HEADER TRANSFERASE 18-AUG-04 1X8K TITLE CRYSTAL STRUCTURE OF RETINOL DEHYDRATASE IN COMPLEX WITH TITLE 2 ANHYDRORETINOL AND INACTIVE COFACTOR PAP COMPND MOL_ID: 1; COMPND 2 MOLECULE: RETINOL DEHYDRATASE; COMPND 3 CHAIN: A, B; COMPND 4 ENGINEERED: YES; COMPND 5 MUTATION: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: SPODOPTERA FRUGIPERDA; SOURCE 3 ORGANISM_COMMON: FALL ARMYWORM; SOURCE 4 ORGANISM_TAXID: 7108; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21(DE3); SOURCE 6 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 7 EXPRESSION_SYSTEM_STRAIN: BL21(DE3); SOURCE 8 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 9 EXPRESSION_SYSTEM_PLASMID: PET-19B KEYWDS SULFOTRANSFERASE, DEHYDRATASE, ANHYDRORETINOL, TRANSFERASE EXPDTA X-RAY DIFFRACTION AUTHOR S.PAKHOMOVA,J.BUCK,M.E.NEWCOMER REVDAT 5 23-AUG-23 1X8K 1 REMARK REVDAT 4 20-OCT-21 1X8K 1 REMARK SEQADV LINK REVDAT 3 24-AUG-11 1X8K 1 HETATM REVDAT 2 24-FEB-09 1X8K 1 VERSN REVDAT 1 08-FEB-05 1X8K 0 JRNL AUTH S.PAKHOMOVA,J.BUCK,M.E.NEWCOMER JRNL TITL THE STRUCTURES OF THE UNIQUE SULFOTRANSFERASE RETINOL JRNL TITL 2 DEHYDRATASE WITH PRODUCT AND INHIBITORS PROVIDE INSIGHT INTO JRNL TITL 3 ENZYME MECHANISM AND INHIBITION. JRNL REF PROTEIN SCI. V. 14 176 2005 JRNL REFN ISSN 0961-8368 JRNL PMID 15608121 JRNL DOI 10.1110/PS.041061105 REMARK 2 REMARK 2 RESOLUTION. 2.75 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.1.24 REMARK 3 AUTHORS : MURSHUDOV,SKUBAK,LEBEDEV,PANNU,STEINER, REMARK 3 : NICHOLLS,WINN,LONG,VAGIN REMARK 3 REMARK 3 REFINEMENT TARGET : MAXIMUM LIKELIHOOD REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.75 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 15.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 95.5 REMARK 3 NUMBER OF REFLECTIONS : 19249 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 + TEST SET) : 0.199 REMARK 3 R VALUE (WORKING SET) : 0.194 REMARK 3 FREE R VALUE : 0.255 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 8.600 REMARK 3 FREE R VALUE TEST SET COUNT : 1822 REMARK 3 REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN. REMARK 3 TOTAL NUMBER OF BINS USED : 20 REMARK 3 BIN RESOLUTION RANGE HIGH (A) : 2.75 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.82 REMARK 3 REFLECTION IN BIN (WORKING SET) : 1000 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : NULL REMARK 3 BIN R VALUE (WORKING SET) : 0.3150 REMARK 3 BIN FREE R VALUE SET COUNT : 82 REMARK 3 BIN FREE R VALUE : 0.3430 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 5696 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 102 REMARK 3 SOLVENT ATOMS : 74 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 16.68 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 0.44000 REMARK 3 B22 (A**2) : -0.86000 REMARK 3 B33 (A**2) : -0.31000 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : -1.04000 REMARK 3 B23 (A**2) : 0.00000 REMARK 3 REMARK 3 ESTIMATED OVERALL COORDINATE ERROR. REMARK 3 ESU BASED ON R VALUE (A): NULL REMARK 3 ESU BASED ON FREE R VALUE (A): 0.406 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.303 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 15.677 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.932 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.870 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 5962 ; 0.012 ; 0.022 REMARK 3 BOND LENGTHS OTHERS (A): NULL ; NULL ; NULL REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 8081 ; 1.525 ; 1.982 REMARK 3 BOND ANGLES OTHERS (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 686 ; 5.789 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): NULL ; NULL ; NULL REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 830 ; 0.103 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 4638 ; 0.006 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): 2781 ; 0.220 ; 0.200 REMARK 3 NON-BONDED CONTACTS OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION OTHERS (A): NULL ; NULL ; NULL REMARK 3 H-BOND (X...Y) REFINED ATOMS (A): 206 ; 0.151 ; 0.200 REMARK 3 H-BOND (X...Y) OTHERS (A): NULL ; NULL ; NULL REMARK 3 POTENTIAL METAL-ION REFINED ATOMS (A): 2 ; 0.051 ; 0.200 REMARK 3 POTENTIAL METAL-ION OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY VDW REFINED ATOMS (A): 55 ; 0.224 ; 0.200 REMARK 3 SYMMETRY VDW OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY H-BOND REFINED ATOMS (A): 10 ; 0.145 ; 0.200 REMARK 3 SYMMETRY H-BOND OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY METAL-ION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY METAL-ION OTHERS (A): NULL ; NULL ; NULL REMARK 3 REMARK 3 ISOTROPIC THERMAL FACTOR RESTRAINTS. COUNT RMS WEIGHT REMARK 3 MAIN-CHAIN BOND REFINED ATOMS (A**2): 3454 ; 0.398 ; 1.500 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 5573 ; 0.809 ; 2.000 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 2508 ; 1.310 ; 3.000 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 2508 ; 2.168 ; 4.500 REMARK 3 SIDE-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 LONG RANGE B REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 LONG RANGE B OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 REMARK 3 ANISOTROPIC THERMAL FACTOR RESTRAINTS. COUNT RMS WEIGHT REMARK 3 RIGID-BOND RESTRAINTS (A**2): NULL ; NULL ; NULL REMARK 3 SPHERICITY; FREE ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SPHERICITY; BONDED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 REMARK 3 NCS RESTRAINTS STATISTICS REMARK 3 NUMBER OF DIFFERENT NCS GROUPS : 1 REMARK 3 REMARK 3 NCS GROUP NUMBER : 1 REMARK 3 CHAIN NAMES : A B REMARK 3 NUMBER OF COMPONENTS NCS GROUP : 1 REMARK 3 COMPONENT C SSSEQI TO C SSSEQI CODE REMARK 3 1 A 6 A 349 4 REMARK 3 1 B 6 B 349 4 REMARK 3 GROUP CHAIN COUNT