HEADER OXIDOREDUCTASE 11-JUL-17 5OFV TITLE CRYSTAL STRUCTURE OF HUMAN 3-PHOSPHOGLYCERATE DEHYDROGENASE IN COMPLEX TITLE 2 WITH 5-FLUORO-2-METHYLBENZOIC ACID COMPND MOL_ID: 1; COMPND 2 MOLECULE: D-3-PHOSPHOGLYCERATE DEHYDROGENASE; COMPND 3 CHAIN: B, A; COMPND 4 SYNONYM: 3-PGDH,2-OXOGLUTARATE REDUCTASE,MALATE DEHYDROGENASE; COMPND 5 EC: 1.1.1.95,1.1.1.399,1.1.1.37; COMPND 6 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 3 ORGANISM_COMMON: HUMAN; SOURCE 4 ORGANISM_TAXID: 9606; SOURCE 5 GENE: PHGDH, PGDH3; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS DEHYDROGENASE, SERINE METABOLISM, FBDD, OXIDOREDUCTASE EXPDTA X-RAY DIFFRACTION AUTHOR J.E.UNTERLASS,A.BASLE,T.J.BLACKBURN,J.TUCKER,C.CANO,M.E.M.NOBLE, AUTHOR 2 N.J.CURTIN REVDAT 5 08-MAY-24 5OFV 1 REMARK REVDAT 4 10-JUL-19 5OFV 1 REMARK REVDAT 3 20-FEB-19 5OFV 1 REMARK LINK REVDAT 2 04-APR-18 5OFV 1 JRNL REVDAT 1 16-AUG-17 5OFV 0 JRNL AUTH J.E.UNTERLASS,A.BASLE,T.J.BLACKBURN,J.TUCKER,C.CANO, JRNL AUTH 2 M.E.M.NOBLE,N.J.CURTIN JRNL TITL VALIDATING AND ENABLING PHOSPHOGLYCERATE DEHYDROGENASE JRNL TITL 2 (PHGDH) AS A TARGET FOR FRAGMENT-BASED DRUG DISCOVERY IN JRNL TITL 3 PHGDH-AMPLIFIED BREAST CANCER. JRNL REF ONCOTARGET V. 9 13139 2018 JRNL REFN ESSN 1949-2553 JRNL PMID 29568346 JRNL DOI 10.18632/ONCOTARGET.11487 REMARK 2 REMARK 2 RESOLUTION. 1.50 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.8.0135 REMARK 3 AUTHORS : MURSHUDOV,SKUBAK,LEBEDEV,PANNU,STEINER, REMARK 3 : NICHOLLS,WINN,LONG,VAGIN REMARK 3 REMARK 3 REFINEMENT TARGET : NULL REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.50 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 50.60 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 89.5 REMARK 3 NUMBER OF REFLECTIONS : 51322 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) : 0.226 REMARK 3 R VALUE (WORKING SET) : 0.224 REMARK 3 FREE R VALUE : 0.273 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.100 REMARK 3 FREE R VALUE TEST SET COUNT : 2775 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) : 1.49 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.53 REMARK 3 REFLECTION IN BIN (WORKING SET) : 3038 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 71.32 REMARK 3 BIN R VALUE (WORKING SET) : 0.4260 REMARK 3 BIN FREE R VALUE SET COUNT : 157 REMARK 3 BIN FREE R VALUE : 0.5030 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 2920 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 22 REMARK 3 SOLVENT ATOMS : 275 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 19.26 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -0.42000 REMARK 3 B22 (A**2) : -0.33000 REMARK 3 B33 (A**2) : -0.08000 REMARK 3 B12 (A**2) : 0.10000 REMARK 3 B13 (A**2) : 0.28000 REMARK 3 B23 (A**2) : 0.69000 REMARK 3 REMARK 3 ESTIMATED OVERALL COORDINATE ERROR. REMARK 3 ESU BASED ON R VALUE (A): 0.142 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.110 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.104 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 6.572 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.903 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.884 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 3175 ; 0.025 ; 0.019 REMARK 3 BOND LENGTHS OTHERS (A): 3093 ; 0.009 ; 0.020 