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HEADER HYDROLYTIC ENZYME 14-MAR-96 1DIN
TITLE DIENELACTONE HYDROLASE AT 2.8 ANGSTROMS
COMPND MOL_ID: 1;
COMPND 2 MOLECULE: DIENELACTONE HYDROLASE;
COMPND 3 CHAIN: NULL;
COMPND 4 SYNONYM: DLH;
COMPND 5 EC: 3.1.1.45;
COMPND 6 ENGINEERED: YES
SOURCE MOL_ID: 1;
SOURCE 2 ORGANISM_SCIENTIFIC: PSEUDOMONAS SP.;
SOURCE 3 STRAIN: B13;
SOURCE 4 EXPRESSION_SYSTEM: EXPRESSED UNDER OWN PROMOTER;
SOURCE 5 EXPRESSION_SYSTEM_PLASMID: PDC100;
SOURCE 6 EXPRESSION_SYSTEM_GENE: CLC D
KEYWDS DIENELACTONE HYDROLASE, AROMATIC HYDROCARBON CATABOLISM,
KEYWDS 2 SERINE ESTERASE, CARBOXYMETHYLENEBUTENOLIDASE,
KEYWDS 3 HYDROLYTIC ENZYME
EXPDTA X-RAY DIFFRACTION
AUTHOR D.L.OLLIS,D.PATHAK
REVDAT 1 17-AUG-96 1DIN 0
JRNL AUTH D.PATHAK,D.OLLIS
JRNL TITL REFINED STRUCTURE OF DIENELACTONE HYDROLASE AT 1.8
JRNL TITL 2 A
JRNL REF J.MOL.BIOL. V. 214 497 1990
JRNL REFN ASTM JMOBAK UK ISSN 0022-2836 0070
REMARK 1
REMARK 1 REFERENCE 1
REMARK 1 AUTH D.PATHAK,K.L.NGAI,D.OLLIS
REMARK 1 TITL X-RAY CRYSTALLOGRAPHIC STRUCTURE OF DIENELACTONE
REMARK 1 TITL 2 HYDROLASE AT 2.8 A
REMARK 1 REF J.MOL.BIOL. V. 204 435 1988
REMARK 1 REFN ASTM JMOBAK UK ISSN 0022-2836 0070
REMARK 1 REFERENCE 2
REMARK 1 AUTH D.L.OLLIS,K.L.NGAI
REMARK 1 TITL CRYSTALLIZATION AND PRELIMINARY X-RAY
REMARK 1 TITL 2 CRYSTALLOGRAPHIC DATA OF DIENELACTONE HYDROLASE
REMARK 1 TITL 3 FROM PSEUDOMONAS SP. B13
REMARK 1 REF J.BIOL.CHEM. V. 260 9818 1985
REMARK 1 REFN ASTM JBCHA3 US ISSN 0021-9258 0071
REMARK 2
REMARK 2 RESOLUTION. 1.8 ANGSTROMS.
REMARK 3
REMARK 3 REFINEMENT.
REMARK 3 PROGRAM : PROLSQ
REMARK 3 AUTHORS : KONNERT,HENDRICKSON
REMARK 3
REMARK 3 DATA USED IN REFINEMENT.
REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.8
REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 10.
REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.0
REMARK 3 COMPLETENESS FOR RANGE (%) : 95.
REMARK 3 NUMBER OF REFLECTIONS : 23835
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) : 0.150
REMARK 3 FREE R VALUE : NULL
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) : NULL
REMARK 3 FREE R VALUE (NO CUTOFF) : NULL
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 : 1780
REMARK 3 NUCLEIC ACID ATOMS : 0
REMARK 3 HETEROGEN ATOMS : 0
REMARK 3 SOLVENT ATOMS : 279
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) : 0.15
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) : 0.014 ; 0.010
REMARK 3 ANGLE DISTANCE (A) : NULL ; NULL
REMARK 3 INTRAPLANAR 1-4 DISTANCE (A) : NULL ; NULL
REMARK 3 H-BOND OR METAL COORDINATION (A) : NULL ; NULL
REMARK 3
REMARK 3 PLANE RESTRAINT (A) : 0.013 ; 0.020
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) : NULL ; NULL
REMARK 3 STAGGERED (DEGREES) : NULL ; NULL
REMARK 3 TRANSVERSE (DEGREES) : NULL ; NULL
REMARK 3
REMARK 3 ISOTROPIC THERMAL FACTOR RESTRAINTS. RMS SIGMA
REMARK 3 MAIN-CHAIN BOND (A**2) : NULL ; NULL
REMARK 3 MAIN-CHAIN ANGLE (A**2) : NULL ; NULL
REMARK 3 SIDE-CHAIN BOND (A**2) : NULL ; NULL
REMARK 3 SIDE-CHAIN ANGLE (A**2) : NULL ; NULL
REMARK 3
REMARK 3 OTHER REFINEMENT REMARKS:
REMARK 3 TNT BY TRONRUD, TEN EYCK, MATTHEWS ALSO WAS USED.
