HEADER OXIDOREDUCTASE 30-SEP-14 4WJI TITLE CRYSTAL STRUCTURE OF CYCLOHEXADIENYL DEHYDROGENASE FROM SINORHIZOBIUM TITLE 2 MELILOTI IN COMPLEX WITH NADP AND TYROSINE COMPND MOL_ID: 1; COMPND 2 MOLECULE: PUTATIVE CYCLOHEXADIENYL DEHYDROGENASE AND ADH PREPHENATE COMPND 3 DEHYDROGENASE; COMPND 4 CHAIN: A; COMPND 5 EC: 1.3.1.-; COMPND 6 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: RHIZOBIUM MELILOTI; SOURCE 3 ORGANISM_COMMON: ENSIFER MELILOTI, SINORHIZOBIUM MELILOTI; SOURCE 4 ORGANISM_TAXID: 266834; SOURCE 5 STRAIN: 1021; SOURCE 6 GENE: TYRC; SOURCE 7 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 8 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 9 EXPRESSION_SYSTEM_STRAIN: BL21 (DE3) RIL; SOURCE 10 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 11 EXPRESSION_SYSTEM_PLASMID: PSGC-HIS KEYWDS CYCLOHEXADIENYL DEHYDROGENASE, NADP, TYROSINE, PSI-BIOLOGY, NYSGRC, KEYWDS 2 STRUCTURAL GENOMICS, NEW YORK STRUCTURAL GENOMICS RESEARCH KEYWDS 3 CONSORTIUM, OXIDOREDUCTASE EXPDTA X-RAY DIFFRACTION AUTHOR I.G.SHABALIN,D.R.COOPER,J.HOU,M.D.ZIMMERMAN,M.STEAD,B.S.HILLERICH, AUTHOR 2 M.AHMED,J.HAMMONDS,J.BONANNO,R.SEIDEL,S.C.ALMO,W.MINOR,NEW YORK AUTHOR 3 STRUCTURAL GENOMICS RESEARCH CONSORTIUM (NYSGRC) REVDAT 5 27-DEC-23 4WJI 1 REMARK REVDAT 4 13-APR-22 4WJI 1 AUTHOR JRNL LINK REVDAT 3 27-NOV-19 4WJI 1 REMARK REVDAT 2 14-OCT-15 4WJI 1 REMARK REVDAT 1 22-OCT-14 4WJI 0 JRNL AUTH I.G.SHABALIN,D.R.COOPER,J.HOU,M.D.ZIMMERMAN,W.MINOR JRNL TITL CRYSTAL STRUCTURE OF CYCLOHEXADIENYL DEHYDROGENASE FROM JRNL TITL 2 SINORHIZOBIUM MELILOTI IN COMPLEX WITH NADP JRNL REF TO BE PUBLISHED JRNL REFN REMARK 2 REMARK 2 RESOLUTION. 1.40 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.8.0073 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) : 1.40 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 50.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 95.6 REMARK 3 NUMBER OF REFLECTIONS : 49707 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) : 0.117 REMARK 3 R VALUE (WORKING SET) : 0.115 REMARK 3 FREE R VALUE : 0.159 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.100 REMARK 3 FREE R VALUE TEST SET COUNT : 2524 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) : 1.40 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.44 REMARK 3 REFLECTION IN BIN (WORKING SET) : 3470 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 95.23 REMARK 3 BIN R VALUE (WORKING SET) : 0.2390 REMARK 3 BIN FREE R VALUE SET COUNT : 186 REMARK 3 BIN FREE R VALUE : 0.2860 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 2162 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 66 REMARK 3 SOLVENT ATOMS : 275 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 11.70 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 15.99 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 0.64000 REMARK 3 B22 (A**2) : -0.19000 REMARK 3 B33 (A**2) : -0.27000 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : -1.20000 REMARK 3 B23 (A**2) : 0.00000 REMARK 3 REMARK 3 ESTIMATED OVERALL COORDINATE ERROR. REMARK 3 ESU BASED ON R VALUE (A): 0.053 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.053 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.038 