RMS WEIGHT REMARK 3 MEDIUM POSITIONAL 1 A (A): 2842 ; 0.19 ; 0.50 REMARK 3 MEDIUM THERMAL 1 A (A**2): 2842 ; 0.41 ; 2.00 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : 2 REMARK 3 REMARK 3 TLS GROUP : 1 REMARK 3 NUMBER OF COMPONENTS GROUP : 1 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : A 6 A 349 REMARK 3 ORIGIN FOR THE GROUP (A): 10.6456 -3.0414 35.6256 REMARK 3 T TENSOR REMARK 3 T11: 0.0632 T22: 0.0431 REMARK 3 T33: 0.0422 T12: -0.0059 REMARK 3 T13: -0.0162 T23: -0.0387 REMARK 3 L TENSOR REMARK 3 L11: 1.7922 L22: 1.8159 REMARK 3 L33: 1.9204 L12: 0.2496 REMARK 3 L13: -0.1956 L23: -0.7647 REMARK 3 S TENSOR REMARK 3 S11: -0.1095 S12: 0.0192 S13: 0.0481 REMARK 3 S21: -0.0347 S22: 0.0808 S23: -0.0694 REMARK 3 S31: 0.0265 S32: -0.0055 S33: 0.0287 REMARK 3 REMARK 3 TLS GROUP : 2 REMARK 3 NUMBER OF COMPONENTS GROUP : 1 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : B 6 B 349 REMARK 3 ORIGIN FOR THE GROUP (A): 54.5514 4.0861 6.9673 REMARK 3 T TENSOR REMARK 3 T11: 0.0544 T22: 0.0375 REMARK 3 T33: 0.0530 T12: -0.0324 REMARK 3 T13: 0.0000 T23: 0.0126 REMARK 3 L TENSOR REMARK 3 L11: 1.5053 L22: 1.8532 REMARK 3 L33: 1.7885 L12: -0.0189 REMARK 3 L13: 0.1992 L23: 0.2513 REMARK 3 S TENSOR REMARK 3 S11: 0.0123 S12: 0.0134 S13: -0.0854 REMARK 3 S21: -0.1195 S22: 0.0736 S23: -0.0031 REMARK 3 S31: -0.0654 S32: 0.0083 S33: -0.0859 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : BABINET MODEL WITH MASK REMARK 3 PARAMETERS FOR MASK CALCULATION REMARK 3 VDW PROBE RADIUS : 1.40 REMARK 3 ION PROBE RADIUS : 0.80 REMARK 3 SHRINKAGE RADIUS : 0.80 REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 1X8K COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 26-AUG-04. REMARK 100 THE DEPOSITION ID IS D_1000030074. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 01-JUN-00 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 6.6 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : N REMARK 200 RADIATION SOURCE : ROTATING ANODE REMARK 200 BEAMLINE : NULL REMARK 200 X-RAY GENERATOR MODEL : RIGAKU RU200 REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.5418 REMARK 200 MONOCHROMATOR : YALE MIRRORS REMARK 200 OPTICS : MIRRORS REMARK 200 REMARK 200 DETECTOR TYPE : IMAGE PLATE REMARK 200 DETECTOR MANUFACTURER : RIGAKU RAXIS IV REMARK 200 INTENSITY-INTEGRATION SOFTWARE : DENZO REMARK 200 DATA SCALING SOFTWARE : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 20545 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.750 REMARK 200 RESOLUTION RANGE LOW (A) : 100.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : -3.