HEADER ISOMERASE 17-MAR-10 3M8C TITLE CRYSTAL STRUCTURE OF KETOSTEROID ISOMERASE D99N FROM PSEUDOMONAS TITLE 2 TESTOSTERONI (TKSI) WITH EQUILENIN BOUND COMPND MOL_ID: 1; COMPND 2 MOLECULE: STEROID DELTA-ISOMERASE; COMPND 3 CHAIN: A, B, C, D; COMPND 4 SYNONYM: DELTA(5)-3-KETOSTEROID ISOMERASE; COMPND 5 EC: 5.3.3.1; COMPND 6 ENGINEERED: YES; COMPND 7 MUTATION: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: COMAMONAS TESTOSTERONI; SOURCE 3 ORGANISM_COMMON: PSEUDOMONAS TESTOSTERONI; SOURCE 4 ORGANISM_TAXID: 285; SOURCE 5 GENE: KSI; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 8 EXPRESSION_SYSTEM_STRAIN: BL21; SOURCE 9 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 10 EXPRESSION_SYSTEM_PLASMID: PKK KEYWDS ISOMERASE, LIPID METABOLISM, STEROID METABOLISM EXPDTA X-RAY DIFFRACTION AUTHOR A.GONZALEZ,Y.TSAI,J.SCHWANS,F.SUNDEN,D.HERSCHLAG REVDAT 3 06-SEP-23 3M8C 1 REMARK REVDAT 2 06-OCT-21 3M8C 1 REMARK SEQADV REVDAT 1 14-APR-10 3M8C 0 JRNL AUTH J.SCHWANS,F.SUNDEN,A.GONZALEZ,Y.TSAI,D.HERSCHLAG JRNL TITL CRYSTAL STRUCTURE OF KETOSTEROID ISOMERASE D99N FROM JRNL TITL 2 PSEUDOMONAS TESTOSTERONI (TKSI) WITH EQUILENIN BOUND JRNL REF TO BE PUBLISHED JRNL REFN REMARK 2 REMARK 2 RESOLUTION. 2.10 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.5.0106 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) : 2.10 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 84.36 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.2 REMARK 3 NUMBER OF REFLECTIONS : 37837 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) : 0.169 REMARK 3 R VALUE (WORKING SET) : 0.166 REMARK 3 FREE R VALUE : 0.222 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT : 1895 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) : 2.10 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.15 REMARK 3 REFLECTION IN BIN (WORKING SET) : 2348 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 89.48 REMARK 3 BIN R VALUE (WORKING SET) : 0.2380 REMARK 3 BIN FREE R VALUE SET COUNT : 118 REMARK 3 BIN FREE R VALUE : 0.3260 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 3756 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 137 REMARK 3 SOLVENT ATOMS : 466 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 24.50 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 26.74 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 1.02000 REMARK 3 B22 (A**2) : 1.02000 REMARK 3 B33 (A**2) : -1.53000 REMARK 3 B12 (A**2) : 0.51000 REMARK 3 B13 (A**2) : 0.00000 REMARK 3 B23 (A**2) : 0.00000 REMARK 3 REMARK 3 ESTIMATED OVERALL COORDINATE ERROR. REMARK 3 ESU BASED ON R VALUE (A): 0.186 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.172 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.111 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 4.127 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.958 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.928 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 4335 ; 0.023 ; 0.022 REMARK 3 BOND LENGTHS OTHERS (A): NULL ; NULL ; NULL REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 5945 ; 1.989 ; 1.976 REMARK 3 BOND ANGLES OTHERS (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 565 ; 6.551 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 