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 2.258 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.983 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.974 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 2291 ; 0.014 ; 0.019 REMARK 3 BOND LENGTHS OTHERS (A): 2173 ; 0.002 ; 0.020 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 3135 ; 1.616 ; 1.981 REMARK 3 BOND ANGLES OTHERS (DEGREES): 4977 ; 1.634 ; 3.000 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 300 ; 4.853 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 86 ;35.792 ;23.023 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 332 ;12.019 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 16 ;14.731 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 371 ; 0.108 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 2587 ; 0.008 ; 0.021 REMARK 3 GENERAL PLANES OTHERS (A): 514 ; 0.006 ; 0.020 REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): NULL ; NULL ; NULL 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): NULL ; NULL ; NULL REMARK 3 H-BOND (X...Y) OTHERS (A): NULL ; NULL ; NULL REMARK 3 POTENTIAL METAL-ION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 POTENTIAL METAL-ION OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY VDW REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY VDW OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY H-BOND REFINED ATOMS (A): NULL ; NULL ; NULL 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): 1182 ; 1.802 ; 1.269 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): 1181 ; 1.801 ; NULL REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 1476 ; 2.219 ; 1.908 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): NULL ; NULL ; NULL 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): 2287 ; 4.816 ; 3.000 REMARK 3 SPHERICITY; FREE ATOMS (A**2): 85 ;20.153 ; 0.010 REMARK 3 SPHERICITY; BONDED ATOMS (A**2): 2432 ;11.494 ; 0.010 REMARK 3 REMARK 3 NCS RESTRAINTS STATISTICS REMARK 3 NUMBER OF DIFFERENT NCS GROUPS : NULL REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : NULL REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : MASK REMARK 3 PARAMETERS FOR MASK CALCULATION REMARK 3 VDW PROBE RADIUS : 1.20 REMARK 3 ION PROBE RADIUS : 0.80 REMARK 3 SHRINKAGE RADIUS : 0.80 REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: HYDROGENS HAVE BEEN ADDED IN THE RIDING REMARK 3 POSITIONS U VALUES : REFINED INDIVIDUALLY REMARK 4 REMARK 4 4WJI COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 01-OCT-14. REMARK 100 THE DEPOSITION ID IS D_1000203931. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 20-JUN-13 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 6.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : APS REMARK 200 BEAMLINE : 21-ID-G REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.97856 REMARK 200 MONOCHROMATOR : DIAMOND [111] REMARK 200 OPTICS : BERYLLIUM LENSES REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : MARMOSAIC 300 MM CCD REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-3000 REMARK 200 DATA SCALING SOFTWARE : HKL-3000, SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 49774 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.400 REMARK 200 RESOLUTION RANGE LOW (A) : 50.