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 96.8 REMARK 200 DATA REDUNDANCY : 3.900 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : 0.11300 REMARK 200 FOR THE DATA SET : 7.8000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.75 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.85 REMARK 200 COMPLETENESS FOR SHELL (%) : 81.5 REMARK 200 DATA REDUNDANCY IN SHELL : 2.30 REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : 0.40400 REMARK 200 FOR SHELL : 1.900 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: CNS REMARK 200 STARTING MODEL: PDB ENTRY 1FMJ REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 52.25 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.58 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 7.5% PEG4000, 0.1M NA HEPES, 0.05M REMARK 280 CALCIUM CHLORIDE, 4% GLYCEROL, PH 6.6, VAPOR DIFFUSION, HANGING REMARK 280 DROP, TEMPERATURE 289K 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 33.33050 REMARK 290 SMTRY3 2 0.000000 0.000000 -1.000000 0.00000 REMARK 290 REMARK 290 REMARK: NULL REMARK 300 REMARK 300 BIOMOLECULE: 1 REMARK 300 SEE REMARK 350 FOR THE AUTHOR PROVIDED AND/OR PROGRAM REMARK 300 GENERATED ASSEMBLY INFORMATION FOR THE STRUCTURE IN REMARK 300 THIS ENTRY. THE REMARK MAY ALSO PROVIDE INFORMATION ON REMARK 300 BURIED SURFACE AREA. REMARK 300 REMARK: THE BIOLOGICAL ASSEMBLY IS A DIMER REMARK 350 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 AUTHOR DETERMINED BIOLOGICAL UNIT: DIMERIC REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, B 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 MET A 1 REMARK 465 GLU A 2 REMARK 465 LYS A 3 REMARK 465 GLN A 4 REMARK 465 GLN A 5 REMARK 465 GLU A 350 REMARK 465 LEU A 351 REMARK 465 MET B 1 REMARK 465 GLU B 2 REMARK 465 LYS B 3 REMARK 465 GLN B 4 REMARK 465 GLN B 5 REMARK 465 GLU B 350 REMARK 465 LEU B 351 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 ASP A 6 CG OD1 OD2 REMARK 470 LYS A 206 CG CD CE NZ REMARK 470 GLU A 326 CG CD OE1 OE2 REMARK 470 ASN A 348 CG OD1 ND2 REMARK 470 ASP B 6 CG OD1 OD2 REMARK 470 LYS B 206 CG CD CE NZ REMARK 470 GLU B 300 CG CD OE1 OE2 REMARK 470 GLU B 326 CG CD OE1 OE2 REMARK 470 ASN B 348 CG OD1 ND2 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 PROTEIN: ENGH AND HUBER, 1999 REMARK 500 EXPECTED VALUES NUCLEIC ACID: CLOWNEY ET AL 1996 REMARK 500 REMARK 500 M RES CSSEQI ATM1 ATM2 ATM3 REMARK 500 ASP A 107 CB - CG - OD2 ANGL. DEV. = 5.9 DEGREES REMARK 500 ASP A 113 CB - CG - OD2 ANGL. DEV. = 6.0 DEGREES REMARK 500 ASP A 212 CB - CG - OD2 ANGL. DEV. = 5.9 DEGREES REMARK 500 ASP A 324 CB - CG - OD2 ANGL. DEV. = 5.7 DEGREES REMARK 500 ASP B 113 CB - CG - OD2 ANGL. DEV. = 6.5 DEGREES REMARK 500 ASP B 176 CB - CG - OD2 ANGL. DEV. = 5.5 DEGREES REMARK 500 ASP B 324 CB - CG - OD2 ANGL. DEV. = 5.4 DEGREES REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: TORSION ANGLES REMARK 500 REMARK 500 TORSION ANGLES OUTSIDE THE EXPECTED RAMACHANDRAN REGIONS: REMARK 500 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 500 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT:(10X,I3,1X,A3,1X,A1,I4,A1,4X,F7.2,3X,F7.2) REMARK 500 REMARK 