEET 4 A 6 ALA A 56 SER A 60 1 N VAL A 57 O VAL A 83
SHEET 5 A 6 LEU A 125 HIS A 130 1 N GLY A 126 O ALA A 56
SHEET 6 A 6 ALA A 149 LEU A 153 1 N ALA A 149 O VAL A 127
SHEET 1 B 3 THR A 169 ALA A 174 0
SHEET 2 B 3 LYS A 199 LEU A 204 1 N ALA A 200 O THR A 169
SHEET 3 B 3 ILE A 251 GLY A 256 -1 N ARG A 255 O TYR A 201
SHEET 1 C 6 THR B 25 VAL B 30 0
SHEET 2 C 6 GLY B 41 PRO B 46 -1 N TYR B 45 O SER B 26
SHEET 3 C 6 VAL B 83 ILE B 87 -1 N THR B 86 O THR B 42
SHEET 4 C 6 ALA B 56 SER B 60 1 N VAL B 57 O VAL B 83
SHEET 5 C 6 LEU B 125 HIS B 130 1 N GLY B 126 O ALA B 56
SHEET 6 C 6 ALA B 149 LEU B 153 1 N ALA B 149 O VAL B 127
SHEET 1 D 3 THR B 169 ALA B 174 0
SHEET 2 D 3 LYS B 199 LEU B 204 1 N ALA B 200 O THR B 169
SHEET 3 D 3 ILE B 251 GLY B 256 -1 N ARG B 255 O TYR B 201
SSBOND 1 CYS A 242 CYS A 258
SSBOND 2 CYS B 242 CYS B 258
CISPEP 1 CYS A 242 PRO A 243 0 0.42
CISPEP 2 CYS A 258 PRO A 259 0 -4.35
CISPEP 3 CYS B 242 PRO B 243 0 -4.16
CISPEP 4 CYS B 258 PRO B 259 0 -4.70
CRYST1 77.500 53.000 81.100 90.00 95.80 90.00 P 1 21 1 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 0.012903 0.000000 0.001311 0.00000
SCALE2 0.000000 0.018868 0.000000 0.00000
SCALE3 0.000000 0.000000 0.012394 0.00000 |