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : -3.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 95.6 REMARK 200 DATA REDUNDANCY : 2.300 REMARK 200 R MERGE (I) : 0.06600 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 14.3000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.40 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.42 REMARK 200 COMPLETENESS FOR SHELL (%) : 93.4 REMARK 200 DATA REDUNDANCY IN SHELL : 1.70 REMARK 200 R MERGE FOR SHELL (I) : 0.36900 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 1.800 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: SAD REMARK 200 SOFTWARE USED: HKL-3000, SHELX, DM REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 41.88 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.12 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.2 UL OF 11 MG/ML PROTEIN IN 20 MM REMARK 280 HEPES PH 7.5, 150 MM NACL, 10% GLYCEROL, 0.1% SODIUM AZID, 0.5 REMARK 280 MM TCEP, 7MM NADP AND 20 MM TYROSINE WERE MIXED WITH 0.2 UL OF REMARK 280 THE INDEX CONDITION #83 (0.2 M MAGNESIUM CHLORIDE HEXAHYDRATE, REMARK 280 0.1 M BIS-TRIS PH 6.5, 25% W/V POLYETHYLENE GLYCOL 3,350) AND REMARK 280 EQUILIBRATED AGAINST 1.5 M NACL SOLUTION IN 96 WELL 3 DROP REMARK 280 CRYSTALLIZATION PLATE (SWISSCI). BEFORE CRYSTALLIZATION PROTEIN REMARK 280 WAS INCUBATED WITH 1/50 V/V OF 2 MG/ML CHYMOTRYPSIN SOLUTION AT REMARK 280 289 K FOR 3 HOURS, VAPOR DIFFUSION, SITTING DROP REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: C 1 2 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,Y,-Z REMARK 290 3555 X+1/2,Y+1/2,Z REMARK 290 4555 -X+1/2,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 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 3 1.000000 0.000000 0.000000 38.20450 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 34.44550 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 4 -1.000000 0.000000 0.000000 38.20450 REMARK 290 SMTRY2 4 0.000000 1.000000 0.000000 34.44550 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 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: BIOLOGICAL UNIT IS THE SAME AS ASYM. 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 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 12120 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 20680 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -143.0 KCAL/MOL 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 350 BIOMT1 2 -1.000000 0.000000 0.000000 72.54224 REMARK 350 BIOMT2 2 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT3 2 0.000000 0.000000 -1.000000 50.95048 REMARK 375 REMARK 375 SPECIAL POSITION REMARK 375 THE FOLLOWING ATOMS ARE FOUND TO BE WITHIN 0.15 ANGSTROMS REMARK 375 OF A SYMMETRY RELATED ATOM AND ARE ASSUMED TO BE ON SPECIAL REMARK 375 POSITIONS. REMARK 375 REMARK 375 ATOM RES CSSEQI REMARK 375 HOH A 504 LIES ON A SPECIAL POSITION. REMARK 375 HOH A 543 LIES ON A SPECIAL POSITION. 