500 EXPECTED VALUES: GJ KLEYWEGT AND TA JONES (1996). PHI/PSI- REMARK 500 CHOLOGY: RAMACHANDRAN REVISITED. STRUCTURE 4, 1395 - 1400 REMARK 500 REMARK 500 M RES CSSEQI PSI PHI REMARK 500 LEU A 7 128.70 -14.86 REMARK 500 SER A 70 149.51 167.10 REMARK 500 ASP A 186 122.24 -39.95 REMARK 500 TYR A 202 37.82 75.56 REMARK 500 THR A 223 115.95 -39.45 REMARK 500 ASP A 254 70.63 -153.40 REMARK 500 ARG A 312 -98.68 -99.75 REMARK 500 LEU B 7 107.07 41.53 REMARK 500 GLN B 72 153.61 -45.53 REMARK 500 ASN B 88 30.32 -96.63 REMARK 500 LEU B 175 2.49 -68.22 REMARK 500 TYR B 202 34.84 70.56 REMARK 500 GLU B 272 -46.91 -27.76 REMARK 500 MET B 295 18.45 57.74 REMARK 500 ARG B 312 -94.24 -97.27 REMARK 500 ASP B 341 74.54 47.30 REMARK 500 THR B 342 143.46 173.49 REMARK 500 REMARK 500 REMARK: NULL REMARK 620 REMARK 620 METAL COORDINATION REMARK 620 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 620 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE): REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 CA A1104 CA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 GLU A 118 O REMARK 620 2 ASN A 121 OD1 84.0 REMARK 620 3 ASP A 122 OD1 91.1 89.2 REMARK 620 N 1 2 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 EMC A1103 HG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS A 318 SG REMARK 620 2 EMC A1103 C1 173.3 REMARK 620 N 1 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 CA B2204 CA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 GLU B 118 O REMARK 620 2 ASN B 121 OD1 70.9 REMARK 620 3 ASP B 122 OD1 87.8 91.6 REMARK 620 N 1 2 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 EMC B2203 HG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS B 318 SG REMARK 620 2 EMC B2203 C1 148.8 REMARK 620 N 1 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE EMC A 1103 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE EMC B 2203 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CA A 1104 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CA B 2204 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE A3P B 1101 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE A3P B 2201 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC7 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ANR A 1102 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC8 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ANR B 2202 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 1FML RELATED DB: PDB REMARK 900 THE SAME PROTEIN COMPLEXED WITH RETINOL REMARK 900 RELATED ID: 1X8J RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF RETINOL DEHYDRATASE IN COMPLEX WITH REMARK 900 ANDROSTERONE AND INACTIVE COFACTOR PAP REMARK 900 RELATED ID: 1X8L RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF RETINOL DEHYDRATASE IN COMPLEX WITH ALL-TRANS- REMARK 900 4-OXORETINOL AND INACTIVE COFACTOR PAP REMARK 999 REMARK 