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 4308 ; 2.296 ; 1.973 REMARK 3 BOND ANGLES OTHERS (DEGREES): 7147 ; 1.566 ; 2.995 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 425 ; 7.579 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 127 ;38.600 ;24.173 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 573 ;16.524 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 25 ;14.792 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 481 ; 0.154 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 3692 ; 0.014 ; 0.021 REMARK 3 GENERAL PLANES OTHERS (A): 693 ; 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): 1652 ; 3.523 ; 1.738 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): 1651 ; 3.506 ; 1.735 REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 2093 ; 3.953 ; 2.606 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): 2094 ; 3.953 ; 2.608 REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 1523 ; 4.176 ; 2.055 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): 1522 ; 4.153 ; 2.054 REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE OTHER ATOMS (A**2): 2216 ; 4.901 ; 2.972 REMARK 3 LONG RANGE B REFINED ATOMS (A**2): 3722 ; 5.079 ;15.060 REMARK 3 LONG RANGE B OTHER ATOMS (A**2): 3723 ; 5.079 ;15.065 REMARK 3 REMARK 3 ANISOTROPIC THERMAL FACTOR RESTRAINTS. COUNT RMS WEIGHT REMARK 3 RIGID-BOND RESTRAINTS (A**2): 6268 ; 6.580 ; 3.000 REMARK 3 SPHERICITY; FREE ATOMS (A**2): 84 ;34.648 ; 5.000 REMARK 3 SPHERICITY; BONDED ATOMS (A**2): 6395 ;16.444 ; 5.000 REMARK 3 REMARK 3 NCS RESTRAINTS STATISTICS REMARK 3 NCS TYPE: LOCAL REMARK 3 NUMBER OF DIFFERENT NCS PAIRS : 1 REMARK 3 GROUP CHAIN1 RANGE CHAIN2 RANGE COUNT RMS WEIGHT REMARK 3 1 B 100 294 A 100 294 23422 0.06 0.05 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : NULL REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : NULL 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 REMARK 4 REMARK 4 5OFV COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 12-JUL-17. REMARK 100 THE DEPOSITION ID IS D_1200004965. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 12-DEC-14 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 7 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : DIAMOND REMARK 200 BEAMLINE : I04-1 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.979 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS PILATUS3 S 6M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XIA2 REMARK 200 DATA SCALING SOFTWARE : XIA2 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 54400 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.500 REMARK 200 RESOLUTION RANGE LOW (A) : 50.600 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 91.4 REMARK 200 DATA REDUNDANCY : 1.930 REMARK 200 R MERGE (I) : 0.08400 REMARK 200 R SYM (I) : NULL REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 5.0000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.50 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.53 REMARK 200 COMPLETENESS FOR SHELL (%) : 90.1 REMARK 200 DATA REDUNDANCY IN SHELL : 1.85 REMARK 200 R MERGE FOR SHELL (I) : 1.24100 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 <I/SIGMA(I)> FOR SHELL : NULL REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: PHASER REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 