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 GLU A 26 CD OE1 OE2 REMARK 470 LYS A 27 CE NZ REMARK 470 LYS A 44 CE NZ REMARK 470 ARG A 54 NE CZ NH1 NH2 REMARK 470 LYS A 115 CG CD CE NZ REMARK 470 ARG A 142 NE CZ NH1 NH2 REMARK 470 LYS A 183 CD CE NZ REMARK 470 GLU A 207 CG CD OE1 OE2 REMARK 470 THR A 208 OG1 CG2 REMARK 470 GLU A 211 CG CD OE1 OE2 REMARK 470 GLU A 249 CD OE1 OE2 REMARK 470 ARG A 253 NE CZ NH1 NH2 REMARK 470 GLU A 256 CG CD OE1 OE2 REMARK 470 ASP A 271 CG OD1 OD2 REMARK 470 LYS A 272 CD CE NZ 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 MSE A 172 CG - SE - CE ANGL. DEV. = -20.1 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 ILE A 13 37.82 -142.06 REMARK 500 SER A 189 -53.02 -134.55 REMARK 500 REMARK 500 REMARK: NULL REMARK 525 REMARK 525 SOLVENT REMARK 525 REMARK 525 THE SOLVENT MOLECULES HAVE CHAIN IDENTIFIERS THAT REMARK 525 INDICATE THE POLYMER CHAIN WITH WHICH THEY ARE MOST REMARK 525 CLOSELY ASSOCIATED. THE REMARK LISTS ALL THE SOLVENT REMARK 525 MOLECULES WHICH ARE MORE THAN 5A AWAY FROM THE REMARK 525 NEAREST POLYMER CHAIN (M = MODEL NUMBER; REMARK 525 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE REMARK 525 NUMBER; I=INSERTION CODE): REMARK 525 REMARK 525 M RES CSSEQI REMARK 525 HOH A 555 DISTANCE = 6.94 ANGSTROMS REMARK 525 HOH A 598 DISTANCE = 5.82 ANGSTROMS 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 MG A 305 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP A 257 OD1 REMARK 620 2 HOH A 404 O 83.7 REMARK 620 3 HOH A 455 O 88.2 88.7 REMARK 620 4 HOH A 479 O 90.0 91.4 178.2 REMARK 620 5 HOH A 482 O 94.1 175.7 95.0 84.9 REMARK 620 6 HOH A 535 O 174.7 92.9 87.7 94.1 89.6 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MG A 303 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HOH A 587 O REMARK 620 2 HOH A 611 O 72.0 REMARK 620 3 HOH A 635 O 167.7 96.5 REMARK 620 4 HOH A 648 O 85.0 156.2 106.9 REMARK 620 5 HOH A 662 O 81.0 78.2 101.3 92.5 REMARK 620 N 1 2 3 4 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MG A 304 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HOH A 613 O REMARK 620 2 HOH A 616 O 109.9 REMARK 620 3 HOH A 634 O 164.6 85.4 REMARK 620 4 HOH A 636 O 89.7 90.8 88.5 REMARK 620 5 HOH A 649 O 82.2 164.6 82.4 79.6 REMARK 620 6 HOH A 651 O 94.6 90.0 86.8 175.1 98.6 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MG A 306 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HOH A 603 O REMARK 620 2 HOH A 623 O 90.9 REMARK 620 3 HOH A 629 O 81.2 94.8 REMARK 620 4 HOH A 652 O 83.2 174.1 84.1 REMARK 620 5 HOH A 653 O 177.5 87.2 100.6 98.6 REMARK 620 6 HOH A 674 O 75.1 90.7 155.8 88.0 103.2 REMARK 620 N 1 2 3 4 5 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue NAP A 301 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue TYR A 302 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue MG A 303 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue MG A 304 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue MG A 305 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue MG A 306 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC7 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue CL A 307 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: NYSGRC-022551 RELATED DB: TARGETTRACK REMARK 999 REMARK 999 SEQUENCE REMARK 999 THE PROTEIN WAS SUBJECTED TO LIMITED PROTEOLYSIS BY CHYMOTRYPSIN REMARK 999 RIGHT BEFORE CRYSTALLIZATION. SUPPOSINGLY THE HIS-TAG AND C- REMARK 999 TERMINAL FRAGMENT WERE CLEAVED ON