999 SEQUENCE AUTHOR STATES THAT THERE IS AN ERROR IN THE SEQUENCE REMARK 999 DATABASE. PHE142 IS ACTUALLY SER142. DBREF 1X8K A 1 351 UNP Q26490 Q26490_SPOFR 1 351 DBREF 1X8K B 1 351 UNP Q26490 Q26490_SPOFR 1 351 SEQADV 1X8K SER A 142 UNP Q26490 PHE 142 SEE REMARK 999 SEQADV 1X8K SER A 258 UNP Q26490 CYS 258 ENGINEERED MUTATION SEQADV 1X8K SER A 279 UNP Q26490 CYS 279 ENGINEERED MUTATION SEQADV 1X8K SER B 142 UNP Q26490 PHE 142 SEE REMARK 999 SEQADV 1X8K SER B 258 UNP Q26490 CYS 258 ENGINEERED MUTATION SEQADV 1X8K SER B 279 UNP Q26490 CYS 279 ENGINEERED MUTATION SEQRES 1 A 351 MET GLU LYS GLN GLN ASP LEU PRO PHE PRO TYR GLU PHE SEQRES 2 A 351 ARG GLU LEU ASN PRO GLU GLU ASP LYS LEU VAL LYS ALA SEQRES 3 A 351 ASN LEU GLY ALA PHE PRO THR THR TYR VAL LYS LEU GLY SEQRES 4 A 351 PRO LYS GLY TYR MET VAL TYR ARG PRO TYR LEU LYS ASP SEQRES 5 A 351 ALA ALA ASN ILE TYR ASN MET PRO LEU ARG PRO THR ASP SEQRES 6 A 351 VAL PHE VAL ALA SER TYR GLN ARG SER GLY THR THR MET SEQRES 7 A 351 THR GLN GLU LEU VAL TRP LEU ILE GLU ASN ASP LEU ASN SEQRES 8 A 351 PHE GLU ALA ALA LYS THR TYR MET SER LEU ARG TYR ILE SEQRES 9 A 351 TYR LEU ASP GLY PHE MET ILE TYR ASP PRO GLU LYS GLN SEQRES 10 A 351 GLU GLU TYR ASN ASP ILE LEU PRO ASN PRO GLU ASN LEU SEQRES 11 A 351 ASP MET GLU ARG TYR LEU GLY LEU LEU GLU TYR SER SER SEQRES 12 A 351 ARG PRO GLY SER SER LEU LEU ALA ALA VAL PRO PRO THR SEQRES 13 A 351 GLU LYS ARG PHE VAL LYS THR HIS LEU PRO LEU SER LEU SEQRES 14 A 351 MET PRO PRO ASN MET LEU ASP THR VAL LYS MET VAL TYR SEQRES 15 A 351 LEU ALA ARG ASP PRO ARG ASP VAL ALA VAL SER SER PHE SEQRES 16 A 351 HIS HIS ALA ARG LEU LEU TYR LEU LEU ASN LYS GLN SER SEQRES 17 A 351 ASN PHE LYS ASP PHE TRP GLU MET PHE HIS ARG GLY LEU SEQRES 18 A 351 TYR THR LEU THR PRO TYR PHE GLU HIS VAL LYS GLU ALA SEQRES 19 A 351 TRP ALA LYS ARG HIS ASP PRO ASN MET LEU PHE LEU PHE SEQRES 20 A 351 TYR GLU ASP TYR LEU LYS ASP LEU PRO GLY SER ILE ALA SEQRES 21 A 351 ARG ILE ALA ASP PHE LEU GLY LYS LYS LEU SER GLU GLU SEQRES 22 A 351 GLN ILE GLN ARG LEU SER GLU HIS LEU ASN PHE GLU LYS SEQRES 23 A 351 PHE LYS ASN ASN GLY ALA VAL ASN MET GLU ASP TYR ARG SEQRES 24 A 351 GLU ILE GLY ILE LEU ALA ASP GLY GLU HIS PHE ILE ARG SEQRES 25 A 351 LYS GLY LYS ALA GLY CYS TRP ARG ASP TYR PHE ASP GLU SEQRES 26 A 351 GLU MET THR LYS GLN ALA GLU LYS TRP ILE LYS ASP ASN SEQRES 27 A 351 LEU LYS ASP THR ASP LEU ARG TYR PRO ASN MET GLU LEU SEQRES 1 B 351 MET GLU LYS GLN GLN ASP LEU PRO PHE PRO TYR GLU PHE SEQRES 2 B 351 ARG GLU LEU ASN PRO GLU GLU ASP LYS LEU VAL LYS ALA SEQRES 3 B 351 ASN LEU GLY ALA PHE PRO THR THR TYR VAL LYS LEU GLY SEQRES 4 B 351 PRO LYS GLY TYR MET VAL TYR ARG PRO TYR LEU LYS ASP SEQRES 5 B 351 ALA ALA ASN ILE TYR ASN MET PRO LEU ARG PRO THR ASP SEQRES 6 B 351 VAL PHE VAL ALA SER TYR GLN ARG SER GLY THR THR MET SEQRES 7 B 351 THR GLN GLU LEU VAL TRP LEU ILE GLU ASN ASP LEU ASN