38.81 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.01 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.1 M PCTP PH 7, 23-25 % PEG 1500, REMARK 280 VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 293K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,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 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 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: 4910 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 15250 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -35.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: B, 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 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 B 93 REMARK 465 LEU B 94 REMARK 465 VAL B 95 REMARK 465 MET B 96 REMARK 465 ASN B 97 REMARK 465 THR B 98 REMARK 465 PRO B 99 REMARK 465 CYS B 295 REMARK 465 GLY B 296 REMARK 465 GLU B 297 REMARK 465 GLU B 298 REMARK 465 ILE B 299 REMARK 465 ALA B 300 REMARK 465 VAL B 301 REMARK 465 GLN B 302 REMARK 465 PHE B 303 REMARK 465 VAL B 304 REMARK 465 ASP B 305 REMARK 465 MET B 306 REMARK 465 VAL B 307 REMARK 465 LYS B 308 REMARK 465 GLY B 309 REMARK 465 LYS B 310 REMARK 465 SER B 311 REMARK 465 LEU B 312 REMARK 465 THR B 313 REMARK 465 GLY B 314 REMARK 465 VAL B 315 REMARK 465 MET A 93 REMARK 465 LEU A 94 REMARK 465 VAL A 95 REMARK 465 MET A 96 REMARK 465 ASN A 97 REMARK 465 THR A 98 REMARK 465 PRO A 99 REMARK 465 CYS A 295 REMARK 465 GLY A 296 REMARK 465 GLU A 297 REMARK 465 GLU A 298 REMARK 465 ILE A 299 REMARK 465 ALA A 300 REMARK 465 VAL A 301 REMARK 465 GLN A 302 REMARK 465 PHE A 303 REMARK 465 VAL A 304 REMARK 465 ASP A 305 REMARK 465 MET A 306 REMARK 465 VAL A 307 REMARK 465 LYS A 308 REMARK 465 GLY A 309 REMARK 465 LYS A 310 REMARK 465 SER A 311 REMARK 465 LEU A 312 REMARK 465 THR A 313 REMARK 465 GLY A 314 REMARK 465 VAL A 315 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 LEU B 284 NH2 ARG A 119 2.08 REMARK 500 NH2 ARG B 119 O LEU A 284 2.13 REMARK 500 REMARK 500 REMARK: NULL 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. AN ATOM LOCATED WITHIN 0.15 REMARK 500 ANGSTROMS OF A SYMMETRY RELATED ATOM IS ASSUMED TO BE ON A REMARK 500 SPECIAL POSITION AND IS, THEREFORE, LISTED IN REMARK 375 REMARK 500 INSTEAD OF REMARK 500. ATOMS WITH NON-BLANK ALTERNATE REMARK 500 LOCATION INDICATORS ARE NOT INCLUDED IN THE CALCULATIONS. REMARK 500 REMARK 500 DISTANCE CUTOFF: REMARK 500 2.2 ANGSTROMS FOR CONTACTS NOT INVOLVING HYDROGEN ATOMS REMARK 500 1.6 ANGSTROMS FOR CONTACTS INVOLVING HYDROGEN ATOMS REMARK 500 REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI SSYMOP DISTANCE REMARK 500 OE2 GLU A 195 NH2 ARG A 268 1455 2.12 REMARK 500 ND2 ASN A 220 O HOH B 603 1444 2.13 REMARK 500 NH1 ARG B 155 OD1 ASN A 100 1565 2.16 REMARK 500 REMARK 500 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 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,2(A3,1X,A1,I4,A1,1X,A4,3X),1X,F6.3) 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 RES CSSEQI ATM2 DEVIATION REMARK 500 CYS B 116 CA CYS B 116 CB -0.100 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 B 119 NE - CZ - NH1 ANGL. DEV. = 6.5 DEGREES REMARK 500 ARG B 119 NE - CZ - NH1 ANGL. DEV. = 3.4 DEGREES REMARK 500 ARG B 119 NE - CZ - NH2 