204 ;34.228 ;23.529 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 662 ;15.560 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 38 ;20.810 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 642 ; 0.146 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 3429 ; 0.010 ; 0.021 REMARK 3 GENERAL PLANES OTHERS (A): NULL ; NULL ; NULL 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): 2697 ; 1.170 ; 1.500 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 4355 ; 2.018 ; 2.000 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 1638 ; 3.223 ; 3.000 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 1590 ; 4.845 ; 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 : 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 : 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: U VALUES : REFINED INDIVIDUALLY REMARK 4 REMARK 4 3M8C COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 18-MAR-10. REMARK 100 THE DEPOSITION ID IS D_1000058235. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 16-JAN-10; 06-JAN-10 REMARK 200 TEMPERATURE (KELVIN) : 100; 100 REMARK 200 PH : 7.2 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y; Y REMARK 200 RADIATION SOURCE : SSRL; SSRL REMARK 200 BEAMLINE : BL9-1; BL9-2 REMARK 200 X-RAY GENERATOR MODEL : NULL; NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : NULL; NULL REMARK 200 WAVELENGTH OR RANGE (A) : 0.98; 0.98 REMARK 200 MONOCHROMATOR : SI SINGLE CRYSTAL; SI DOUBLE REMARK 200 CRYSTAL REMARK 200 OPTICS : NULL; NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL; CCD REMARK 200 DETECTOR MANUFACTURER : DECTRIS PILATUS 6M; MARMOSAIC REMARK 200 325 MM CCD REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : SCALA REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 38027 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.100 REMARK 200 RESOLUTION RANGE LOW (A) : 33.630 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 0.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.2 REMARK 200 DATA REDUNDANCY : 11.70 REMARK 200 R MERGE (I) : 0.09400 REMARK 200 R SYM (I) : NULL REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 20.6000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.10 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.21 REMARK 200 COMPLETENESS FOR SHELL (%) : 94.8 REMARK 200 DATA REDUNDANCY IN SHELL : 8.10 REMARK 200 R MERGE FOR SHELL (I) : 0.41600 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 <I/SIGMA(I)> FOR SHELL : 4.900 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH; SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: MOLREP REMARK 200 STARTING MODEL: 8CHO REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 56.33 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.82 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 1.4 M AMMONIUM SULFATE, 40 MM REMARK 280 POTASSIUM PHOSPHATE, 1 MM EDTA, 2 MM DTT, PH 7.2, SITTING DROP, REMARK 280 TEMPERATURE 298K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 61 2 2 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -Y,X-Y,Z+1/3 REMARK 290 3555 -X+Y,-X,Z+2/3 REMARK 290 4555 -X,-Y,Z+1/2 REMARK 290 5555 Y,-X+Y,Z+5/6 REMARK 290 6555 X-Y,X,Z+1/6 REMARK 290 7555 Y,X,-Z+1/3 REMARK 290 