SEQRES 8 B 351 PHE GLU ALA ALA LYS THR TYR MET SER LEU ARG TYR ILE SEQRES 9 B 351 TYR LEU ASP GLY PHE MET ILE TYR ASP PRO GLU LYS GLN SEQRES 10 B 351 GLU GLU TYR ASN ASP ILE LEU PRO ASN PRO GLU ASN LEU SEQRES 11 B 351 ASP MET GLU ARG TYR LEU GLY LEU LEU GLU TYR SER SER SEQRES 12 B 351 ARG PRO GLY SER SER LEU LEU ALA ALA VAL PRO PRO THR SEQRES 13 B 351 GLU LYS ARG PHE VAL LYS THR HIS LEU PRO LEU SER LEU SEQRES 14 B 351 MET PRO PRO ASN MET LEU ASP THR VAL LYS MET VAL TYR SEQRES 15 B 351 LEU ALA ARG ASP PRO ARG ASP VAL ALA VAL SER SER PHE SEQRES 16 B 351 HIS HIS ALA ARG LEU LEU TYR LEU LEU ASN LYS GLN SER SEQRES 17 B 351 ASN PHE LYS ASP PHE TRP GLU MET PHE HIS ARG GLY LEU SEQRES 18 B 351 TYR THR LEU THR PRO TYR PHE GLU HIS VAL LYS GLU ALA SEQRES 19 B 351 TRP ALA LYS ARG HIS ASP PRO ASN MET LEU PHE LEU PHE SEQRES 20 B 351 TYR GLU ASP TYR LEU LYS ASP LEU PRO GLY SER ILE ALA SEQRES 21 B 351 ARG ILE ALA ASP PHE LEU GLY LYS LYS LEU SER GLU GLU SEQRES 22 B 351 GLN ILE GLN ARG LEU SER GLU HIS LEU ASN PHE GLU LYS SEQRES 23 B 351 PHE LYS ASN ASN GLY ALA VAL ASN MET GLU ASP TYR ARG SEQRES 24 B 351 GLU ILE GLY ILE LEU ALA ASP GLY GLU HIS PHE ILE ARG SEQRES 25 B 351 LYS GLY LYS ALA GLY CYS TRP ARG ASP TYR PHE ASP GLU SEQRES 26 B 351 GLU MET THR LYS GLN ALA GLU LYS TRP ILE LYS ASP ASN SEQRES 27 B 351 LEU LYS ASP THR ASP LEU ARG TYR PRO ASN MET GLU LEU HET EMC A1103 3 HET CA A1104 1 HET ANR A1102 20 HET EMC B2203 3 HET CA B2204 1 HET A3P B1101 27 HET A3P B2201 27 HET ANR B2202 20 HETNAM EMC ETHYL MERCURY ION HETNAM CA CALCIUM ION HETNAM ANR ANHYDRORETINOL HETNAM A3P ADENOSINE-3'-5'-DIPHOSPHATE HETSYN ANR (6E)-6-[(2E,4E,6E)-3,7-DIMETHYLNONA-2,4,6,8- HETSYN 2 ANR TETRAENYLIDENE]-1,5,5-TRIMETHYLCYCLOHEXENE FORMUL 3 EMC 2(C2 H5 HG 1+) FORMUL 4 CA 2(CA 2+) FORMUL 5 ANR 2(C20 H28) FORMUL 8 A3P 2(C10 H15 N5 O10 P2) FORMUL 11 HOH *74(H2 O) HELIX 1 1 ASN A 17 GLY A 29 1 13 HELIX 2 2 PRO A 48 LYS A 51 5 4 HELIX 3 3 ASP A 52 ASN A 58 1 7 HELIX 4 4 GLY A 75 ASN A 88 1 14 HELIX 5 5 PHE A 92 THR A 97 5 6 HELIX 6 6 TYR A 98 TYR A 103 1 6 HELIX 7 7 ASP A 107 TYR A 112 5 6 HELIX 8 8 ASP A 113 LEU A 124 5 12 HELIX 9 9 ASN A 126 LEU A 130 5 5 HELIX 10 10 ASP A 131 ARG A 144 1 14 HELIX 11 11 PRO A 145 VAL A 153 1 9 HELIX 12 12 PRO A 166 MET A 170 5 5 HELIX 13 13 ASN A 173 THR A 177 5 5 HELIX 14 14 ASP A 186 TYR A 202 1 17 HELIX 15 15 ASN A 209 ARG A 219 1 11 HELIX 16 16 PRO A 226 ALA A 236 1 11 HELIX 17 17 TYR A 248 ASP A 254 1 7 HELIX 18 18 ASP A 254 LEU A 266 1 13 HELIX 19 19 SER A 271 LEU A 282 1 12 HELIX 20 20 ASN A 283 ASN A 289 1 7 HELIX 21 21 GLU A 296 GLY A 302 1 7 HELIX 22 22 GLY A 317 TYR A 322 5 6 HELIX 23 23 ASP A 324 LYS A 340 1 17 HELIX 24 24 ASN B 17 GLY B 29 1 13 HELIX 25 25 TYR B 49 MET B 59 1 11 HELIX 26 26 GLY B 75 ASN B 88 1 14 HELIX 27 27 GLU B 93 THR B 97 5 5 HELIX 28 28 TYR B 98 TYR B 103 1 6 HELIX 29 29 ASP B 107 TYR B 112 5 6 HELIX 