REMARK 3 BOND ANGLES 3.4(3.00)
REMARK 4
REMARK 4 1DIN COMPLIES WITH FORMAT V. 2.0, 16-FEB-1996
REMARK 6
REMARK 6 THERE IS MICROHETEROGENEITY AT RESIDUE 123. ONE OF THE
REMARK 6 RESIDUES IS CYSTEINE AND THE OTHER IS OXIDIZED CYSTEINE
REMARK 6 WHICH IS PRESENTED AS RESIDUE CSD. ONLY CSD IS LISTED ON
REMARK 6 THE SEQRES RECORDS BELOW; BOTH CYS AND CSD ARE LISTED ON
REMARK 6 SEQADV RECORDS. COORDINATES ARE PRESENTED FOR CYS AND
REMARK 6 CSD.
REMARK 200
REMARK 200 EXPERIMENTAL DETAILS
REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION
REMARK 200 DATE OF DATA COLLECTION : 1987
REMARK 200 TEMPERATURE (KELVIN) : NULL
REMARK 200 PH : NULL
REMARK 200 NUMBER OF CRYSTALS USED : NULL
REMARK 200
REMARK 200 SYNCHROTRON (Y/N) : N
REMARK 200 RADIATION SOURCE : NULL
REMARK 200 BEAMLINE : NULL
REMARK 200 X-RAY GENERATOR MODEL : NULL
REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M
REMARK 200 WAVELENGTH OR RANGE (A) : 1.5418
REMARK 200 MONOCHROMATOR : NULL
REMARK 200 OPTICS : NULL
REMARK 200
REMARK 200 DETECTOR TYPE : NICOLET
REMARK 200 DETECTOR MANUFACTURER : NULL
REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XENGEN
REMARK 200 DATA SCALING SOFTWARE : NULL
REMARK 200
REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 29488
REMARK 200 RESOLUTION RANGE HIGH (A) : NULL
REMARK 200 RESOLUTION RANGE LOW (A) : NULL
REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL
REMARK 200
REMARK 200 OVERALL.
REMARK 200 COMPLETENESS FOR RANGE (%) : 95.
REMARK 200 DATA REDUNDANCY : 6.
REMARK 200 R MERGE (I) : 0.057
REMARK 200 R SYM (I) : NULL
REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : NULL
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: NULL
REMARK 200 SOFTWARE USED: NULL
REMARK 200 STARTING MODEL: NULL
REMARK 200
REMARK 200 REMARK: NULL
REMARK 280
REMARK 280 CRYSTAL
REMARK 280 SOLVENT CONTENT, VS (%): NULL
REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): NULL
REMARK 280
REMARK 280 CRYSTALLIZATION CONDITIONS: NULL
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 24.44988
REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000
REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 39.12057
REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000
REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 35.72449
REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 39.12057
REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 24.44988
REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 35.72449
REMARK 290 SMTRY3 4 0.000000 0.000000 -1.000000 0.00000
REMARK 290
REMARK 290 REMARK: NULL
REMARK 470
REMARK 470 MISSING ATOM
REMARK 470 THE FOLLOWING RESIDUES HAVE MISSING ATOMS (M=MODEL NUMBER;
REMARK 470 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER;
REMARK 470 I=INSERTION CODE):
REMARK 470 M RES CSSEQI ATOMS
REMARK 470 SER 233 O
REMARK 500
REMARK 500 GEOMETRY AND STEREOCHEMISTRY
REMARK 500 SUBTOPIC: CLOSE CONTACTS
REMARK 500
REMARK 500 THE FOLLOWING ATOMS THAT ARE RELATED BY CRYSTALLOGRAPHIC
REMARK 500 SYMMETRY ARE IN CLOSE CONTACT. SOME OF THESE MAY BE ATOMS
REMARK 500 LOCATED ON SPECIAL POSITIONS IN THE CELL.
REMARK 500
REMARK 500 DISTANCE CUTOFF: 2.2 ANGSTROMS
REMARK 500
REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI SSYMOP DISTANCE
REMARK 500 O HOH 509 O HOH 481 2665 1.63
REMARK 999
REMARK 999 SEQUENCE
REMARK 999 1DIN SWS P11453 234 - 236 NOT IN ATOMS LIST
REMARK 999
REMARK 999 THE ORIGINAL SEQUENCE WAS INCORRECT AT POSITION 79. THE
REMARK 999 CORRECT SEQUENCE IS REPORTED IN CHEAH, E., AUSTIN, C.,
REMARK 999 ASHLEY, G., OLLIS, D., PROTEIN ENGINEERING, VOL 6,
REMARK 999 PAGES 575-583 (1993).