8555 X-Y,-Y,-Z REMARK 290 9555 -X,-X+Y,-Z+2/3 REMARK 290 10555 -Y,-X,-Z+5/6 REMARK 290 11555 -X+Y,Y,-Z+1/2 REMARK 290 12555 X,X-Y,-Z+1/6 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 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 2 0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 168.72467 REMARK 290 SMTRY1 3 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 3 -0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 337.44933 REMARK 290 SMTRY1 4 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 253.08700 REMARK 290 SMTRY1 5 0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 5 -0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 5 0.000000 0.000000 1.000000 421.81167 REMARK 290 SMTRY1 6 0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 6 0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 6 0.000000 0.000000 1.000000 84.36233 REMARK 290 SMTRY1 7 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 7 0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 168.72467 REMARK 290 SMTRY1 8 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 8 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 8 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 9 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 9 -0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 9 0.000000 0.000000 -1.000000 337.44933 REMARK 290 SMTRY1 10 0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 10 -0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 10 0.000000 0.000000 -1.000000 421.81167 REMARK 290 SMTRY1 11 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 11 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 11 0.000000 0.000000 -1.000000 253.08700 REMARK 290 SMTRY1 12 0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 12 0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 12 0.000000 0.000000 -1.000000 84.36233 REMARK 290 REMARK 290 REMARK: NULL REMARK 300 REMARK 300 BIOMOLECULE: 1, 2 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 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: 4110 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 12080 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -70.0 KCAL/MOL 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 350 REMARK 350 BIOMOLECULE: 2 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: 3930 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 12010 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -57.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: C, D 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 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 B 377 LIES ON A SPECIAL POSITION. REMARK 375 HOH C 559 LIES ON A SPECIAL POSITION. 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 ALA A 125 REMARK 465 ALA B 125 REMARK 465 ALA C 125 REMARK 465 ALA D 125 REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CLOSE CONTACTS IN SAME ASYMMETRIC UNIT REMARK 500 REMARK 500 THE FOLLOWING ATOMS ARE IN CLOSE CONTACT. REMARK 500 REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI DISTANCE REMARK 500 O ALA C 75 O HOH C 384 2.01 REMARK 500 N GLY A 105 O3 SO4 A 130 2.17 REMARK 500 REMARK 500 REMARK: NULL 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 