30 30 ASP B 113 LEU B 124 5 12 HELIX 31 31 ASN B 126 LEU B 130 5 5 HELIX 32 32 ASP B 131 SER B 143 1 13 HELIX 33 33 PRO B 145 VAL B 153 1 9 HELIX 34 34 PRO B 166 MET B 170 5 5 HELIX 35 35 ASN B 173 THR B 177 5 5 HELIX 36 36 ASP B 186 LEU B 201 1 16 HELIX 37 37 ASN B 209 ARG B 219 1 11 HELIX 38 38 PRO B 226 LYS B 237 1 12 HELIX 39 39 TYR B 248 ASP B 254 1 7 HELIX 40 40 ASP B 254 LEU B 266 1 13 HELIX 41 41 SER B 271 LEU B 282 1 12 HELIX 42 42 ASN B 283 ASN B 289 1 7 HELIX 43 43 GLU B 296 GLY B 302 1 7 HELIX 44 44 GLY B 317 TYR B 322 5 6 HELIX 45 45 ASP B 324 LYS B 340 1 17 SHEET 1 A 3 PHE A 13 ARG A 14 0 SHEET 2 A 3 TYR A 35 LEU A 38 -1 O LYS A 37 N ARG A 14 SHEET 3 A 3 TYR A 43 TYR A 46 -1 O TYR A 43 N LEU A 38 SHEET 1 B 5 ILE A 104 TYR A 105 0 SHEET 2 B 5 PHE A 160 THR A 163 1 O LYS A 162 N ILE A 104 SHEET 3 B 5 VAL A 66 SER A 70 1 N VAL A 68 O VAL A 161 SHEET 4 B 5 LYS A 179 ALA A 184 1 O LYS A 179 N PHE A 67 SHEET 5 B 5 MET A 243 PHE A 247 1 O LEU A 244 N TYR A 182 SHEET 1 C 3 PHE B 13 ARG B 14 0 SHEET 2 C 3 TYR B 35 LEU B 38 -1 O LYS B 37 N ARG B 14 SHEET 3 C 3 TYR B 43 TYR B 46 -1 O TYR B 43 N LEU B 38 SHEET 1 D 5 ILE B 104 TYR B 105 0 SHEET 2 D 5 PHE B 160 THR B 163 1 O PHE B 160 N ILE B 104 SHEET 3 D 5 VAL B 66 SER B 70 1 N VAL B 68 O VAL B 161 SHEET 4 D 5 LYS B 179 ALA B 184 1 O LYS B 179 N PHE B 67 SHEET 5 D 5 MET B 243 PHE B 247 1 O LEU B 244 N TYR B 182 LINK O GLU A 118 CA CA A1104 1555 1555 2.69 LINK OD1 ASN A 121 CA CA A1104 1555 1555 2.35 LINK OD1 ASP A 122 CA CA A1104 1555 1555 2.41 LINK SG CYS A 318 HG EMC A1103 1555 1555 2.83 LINK O GLU B 118 CA CA B2204 1555 1555 2.46 LINK OD1 ASN B 121 CA CA B2204 1555 1555 2.55 LINK OD1 ASP B 122 CA CA B2204 1555 1555 2.60 LINK SG CYS B 318 HG EMC B2203 1555 1555 2.76 CISPEP 1 THR A 225 PRO A 226 0 0.16 CISPEP 2 THR B 225 PRO B 226 0 8.00 SITE 1 AC1 2 GLY A 317 CYS A 318 SITE 1 AC2 2 GLY B 317 CYS B 318 SITE 1 AC3 3 GLU A 118 ASN A 121 ASP A 122 SITE 1 AC4 3 GLU B 118 ASN B 121 ASP B 122 SITE 1 AC5 17 ARG A 73 SER A 74 GLY A 75 THR A 76 SITE 2 AC5 17 THR A 77 MET A 78 ARG A 185 SER A 193 SITE 3 AC5 17 TYR A 248 LEU A 282 PHE A 284 PHE A 287 SITE 4 AC5 17 ILE A 311 ARG A 312 LYS A 313 GLY A 314 SITE 5 AC5 17 HOH B2207 SITE 1 AC6 17 ARG B 73 SER B 74 GLY B 75 THR B 76 SITE 2 AC6 17 THR B 77 MET B 78 ARG B 185 SER B 193 SITE 3 AC6 17 TYR B 248 LEU B 282 PHE B 284 PHE B 287 SITE 4 AC6 17 ILE B 311 ARG B 312 LYS B 313 GLY B 314 SITE 5 AC6 17 HOH B2213 SITE 1 AC7 8 PHE A 31 LEU A 138 LEU A 139 LYS A 162 SITE 2 AC7 8 HIS A 164 HIS A 197 LEU A 201 PHE A 310 SITE 1 AC8 8 PHE B 31 LEU B 138 LEU B 139 LYS B 162 SITE 2 AC8 8 HIS B 164 HIS B 197 LEU B 201 PHE B 310 CRYST1 81.286 66.661 84.464 90.00 110.66 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 0.012302 0.000000 0.004639 0.00000 SCALE2 0.000000 0.015001 0.000000 0.00000 SCALE3 0.000000 0.000000 0.012653 0.00000