ANGL. DEV. = -8.3 DEGREES REMARK 500 ARG B 236 NE - CZ - NH2 ANGL. DEV. = -3.1 DEGREES REMARK 500 ARG B 294 NE - CZ - NH1 ANGL. DEV. = 3.4 DEGREES REMARK 500 ARG A 119 NE - CZ - NH1 ANGL. DEV. = 8.2 DEGREES REMARK 500 ARG A 119 NE - CZ - NH2 ANGL. DEV. = -6.6 DEGREES REMARK 500 ASN A 220 CB - CA - C ANGL. DEV. = 12.8 DEGREES REMARK 500 ARG A 236 CG - CD - NE ANGL. DEV. = 13.2 DEGREES REMARK 500 ARG A 236 CD - NE - CZ ANGL. DEV. = 11.5 DEGREES REMARK 500 ARG A 236 NE - CZ - NH1 ANGL. DEV. = 6.3 DEGREES REMARK 500 ARG A 236 NE - CZ - NH2 ANGL. DEV. = -5.9 DEGREES REMARK 500 ARG A 294 NE - CZ - NH1 ANGL. DEV. = 4.3 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 GLU B 134 79.73 -116.37 REMARK 500 ALA B 235 -79.20 -108.58 REMARK 500 GLU A 134 77.93 -113.61 REMARK 500 HIS A 206 53.28 -140.61 REMARK 500 ALA A 235 -75.83 -105.68 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: NON-CIS, NON-TRANS REMARK 500 REMARK 500 THE FOLLOWING PEPTIDE BONDS DEVIATE SIGNIFICANTLY FROM BOTH REMARK 500 CIS AND TRANS CONFORMATION. CIS BONDS, IF ANY, ARE LISTED REMARK 500 ON CISPEP RECORDS. TRANS IS DEFINED AS 180 +/- 30 AND REMARK 500 CIS IS DEFINED AS 0 +/- 30 DEGREES. REMARK 500 MODEL OMEGA REMARK 500 ASN B 100 GLY B 101 134.05 REMARK 500 ASN A 100 GLY A 101 135.85 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: MAIN CHAIN PLANARITY REMARK 500 REMARK 500 THE FOLLOWING RESIDUES HAVE A PSEUDO PLANARITY REMARK 500 TORSION ANGLE, C(I) - CA(I) - N(I+1) - O(I), GREATER REMARK 500 10.0 DEGREES. (M=MODEL NUMBER; RES=RESIDUE NAME; REMARK 500 C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; REMARK 500 I=INSERTION CODE). REMARK 500 REMARK 500 M RES CSSEQI ANGLE REMARK 500 ILE A 172 -10.13 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 9TZ B 401 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue 9TZ A 401 DBREF 5OFV B 94 315 UNP O43175 SERA_HUMAN 94 315 DBREF 5OFV A 94 315 UNP O43175 SERA_HUMAN 94 315 SEQADV 5OFV MET B 93 UNP O43175 INITIATING METHIONINE SEQADV 5OFV MET A 93 UNP O43175 INITIATING METHIONINE SEQRES 1 B 223 MET LEU VAL MET ASN THR PRO ASN GLY ASN SER LEU SER SEQRES 2 B 223 ALA ALA GLU LEU THR CYS GLY MET ILE MET CYS LEU ALA SEQRES 3 B 223 ARG GLN ILE PRO GLN ALA THR ALA SER MET LYS ASP GLY SEQRES 4 B 223 LYS TRP GLU ARG LYS LYS PHE MET GLY THR GLU LEU ASN SEQRES 5 B 223 GLY LYS THR LEU GLY ILE LEU GLY LEU GLY ARG ILE GLY SEQRES 6 B 223 ARG GLU VAL ALA THR ARG MET GLN SER PHE GLY MET LYS SEQRES 7 B 223 THR ILE GLY TYR ASP PRO ILE ILE SER PRO GLU VAL SER SEQRES 8 B 223 ALA SER PHE GLY VAL GLN GLN LEU PRO LEU GLU GLU ILE SEQRES 9 B 223 TRP PRO LEU CYS ASP PHE ILE THR VAL HIS THR PRO LEU SEQRES 10 B 223 LEU PRO SER THR THR GLY LEU LEU ASN ASP ASN THR PHE SEQRES 11 B 223 ALA GLN CYS LYS LYS GLY VAL ARG VAL VAL ASN CYS ALA SEQRES 12 B 223 ARG GLY GLY ILE VAL ASP GLU GLY ALA LEU LEU ARG ALA SEQRES 13 B 223 LEU GLN SER GLY GLN CYS ALA GLY ALA ALA LEU ASP VAL SEQRES 14 B 223 PHE THR GLU GLU PRO PRO ARG ASP ARG ALA LEU VAL ASP SEQRES 15 B 223 HIS GLU ASN VAL ILE SER CYS PRO HIS LEU GLY ALA SER SEQRES 16 B 223 THR LYS GLU ALA GLN SER ARG CYS GLY GLU GLU ILE ALA SEQRES 17 B 223 VAL GLN PHE VAL ASP MET VAL LYS GLY LYS SER LEU THR SEQRES 18 B 223 GLY VAL SEQRES 1 A 223 MET LEU VAL MET ASN THR PRO ASN GLY ASN SER LEU SER