DBREF 1DIN 1 233 SWS P11453 CLCD_PSEPU 1 233
SEQADV 1DIN CSD 123 SWS P11453 CYS 123 CONFLICT
SEQADV 1DIN CYS 123 SWS P11453 CYS 123 MICROHETEROGENEITY
SEQADV 1DIN ASN 154 SWS P11453 LYS 154 CONFLICT
SEQADV 1DIN THR 224 SWS P11453 ARG 224 CONFLICT
SEQRES 1 236 MET LEU THR GLU GLY ILE SER ILE GLN SER TYR ASP GLY
SEQRES 2 236 HIS THR PHE GLY ALA LEU VAL GLY SER PRO ALA LYS ALA
SEQRES 3 236 PRO ALA PRO VAL ILE VAL ILE ALA GLN GLU ILE PHE GLY
SEQRES 4 236 VAL ASN ALA PHE MET ARG GLU THR VAL SER TRP LEU VAL
SEQRES 5 236 ASP GLN GLY TYR ALA ALA VAL CYS PRO ASP LEU TYR ALA
SEQRES 6 236 ARG GLN ALA PRO GLY THR ALA LEU ASP PRO GLN ASP GLU
SEQRES 7 236 ARG GLN ARG GLU GLN ALA TYR LYS LEU TRP GLN ALA PHE
SEQRES 8 236 ASP MET GLU ALA GLY VAL GLY ASP LEU GLU ALA ALA ILE
SEQRES 9 236 ARG TYR ALA ARG HIS GLN PRO TYR SER ASN GLY LYS VAL
SEQRES 10 236 GLY LEU VAL GLY TYR CSD LEU GLY GLY ALA LEU ALA PHE
SEQRES 11 236 LEU VAL ALA ALA LYS GLY TYR VAL ASP ARG ALA VAL GLY
SEQRES 12 236 TYR TYR GLY VAL GLY LEU GLU LYS GLN LEU ASN LYS VAL
SEQRES 13 236 PRO GLU VAL LYS HIS PRO ALA LEU PHE HIS MET GLY GLY
SEQRES 14 236 GLN ASP HIS PHE VAL PRO ALA PRO SER ARG GLN LEU ILE
SEQRES 15 236 THR GLU GLY PHE GLY ALA ASN PRO LEU LEU GLN VAL HIS
SEQRES 16 236 TRP TYR GLU GLU ALA GLY HIS SER PHE ALA ARG THR SER
SEQRES 17 236 SER SER GLY TYR VAL ALA SER ALA ALA ALA LEU ALA ASN
SEQRES 18 236 GLU ARG THR LEU ASP PHE LEU ALA PRO LEU GLN SER LYS
SEQRES 19 236 LYS PRO
MODRES 1DIN CSD 123 CYS MODIFIED CYSTEINE
HET CSD 123 8
HETNAM CSD 3-SULFINOALANINE
HETSYN CSD S-CYSTEINESULFINIC ACID; S-SULFINOCYSTEINE
FORMUL 1 CSD C3 H7 N1 O4 S1
FORMUL 2 HOH *279(H2 O1)
HELIX 1 2 LEU 63 ALA 68 5 6
HELIX 2 3 GLU 78 GLN 89 1 12
HELIX 3 4 MET 93 HIS 109 1 17
HELIX 4 5 GLY 125 LYS 135 1 11
HELIX 5 6 LEU 149 GLU 158 5 10
HELIX 6 7 ALA 176 ALA 188 1 13
HELIX 7 8 ALA 214 LEU 231 1 18
SHEET 1 A 7 ALA 18 GLY 21 0
SHEET 2 A 7 ALA 57 PRO 61 -1 N CYS 60 O LEU 19
SHEET 3 A 7 VAL 30 ALA 34 1 N ILE 31 O ALA 57
SHEET 4 A 7 VAL 117 GLY 121 1 N GLY 118 O VAL 30
SHEET 5 A 7 ARG 140 TYR 144 1 N ARG 140 O LEU 119
SHEET 6 A 7 ALA 163 GLY 168 1 N LEU 164 O ALA 141
SHEET 7 A 7 LEU 192 TYR 197 1 N GLN 193 O ALA 163
LINK N CSD 123 C TYR 122
LINK C CSD 123 N LEU 124
CISPEP 1 ALA 26 PRO 27 0 -1.55
CRYST1 48.900 71.450 78.240 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 0.020450 0.000000 0.000000 0.00000
SCALE2 0.000000 0.013996 0.000000 0.00000
SCALE3 0.000000 0.000000 0.012781 0.00000 |