ARG C 52 NE - CZ - NH1 ANGL. DEV. = 3.3 DEGREES REMARK 500 PRO D 44 C - N - CA ANGL. DEV. = 11.2 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 ALA A 75 -126.16 54.16 REMARK 500 ASP B 38 109.93 -160.70 REMARK 500 ALA B 75 -121.58 58.62 REMARK 500 ALA C 75 -120.39 52.00 REMARK 500 ALA D 75 -121.09 54.32 REMARK 500 REMARK 500 REMARK: NULL REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE GOL A 126 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE GOL A 127 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SO4 A 128 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SO4 A 129 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SO4 A 130 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SO4 B 126 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC7 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SO4 B 127 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC8 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SO4 B 128 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC9 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SO4 B 129 REMARK 800 REMARK 800 SITE_IDENTIFIER: BC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE EQU B 130 REMARK 800 REMARK 800 SITE_IDENTIFIER: BC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SO4 C 126 REMARK 800 REMARK 800 SITE_IDENTIFIER: BC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SO4 C 127 REMARK 800 REMARK 800 SITE_IDENTIFIER: BC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SO4 C 128 REMARK 800 REMARK 800 SITE_IDENTIFIER: BC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE EQU C 129 REMARK 800 REMARK 800 SITE_IDENTIFIER: BC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SO4 D 126 REMARK 800 REMARK 800 SITE_IDENTIFIER: BC7 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SO4 D 127 REMARK 800 REMARK 800 SITE_IDENTIFIER: BC8 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SO4 D 128 REMARK 800 REMARK 800 SITE_IDENTIFIER: BC9 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE EQU D 129 DBREF 3M8C A 1 125 UNP P00947 SDIS_COMTE 1 125 DBREF 3M8C B 1 125 UNP P00947 SDIS_COMTE 1 125 DBREF 3M8C C 1 125 UNP P00947 SDIS_COMTE 1 125 DBREF 3M8C D 1 125 UNP P00947 SDIS_COMTE 1 125 SEQADV 3M8C ASN A 99 UNP P00947 ASP 99 ENGINEERED MUTATION SEQADV 3M8C ASN B 99 UNP P00947 ASP 99 ENGINEERED MUTATION SEQADV 3M8C ASN C 99 UNP P00947 ASP 99 ENGINEERED MUTATION SEQADV 3M8C ASN D 99 UNP P00947 ASP 99 ENGINEERED MUTATION SEQRES 1 A 125 MET ASN THR PRO GLU HIS MET THR ALA VAL VAL GLN ARG SEQRES 2 A 125 TYR VAL ALA ALA LEU ASN ALA GLY ASP LEU ASP GLY ILE SEQRES 3 A 125 VAL ALA LEU PHE ALA ASP ASP ALA THR VAL GLU ASP PRO SEQRES 4 A 125 VAL GLY SER GLU PRO ARG SER GLY THR ALA ALA ILE ARG SEQRES 5 A 125 GLU PHE TYR ALA ASN SER LEU LYS LEU PRO LEU ALA VAL SEQRES 6 A 125 GLU LEU THR GLN GLU VAL ARG ALA VAL ALA ASN GLU ALA SEQRES 7 A 125 ALA PHE ALA PHE THR VAL SER PHE GLU TYR GLN GLY ARG SEQRES 8 A 125 LYS THR VAL VAL ALA PRO ILE ASN HIS PHE ARG PHE ASN SEQRES 9 A 125 GLY ALA GLY LYS VAL VAL SER MET ARG ALA LEU PHE GLY SEQRES 10 A 125 GLU LYS ASN ILE HIS ALA GLY ALA SEQRES 1 B 125 MET ASN THR PRO GLU HIS MET THR ALA VAL VAL GLN ARG SEQRES 2 B 125 TYR VAL ALA ALA LEU ASN ALA GLY ASP LEU ASP