ONE OF THE POSSIBLE SITES. THE REMARK 999 MAIN SUBSTRATES OF CHYMOTRYPSIN INCLUDE TRYPTOPHAN, TYROSINE, REMARK 999 PHENYLALANINE, LEUCINE, AND METHIONINE, WHICH ARE CLEAVED AT THE REMARK 999 CARBOXYL TERMINAL. DBREF 4WJI A 2 294 UNP Q92MG1 Q92MG1_RHIME 2 294 SEQRES 1 A 293 ALA GLN GLN PHE GLN THR ILE ALA LEU ILE GLY ILE GLY SEQRES 2 A 293 LEU ILE GLY SER SER ILE ALA ARG ASP ILE ARG GLU LYS SEQRES 3 A 293 GLN LEU ALA GLY THR ILE VAL VAL THR THR ARG SER GLU SEQRES 4 A 293 ALA THR LEU LYS ARG ALA GLY GLU LEU GLY LEU GLY ASP SEQRES 5 A 293 ARG TYR THR LEU SER ALA ALA GLU ALA VAL GLU GLY ALA SEQRES 6 A 293 ASP LEU VAL VAL VAL SER VAL PRO VAL GLY ALA SER GLY SEQRES 7 A 293 ALA VAL ALA ALA GLU ILE ALA ALA HIS LEU LYS PRO GLY SEQRES 8 A 293 ALA ILE VAL THR ASP VAL GLY SER THR LYS GLY SER VAL SEQRES 9 A 293 ILE ALA GLN MSE ALA PRO HIS LEU PRO LYS ASP VAL HIS SEQRES 10 A 293 PHE VAL PRO GLY HIS PRO ILE ALA GLY THR GLU HIS SER SEQRES 11 A 293 GLY PRO ASP ALA GLY PHE ALA GLY LEU PHE ARG GLY ARG SEQRES 12 A 293 TRP CYS ILE LEU THR PRO PRO ALA GLY THR ASP GLU GLU SEQRES 13 A 293 ALA VAL ALA ARG LEU ARG LEU PHE TRP GLU THR LEU GLY SEQRES 14 A 293 SER MSE VAL ASP GLU MSE ASP PRO LYS HIS HIS ASP LYS SEQRES 15 A 293 VAL LEU ALA ILE VAL SER HIS LEU PRO HIS ILE ILE ALA SEQRES 16 A 293 TYR ASN ILE VAL GLY THR ALA ASP ASP LEU GLU THR VAL SEQRES 17 A 293 THR GLU SER GLU VAL ILE LYS TYR SER ALA SER GLY PHE SEQRES 18 A 293 ARG ASP PHE THR ARG LEU ALA ALA SER ASP PRO THR MSE SEQRES 19 A 293 TRP ARG ASP VAL CYS LEU HIS ASN LYS ASP ALA ILE LEU SEQRES 20 A 293 GLU MSE LEU ALA ARG PHE SER GLU ASP LEU ALA SER LEU SEQRES 21 A 293 GLN ARG ALA ILE ARG TRP GLY ASP GLY ASP LYS LEU PHE SEQRES 22 A 293 ASP LEU PHE THR ARG THR ARG ALA ILE ARG ARG SER ILE SEQRES 23 A 293 VAL GLN ALA GLY GLN ASP THR MODRES 4WJI MSE A 109 MET MODIFIED RESIDUE MODRES 4WJI MSE A 172 MET MODIFIED RESIDUE MODRES 4WJI MSE A 176 MET MODIFIED RESIDUE MODRES 4WJI MSE A 235 MET MODIFIED RESIDUE MODRES 4WJI MSE A 250 MET MODIFIED RESIDUE HET MSE A 109 8 HET MSE A 172 8 HET MSE A 176 8 HET MSE A 235 8 HET MSE A 250 8 HET NAP A 301 48 HET TYR A 302 13 HET MG A 303 1 HET MG A 304 1 HET MG A 305 1 HET MG A 306 1 HET CL A 307 1 HETNAM MSE SELENOMETHIONINE HETNAM NAP NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE HETNAM TYR TYROSINE HETNAM MG MAGNESIUM ION HETNAM CL CHLORIDE ION HETSYN NAP 2'-MONOPHOSPHOADENOSINE 5'-DIPHOSPHORIBOSE FORMUL 1 MSE 5(C5 H11 N O2 SE) FORMUL 2 NAP C21 H28 N7 O17 P3 FORMUL 3 TYR C9 H11 N O3 FORMUL 4 MG 4(MG 2+) FORMUL 8 CL CL 1- FORMUL 9 HOH *275(H2 O) HELIX 1 AA1 GLY A 14 GLN A 28 1 15 HELIX 2 AA2 SER A 39 GLY A 50 1 12 HELIX 3 AA3 SER A 58 VAL A 63 1 6 HELIX 4 AA4 PRO A 74 GLY A 76 5 3 HELIX 5 AA5 ALA A 77 ALA A 86 1 10 HELIX 6 AA6 ALA A 87 LEU A 89 5 3 HELIX 7 AA7 LYS A 102 ALA A 110 1 9 HELIX 8 AA8 GLY A 132 GLY A 136 5 5 HELIX 9 AA9 ASP A 155 LEU A 169 1 15 HELIX 10 AB1 ASP A 177 SER A 189 1 13 HELIX 11 AB2 SER A 189 ASP A 205 1 17 HELIX 12 AB3 THR A 210 TYR A 217 1 8 HELIX 13 AB4 SER A 218 SER A 220 5 3 HELIX 14 AB5 GLY A 221 ALA A 229 1 9 HELIX 15 AB6 ASP A 232 ASN A 243 1 12 HELIX 16 AB7 ASN A 243 TRP A 267 1 25 HELIX 17 AB8 ASP A 269 THR A 280 1 12 HELIX 18 AB9 THR A 280 GLY A 291 1 12 SHEET 