SEQRES 2 A 223 ALA ALA GLU LEU THR CYS GLY MET ILE MET CYS LEU ALA SEQRES 3 A 223 ARG GLN ILE PRO GLN ALA THR ALA SER MET LYS ASP GLY SEQRES 4 A 223 LYS TRP GLU ARG LYS LYS PHE MET GLY THR GLU LEU ASN SEQRES 5 A 223 GLY LYS THR LEU GLY ILE LEU GLY LEU GLY ARG ILE GLY SEQRES 6 A 223 ARG GLU VAL ALA THR ARG MET GLN SER PHE GLY MET LYS SEQRES 7 A 223 THR ILE GLY TYR ASP PRO ILE ILE SER PRO GLU VAL SER SEQRES 8 A 223 ALA SER PHE GLY VAL GLN GLN LEU PRO LEU GLU GLU ILE SEQRES 9 A 223 TRP PRO LEU CYS ASP PHE ILE THR VAL HIS THR PRO LEU SEQRES 10 A 223 LEU PRO SER THR THR GLY LEU LEU ASN ASP ASN THR PHE SEQRES 11 A 223 ALA GLN CYS LYS LYS GLY VAL ARG VAL VAL ASN CYS ALA SEQRES 12 A 223 ARG GLY GLY ILE VAL ASP GLU GLY ALA LEU LEU ARG ALA SEQRES 13 A 223 LEU GLN SER GLY GLN CYS ALA GLY ALA ALA LEU ASP VAL SEQRES 14 A 223 PHE THR GLU GLU PRO PRO ARG ASP ARG ALA LEU VAL ASP SEQRES 15 A 223 HIS GLU ASN VAL ILE SER CYS PRO HIS LEU GLY ALA SER SEQRES 16 A 223 THR LYS GLU ALA GLN SER ARG CYS GLY GLU GLU ILE ALA SEQRES 17 A 223 VAL GLN PHE VAL ASP MET VAL LYS GLY LYS SER LEU THR SEQRES 18 A 223 GLY VAL HET 9TZ B 401 11 HET 9TZ A 401 11 HETNAM 9TZ 5-FLUORANYL-2-METHYL-BENZOIC ACID FORMUL 3 9TZ 2(C8 H7 F O2) FORMUL 5 HOH *275(H2 O) HELIX 1 AA1 ASN B 102 GLN B 120 1 19 HELIX 2 AA2 GLN B 120 ASP B 130 1 11 HELIX 3 AA3 GLY B 154 SER B 166 1 13 HELIX 4 AA4 SER B 179 PHE B 186 1 8 HELIX 5 AA5 PRO B 192 TRP B 197 1 6 HELIX 6 AA6 PRO B 198 CYS B 200 5 3 HELIX 7 AA7 ASN B 218 ALA B 223 1 6 HELIX 8 AA8 ASP B 241 GLY B 252 1 12 HELIX 9 AA9 ARG B 270 HIS B 275 1 6 HELIX 10 AB1 THR B 288 SER B 293 1 6 HELIX 11 AB2 ASN A 102 GLN A 120 1 19 HELIX 12 AB3 GLN A 120 ASP A 130 1 11 HELIX 13 AB4 GLY A 154 PHE A 167 1 14 HELIX 14 AB5 SER A 179 PHE A 186 1 8 HELIX 15 AB6 PRO A 192 TRP A 197 1 6 HELIX 16 AB7 PRO A 198 CYS A 200 5 3 HELIX 17 AB8 ASN A 218 ALA A 223 1 6 HELIX 18 AB9 ASP A 241 GLY A 252 1 12 HELIX 19 AC1 THR A 288 SER A 293 1 6 SHEET 1 AA1 7 GLN B 189 GLN B 190 0 SHEET 2 AA1 7 LYS B 170 TYR B 174 1 N GLY B 173 O GLN B 189 SHEET 3 AA1 7 THR B 147 LEU B 151 1 N LEU B 148 O LYS B 170 SHEET 4 AA1 7 PHE B 202 VAL B 205 1 O PHE B 202 N GLY B 149 SHEET 5 AA1 7 VAL B 229 ASN B 233 1 O ARG B 230 N ILE B 203 SHEET 6 AA1 7 CYS B 254 LEU B 259 1 O ALA B 258 N ASN B 233 SHEET 7 AA1 7 VAL B 278 SER B 280 1 O ILE B 279 N LEU B 259 SHEET 1 AA2 7 GLN A 189 GLN A 190 0 SHEET 2 AA2 7 LYS A 170 TYR A 174 1 N THR A 171 O GLN A 189 SHEET 3 AA2 7 THR A 147 LEU A 151 1 N LEU A 148 O LYS A 170 SHEET 4 AA2 7 PHE A 202 VAL A 205 1 O PHE A 202 N GLY A 149 SHEET 5 AA2 7 VAL A 229 ASN A 233 1 O VAL A 232 N ILE A 203 SHEET 6 AA2 7 CYS A 254 LEU A 259 1 O ALA A 258 N ASN A 233 SHEET 7 AA2 7 VAL A 278 SER A 280 1 O ILE A 279 N LEU A 259 CISPEP 1 GLU B 265 PRO B 266 0 -12.85 CISPEP 2 GLU A 265 PRO A 266 0 -9.23 SITE 1 AC1 9 GLY B 152 TYR B 174 ASP B 175 PRO B 176 SITE 2 AC1 9 THR B 207 PRO B 208 SER B 212 THR B 213 SITE 3 AC1 9 LEU B 216 SITE 1 AC2 9 GLY A 152 TYR A 174 ASP A 175 PRO A 176 SITE 2 AC2 9 THR A 207 PRO A 208 SER A 212 THR A 213 SITE 3 AC2 9 LEU A 216 CRYST1 43.342 45.608 56.269 98.02 111.14 105.85 P 1 2 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 0.023072 0.006551 0.011053 0.00000 SCALE2 0.000000 0.022793 0.006269 0.00000 SCALE3 0.000000 0.000000 0.019761 0.00000