GLY ILE SEQRES 3 B 125 VAL ALA LEU PHE ALA ASP ASP ALA THR VAL GLU ASP PRO SEQRES 4 B 125 VAL GLY SER GLU PRO ARG SER GLY THR ALA ALA ILE ARG SEQRES 5 B 125 GLU PHE TYR ALA ASN SER LEU LYS LEU PRO LEU ALA VAL SEQRES 6 B 125 GLU LEU THR GLN GLU VAL ARG ALA VAL ALA ASN GLU ALA SEQRES 7 B 125 ALA PHE ALA PHE THR VAL SER PHE GLU TYR GLN GLY ARG SEQRES 8 B 125 LYS THR VAL VAL ALA PRO ILE ASN HIS PHE ARG PHE ASN SEQRES 9 B 125 GLY ALA GLY LYS VAL VAL SER MET ARG ALA LEU PHE GLY SEQRES 10 B 125 GLU LYS ASN ILE HIS ALA GLY ALA SEQRES 1 C 125 MET ASN THR PRO GLU HIS MET THR ALA VAL VAL GLN ARG SEQRES 2 C 125 TYR VAL ALA ALA LEU ASN ALA GLY ASP LEU ASP GLY ILE SEQRES 3 C 125 VAL ALA LEU PHE ALA ASP ASP ALA THR VAL GLU ASP PRO SEQRES 4 C 125 VAL GLY SER GLU PRO ARG SER GLY THR ALA ALA ILE ARG SEQRES 5 C 125 GLU PHE TYR ALA ASN SER LEU LYS LEU PRO LEU ALA VAL SEQRES 6 C 125 GLU LEU THR GLN GLU VAL ARG ALA VAL ALA ASN GLU ALA SEQRES 7 C 125 ALA PHE ALA PHE THR VAL SER PHE GLU TYR GLN GLY ARG SEQRES 8 C 125 LYS THR VAL VAL ALA PRO ILE ASN HIS PHE ARG PHE ASN SEQRES 9 C 125 GLY ALA GLY LYS VAL VAL SER MET ARG ALA LEU PHE GLY SEQRES 10 C 125 GLU LYS ASN ILE HIS ALA GLY ALA SEQRES 1 D 125 MET ASN THR PRO GLU HIS MET THR ALA VAL VAL GLN ARG SEQRES 2 D 125 TYR VAL ALA ALA LEU ASN ALA GLY ASP LEU ASP GLY ILE SEQRES 3 D 125 VAL ALA LEU PHE ALA ASP ASP ALA THR VAL GLU ASP PRO SEQRES 4 D 125 VAL GLY SER GLU PRO ARG SER GLY THR ALA ALA ILE ARG SEQRES 5 D 125 GLU PHE TYR ALA ASN SER LEU LYS LEU PRO LEU ALA VAL SEQRES 6 D 125 GLU LEU THR GLN GLU VAL ARG ALA VAL ALA ASN GLU ALA SEQRES 7 D 125 ALA PHE ALA PHE THR VAL SER PHE GLU TYR GLN GLY ARG SEQRES 8 D 125 LYS THR VAL VAL ALA PRO ILE ASN HIS PHE ARG PHE ASN SEQRES 9 D 125 GLY ALA GLY LYS VAL VAL SER MET ARG ALA LEU PHE GLY SEQRES 10 D 125 GLU LYS ASN ILE HIS ALA GLY ALA HET GOL A 126 6 HET GOL A 127 6 HET SO4 A 128 5 HET SO4 A 129 5 HET SO4 A 130 5 HET SO4 B 126 5 HET SO4 B 127 5 HET SO4 B 128 5 HET SO4 B 129 5 HET EQU B 130 20 HET SO4 C 126 5 HET SO4 C 127 5 HET SO4 C 128 5 HET EQU C 129 20 HET SO4 D 126 5 HET SO4 D 127 5 HET SO4 D 128 5 HET EQU D 129 20 HETNAM GOL GLYCEROL HETNAM SO4 SULFATE ION HETNAM EQU EQUILENIN HETSYN GOL GLYCERIN; PROPANE-1,2,3-TRIOL FORMUL 5 GOL 2(C3 H8 O3) FORMUL 7 SO4 13(O4 S 2-) FORMUL 14 EQU 3(C18 H18 O2) FORMUL 23 HOH *466(H2 O) HELIX 1 1 THR A 3 GLY A 21 1 19 HELIX 2 2 ASP A 22 ALA A 28 1 7 HELIX 3 3 GLY A 47 LEU A 59 1 13 HELIX 4 4 GLY A 117 LYS A 119 5 3 HELIX 5 5 THR B 3 GLY B 21 1 19 HELIX 6 6 ASP B 22 ALA B 28 1 7 HELIX 7 7 GLY B 47 LEU B 59 1 13 HELIX 8 8 GLY B 117 LYS B 119 5 3 HELIX 9 9 THR C 3 ALA C 20 1 18 HELIX 10 10 ASP C 22 ALA C 28 1 7 HELIX 11 11 GLY C 47 LEU C 59 1 13 HELIX 12 12 GLY C 117 LYS C 119 5 3 HELIX 13 13 THR D 3 ALA D 20 1 18 HELIX 14 14 ASP D 22 LEU D 29 1 8 HELIX 15 15 GLY D 47 LEU D 59 1 13 HELIX 16 16 GLY D 117 LYS D 119 5 3 SHEET 1 A 6 ARG A 45 SER A 46 0 SHEET 2 A 6 PHE A 30 GLU A 37 -1 N VAL A 36 O ARG A 45 SHEET 3 A 6 VAL A 109 LEU A 115 1 O ALA A 114 N GLU A 37 SHEET 4 A 6 ILE A 98 PHE A 103 -1 N ILE A 98 O LEU A 115 SHEET 5 A 6 GLU A 77 TYR A 88 -1 N PHE A 80 O ASN A 99 SHEET 6 A 6 ARG A 72 VAL A 74 -1 N ARG A 72 O ALA A 79 SHEET 1 B 4 ALA A 64 LEU A 67 0 SHEET 2 B 4 GLU A 77 TYR A 88 -1 O SER A 85 N ALA A 64 SHEET 3 B 4 ARG A 91 VAL A 95 -1 O THR A 93 N PHE A 86 SHEET 4 B 4 ILE A 121 ALA A 123 -1 O HIS A 122 N VAL A 94 SHEET 1 C 6 ARG B 45 SER B 46 0 SHEET 2 C 6 PHE B 30 GLU B 37 -1 N VAL B 36 O ARG B 45 SHEET 3 C 6 VAL B 109 LEU B 115 1 O VAL B 109 N ALA B 31 SHEET 4 C 6 ILE B 98 PHE B 103 -1 N ILE B 98 O LEU B 115 SHEET 5 C 6 GLU B 77 TYR B 88 -1 N ALA B 78 O PHE B 101 SHEET 6 C 6 ARG B 72 VAL B 74 -1 N ARG B 72 O ALA B 79 SHEET 1 D 4 ALA B 64 LEU B 67 0 SHEET 2 D 4 GLU B 77 TYR B 88 -1 O THR B 83 N GLU B 66 SHEET 3 D 4 ARG B 91 VAL B 95 -1 O THR B 93 N PHE B 86 SHEET 4 D 4 ILE B 121 GLY B 124 -1 O HIS B 122 N VAL B 94 SHEET 1 E 6 ARG C 45 SER C 46 0 SHEET 2 E 6 PHE C 30 GLU C 37 -1 N VAL C 36 O ARG C 45 SHEET 3 E 6 VAL C 109 LEU C 115 1 O VAL C 109 N ALA C 31 SHEET 4 E 6 ILE C 98 PHE C 103 -1 N ILE C 98 O LEU C 115 SHEET 5 E 6 GLU C 77 TYR C 88 -1 N ALA C 78 O PHE C 101 SHEET 6 E 6 ARG C 72 VAL C 74 -1 N VAL C 74 O GLU C 77 SHEET 1 F 4 ALA C 64 LEU C 67 0 SHEET 2 F 4 GLU C 77 TYR C 88 -1 O SER C 85 N ALA C 64 SHEET 3 F 4 ARG C 91 VAL C 95 -1 O VAL C 95 N VAL C 84 SHEET 4 F 4 ILE C 121 HIS C 122 -1 O HIS C 122 N VAL C 94 SHEET 1 G 6 ARG D 45 SER D 46 0 SHEET 2 G 6 PHE D 30 GLU D 37 -1 N VAL D 36 O ARG D 45 SHEET 3 G 6 VAL D 109 LEU D 115 1 O VAL D 109 N ALA D 31 SHEET 4 G 6 ILE D 98 PHE D 103 -1 N ILE D 98 O LEU D 115 SHEET 5 G 6 GLU D 77 TYR D 88 -1 N ALA D 78 O PHE D 101 SHEET 6 G 6 ARG D 72 VAL D 74 -1 N ARG D 72 O ALA D 79 SHEET 1 H 4 ALA D 64 LEU D 67 0 SHEET 2 H 4 GLU D 77 TYR D 88 -1 O SER D 85 N ALA D 64 SHEET 3 H 4 ARG D 91 VAL D 95 -1 O VAL D 95 N VAL D 84 SHEET 4 H 4 ILE D 121 ALA D 123 -1 O HIS D 122 N VAL D 94 CISPEP 1 ASP A 38 PRO A 39 0 1.55 CISPEP 2 ASP B 38 PRO B 39 0 3.33 CISPEP 3 ASP C 38 PRO C 39 0 -1.19 CISPEP 4 ASP D 38 PRO D 39 0 -14.68 SITE 1 AC1 6 GLU A 87 TYR A 88 GLN A 89 GLY A 90 SITE 2 AC1 6 HOH A 493 HOH A 561 SITE 1 AC2 4 HIS A 100 ARG A 113 HIS B 100 ARG B 113 SITE 1 AC3 3 HIS A 6 ARG A 13 HOH A 350 SITE 1 AC4 2 HIS A 122 ALA A 123 SITE 1 AC5 3 ASN A 104 GLY A 105 HOH A 547 SITE 1 AC6 3 ASN B 104 GLY B 105 HOH B 311 SITE 1 AC7 6 ARG B 91 ALA B 123 HOH B 152 HOH B 294 SITE 2 AC7 6 ARG D 91 THR D 93 SITE 1 AC8 3 ARG B 102 SER B 111 HOH B 362 SITE 1 AC9 4 ILE B 121 HIS B 122 ALA B 123 HOH B 367 SITE 1 BC1 12 TYR B 14 LEU B 18 ASP B 38 PHE B 54 SITE 2 BC1 12 PHE B 86 ASN B 99 MET B 112 PHE B 116 SITE 3 BC1 12 HOH B 237 TYR D 88 GLN D 89 ARG D 91 SITE 1 BC2 4 HIS B 6 ARG B 13 HOH C 249 HOH C 304 SITE 1 BC3 3 HIS C 6 ARG C 13 HOH C 513 SITE 1 BC4 2 HIS C 122 ALA C 123 SITE 1 BC5 13 TYR A 88 GLN A 89 ARG A 91 HOH A 134 SITE 2 BC5 13 TYR C 14 LEU C 18 PHE C 54 VAL C 84 SITE 3 BC5 13 PHE C 86 VAL C 95 ASN C 99 MET C 112 SITE 4 BC5 13 PHE C 116 SITE 1 BC6 2 HIS D 122 ALA D 123 SITE 1 BC7 3 HIS D 6 ARG D 13 HOH D 407 SITE 1 BC8 3 ASN D 104 GLY D 105 HOH D 354 SITE 1 BC9 12 TYR B 88 GLN B 89 TYR D 14 LEU D 18 SITE 2 BC9 12 ASP D 38 PHE D 54 VAL D 84 PHE D 86 SITE 3 BC9 12 ASN D 99 MET D 112 PHE D 116 HOH D 138 CRYST1 64.312 64.312 506.174 90.00 90.00 120.00 P 61 2 2 48 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 0.015549 0.008977 0.000000 0.00000 SCALE2 0.000000 0.017955 0.000000 0.00000 SCALE3 0.000000 0.000000 0.001976 0.00000