1 AA1 6 ARG A 54 THR A 56 0 SHEET 2 AA1 6 ALA A 30 THR A 36 1 N VAL A 35 O ARG A 54 SHEET 3 AA1 6 PHE A 5 ILE A 11 1 N LEU A 10 O VAL A 34 SHEET 4 AA1 6 LEU A 68 VAL A 71 1 O VAL A 70 N ALA A 9 SHEET 5 AA1 6 ILE A 94 ASP A 97 1 O THR A 96 N VAL A 69 SHEET 6 AA1 6 HIS A 118 PHE A 119 1 O HIS A 118 N VAL A 95 SHEET 1 AA2 3 GLY A 122 PRO A 124 0 SHEET 2 AA2 3 TRP A 145 LEU A 148 -1 O ILE A 147 N HIS A 123 SHEET 3 AA2 3 MSE A 172 GLU A 175 1 O ASP A 174 N LEU A 148 LINK C GLN A 108 N MSE A 109 1555 1555 1.34 LINK C MSE A 109 N ALA A 110 1555 1555 1.33 LINK C SER A 171 N MSE A 172 1555 1555 1.32 LINK C MSE A 172 N VAL A 173 1555 1555 1.32 LINK C GLU A 175 N MSE A 176 1555 1555 1.32 LINK C MSE A 176 N ASP A 177 1555 1555 1.32 LINK C THR A 234 N MSE A 235 1555 1555 1.34 LINK C MSE A 235 N TRP A 236 1555 1555 1.35 LINK C GLU A 249 N MSE A 250 1555 1555 1.32 LINK C MSE A 250 N LEU A 251 1555 1555 1.35 LINK OD1 ASP A 257 MG MG A 305 1555 1555 2.01 LINK MG MG A 303 O HOH A 587 1555 1555 2.34 LINK MG MG A 303 O HOH A 611 1555 1555 2.43 LINK MG MG A 303 O HOH A 635 1555 1555 1.93 LINK MG MG A 303 O HOH A 648 1555 1555 2.20 LINK MG MG A 303 O HOH A 662 1555 1555 1.99 LINK MG MG A 304 O HOH A 613 1555 1555 2.00 LINK MG MG A 304 O HOH A 616 1555 1555 2.11 LINK MG MG A 304 O HOH A 634 1555 1555 1.90 LINK MG MG A 304 O HOH A 636 1555 1555 2.24 LINK MG MG A 304 O HOH A 649 1555 1555 2.12 LINK MG MG A 304 O HOH A 651 1555 1555 2.04 LINK MG MG A 305 O HOH A 404 1555 1555 2.01 LINK MG MG A 305 O HOH A 455 1555 1555 2.02 LINK MG MG A 305 O HOH A 479 1555 1555 2.16 LINK MG MG A 305 O HOH A 482 1555 1555 2.02 LINK MG MG A 305 O HOH A 535 1555 1555 2.02 LINK MG MG A 306 O HOH A 603 1555 1555 2.27 LINK MG MG A 306 O HOH A 623 1555 1555 2.09 LINK MG MG A 306 O HOH A 629 1555 1555 2.33 LINK MG MG A 306 O HOH A 652 1555 1555 2.10 LINK MG MG A 306 O HOH A 653 1555 1555 2.31 LINK MG MG A 306 O HOH A 674 1555 1555 1.97 SITE 1 AC1 37 GLY A 12 ILE A 13 GLY A 14 LEU A 15 SITE 2 AC1 37 ILE A 16 THR A 37 ARG A 38 SER A 39 SITE 3 AC1 37 THR A 42 SER A 72 VAL A 73 PRO A 74 SITE 4 AC1 37 VAL A 75 ALA A 77 VAL A 98 GLY A 99 SITE 5 AC1 37 SER A 100 PRO A 124 ALA A 126 GLY A 127 SITE 6 AC1 37 THR A 128 SER A 131 GLY A 132 MSE A 235 SITE 7 AC1 37 TYR A 302 HOH A 418 HOH A 547 HOH A 549 SITE 8 AC1 37 HOH A 565 HOH A 575 HOH A 579 HOH A 580 SITE 9 AC1 37 HOH A 592 HOH A 597 HOH A 632 HOH A 654 SITE 10 AC1 37 HOH A 655 SITE 1 AC2 14 SER A 100 HIS A 123 GLY A 127 THR A 128 SITE 2 AC2 14 GLU A 129 ALA A 219 SER A 220 ARG A 227 SITE 3 AC2 14 MSE A 235 NAP A 301 HOH A 437 HOH A 438 SITE 4 AC2 14 HOH A 445 HOH A 562 SITE 1 AC3 6 HIS A 88 HOH A 587 HOH A 611 HOH A 635 SITE 2 AC3 6 HOH A 648 HOH A 662 SITE 1 AC4 6 HOH A 613 HOH A 616 HOH A 634 HOH A 636 SITE 2 AC4 6 HOH A 649 HOH A 651 SITE 1 AC5 6 ASP A 257 HOH A 404 HOH A 455 HOH A 479 SITE 2 AC5 6 HOH A 482 HOH A 535 SITE 1 AC6 6 HOH A 603 HOH A 623 HOH A 629 HOH A 652 SITE 2 AC6 6 HOH A 653 HOH A 674 SITE 1 AC7 3 GLN A 6 ASP A 67 ARG A 161 CRYST1 76.409 68.891 51.097 90.00 94.34 90.00 C 1 2 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 0.013087 0.000000 0.000994 0.00000 SCALE2 0.000000 0.014516 0.000000 0.00000 SCALE3 0.000000 0.000000 0.019627 0.00000