HEADER OXIDOREDUCTASE 22-JAN-09 3FY8 TITLE CRYSTAL STRUCTURE OF STAPH. AUREUS DHFR COMPLEXED WITH NADPH AND AR- TITLE 2 101 COMPND MOL_ID: 1; COMPND 2 MOLECULE: DIHYDROFOLATE REDUCTASE; COMPND 3 CHAIN: X; COMPND 4 SYNONYM: DHFR; COMPND 5 EC: 1.5.1.3; COMPND 6 ENGINEERED: YES; COMPND 7 MUTATION: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: STAPHYLOCOCCUS AUREUS; SOURCE 3 ORGANISM_TAXID: 1280; SOURCE 4 GENE: FOLA; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS DHFR, NADP, ONE-CARBON METABOLISM, OXIDOREDUCTASE EXPDTA X-RAY DIFFRACTION AUTHOR C.OEFNER,G.E.DALE REVDAT 5 29-MAY-24 3FY8 1 REMARK REVDAT 4 10-NOV-21 3FY8 1 REMARK SEQADV REVDAT 3 23-APR-14 3FY8 1 FORMUL HET HETATM HETNAM REVDAT 2 20-NOV-13 3FY8 1 HET HETATM HETNAM VERSN REVDAT 1 04-AUG-09 3FY8 0 JRNL AUTH C.OEFNER,S.PARISI,H.SCHULZ,S.LOCIURO,G.E.DALE JRNL TITL INHIBITORY PROPERTIES AND X-RAY CRYSTALLOGRAPHIC STUDY OF JRNL TITL 2 THE BINDING OF AR-101, AR-102 AND ICLAPRIM IN TERNARY JRNL TITL 3 COMPLEXES WITH NADPH AND DIHYDROFOLATE REDUCTASE FROM JRNL TITL 4 STAPHYLOCOCCUS AUREUS JRNL REF ACTA CRYSTALLOGR.,SECT.D V. 65 751 2009 JRNL REFN ISSN 0907-4449 JRNL PMID 19622858 JRNL DOI 10.1107/S0907444909013936 REMARK 2 REMARK 2 RESOLUTION. 2.20 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.2.0019 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) : 2.20 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 20.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 90.6 REMARK 3 NUMBER OF REFLECTIONS : 9373 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) : 0.255 REMARK 3 R VALUE (WORKING SET) : 0.251 REMARK 3 FREE R VALUE : 0.335 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.900 REMARK 3 FREE R VALUE TEST SET COUNT : 480 REMARK 3 REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN. REMARK 3 TOTAL NUMBER OF BINS USED : 10 REMARK 3 BIN RESOLUTION RANGE HIGH (A) : 2.20 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.32 REMARK 3 REFLECTION IN BIN (WORKING SET) : 655 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 45.32 REMARK 3 BIN R VALUE (WORKING SET) : 0.5360 REMARK 3 BIN FREE R VALUE SET COUNT : 37 REMARK 3 BIN FREE R VALUE : 0.6200 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 1273 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 74 REMARK 3 SOLVENT ATOMS : 157 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 15.91 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -0.08000 REMARK 3 B22 (A**2) : -0.08000 REMARK 3 B33 (A**2) : 0.13000 REMARK 3 B12 (A**2) : -0.04000 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): 0.389 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.311 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.270 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 11.971 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.893 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.791 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 1387 ; 0.011 ; 0.022 REMARK 3 BOND LENGTHS OTHERS (A): 916 ; 0.000 ; 0.020 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 1894 ; 1.593 ; 2.017 REMARK 3 BOND ANGLES OTHERS (DEGREES): 2236 ; 0.944 ; 3.000 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 156 ;11.010 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 62 ;39.384 ;24.194 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 226 ;21.213 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 6 ;21.994 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 209 ; 0.072 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 1473 ; 0.004 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): 271 ; 0.000 ; 0.020 REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): 357 ; 0.300 ; 0.200 REMARK 3 NON-BONDED CONTACTS OTHERS (A): 1065 ; 0.278 ; 0.200 REMARK 3 NON-BONDED TORSION REFINED ATOMS (A): 655 ; 0.205 ; 0.200 REMARK 3 NON-BONDED TORSION OTHERS (A): 753 ; 0.096 ; 0.200 REMARK 3 H-BOND (X...Y) REFINED ATOMS (A): 115 ; 0.293 ; 0.200 REMARK 3 H-BOND (X...Y) OTHERS (A): 1 ; 0.096 ; 0.200 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): 16 ; 0.483 ; 0.200 REMARK 3 SYMMETRY VDW OTHERS (A): 35 ; 0.302 ; 0.200 REMARK 3 SYMMETRY H-BOND REFINED ATOMS (A): 16 ; 0.365 ; 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): 994 ; 0.949 ; 2.000 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): 316 ; 0.148 ; 2.000 REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 1280 ; 1.190 ; 3.000 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 706 ; 0.626 ; 2.000 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 611 ; 0.942 ; 3.000 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 : 1.20 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 3FY8 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 26-JAN-09. REMARK 100 THE DEPOSITION ID IS D_1000051187. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 02-NOV-07 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 5.5 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 : ENRAF-NONIUS FR591 REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.5418 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : MIRRORS REMARK 200 REMARK 200 DETECTOR TYPE : IMAGE PLATE REMARK 200 DETECTOR MANUFACTURER : MAR SCANNER 345 MM PLATE REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XFIT, DENZO REMARK 200 DATA SCALING SOFTWARE : SCALA REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 10269 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.200 REMARK 200 RESOLUTION RANGE LOW (A) : 20.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 4.100 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 93.8 REMARK 200 DATA REDUNDANCY : NULL REMARK 200 R MERGE (I) : 0.16700 REMARK 200 R SYM (I) : 0.16700 REMARK 200 FOR THE DATA SET : NULL REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : NULL REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : NULL REMARK 200 COMPLETENESS FOR SHELL (%) : NULL REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : NULL REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MIR REMARK 200 SOFTWARE USED: XFIT REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 55.13 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.74 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 25% PEG3350, 200MM NACL, 100MM BIS REMARK 280 -TRIS, PH5.5 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 36.31933 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 72.63867 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 54.47900 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 90.79833 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 18.15967 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 36.31933 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 72.63867 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 90.79833 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 54.47900 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 18.15967 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: MONOMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: MONOMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 APPLY THE FOLLOWING TO CHAINS: X 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 LYS X 158 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 CA LEU X 141 O HOH X 314 1.23 REMARK 500 CB LEU X 141 O HOH X 314 1.32 REMARK 500 N LEU X 141 O HOH X 314 1.63 REMARK 500 C LEU X 141 O HOH X 314 1.91 REMARK 500 NE2 GLN X 11 O HOH X 234 1.94 REMARK 500 O ASP X 81 O HOH X 268 2.05 REMARK 500 O HOH X 278 O HOH X 313 2.18 REMARK 500 O HOH X 237 O HOH X 284 2.19 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 O HOH X 190 O HOH X 224 6555 1.67 REMARK 500 OE2 GLU X 48 OE2 GLU X 48 10665 1.93 REMARK 500 O HOH X 284 O HOH X 298 8556 2.19 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 PRO X 55 C - N - CA ANGL. DEV. = 10.3 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 LEU X 24 78.28 -152.39 REMARK 500 HIS X 38 -163.64 -129.34 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 PRO X 86 GLY X 87 148.15 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 NDP X 301 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE XCF X 300 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 3FY9 RELATED DB: PDB REMARK 900 RELATED ID: 3FYV RELATED DB: PDB REMARK 900 RELATED ID: 3FYW RELATED DB: PDB DBREF 3FY8 X 1 158 UNP P0A017 DYR_STAAU 2 159 SEQADV 3FY8 TYR X 98 UNP P0A017 PHE 99 ENGINEERED MUTATION SEQRES 1 X 158 THR LEU SER ILE LEU VAL ALA HIS ASP LEU GLN ARG VAL SEQRES 2 X 158 ILE GLY PHE GLU ASN GLN LEU PRO TRP HIS LEU PRO ASN SEQRES 3 X 158 ASP LEU LYS HIS VAL LYS LYS LEU SER THR GLY HIS THR SEQRES 4 X 158 LEU VAL MET GLY ARG LYS THR PHE GLU SER ILE GLY LYS SEQRES 5 X 158 PRO LEU PRO ASN ARG ARG ASN VAL VAL LEU THR SER ASP SEQRES 6 X 158 THR SER PHE ASN VAL GLU GLY VAL ASP VAL ILE HIS SER SEQRES 7 X 158 ILE GLU ASP ILE TYR GLN LEU PRO GLY HIS VAL PHE ILE SEQRES 8 X 158 PHE GLY GLY GLN THR LEU TYR GLU GLU MET ILE ASP LYS SEQRES 9 X 158 VAL ASP ASP MET TYR ILE THR VAL ILE GLU GLY LYS PHE SEQRES 10 X 158 ARG GLY ASP THR PHE PHE PRO PRO TYR THR PHE GLU ASP SEQRES 11 X 158 TRP GLU VAL ALA SER SER VAL GLU GLY LYS LEU ASP GLU SEQRES 12 X 158 LYS ASN THR ILE PRO HIS THR PHE LEU HIS LEU ILE ARG SEQRES 13 X 158 LYS LYS HET NDP X 301 48 HET XCF X 300 26 HETNAM NDP NADPH DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDE HETNAM 2 NDP PHOSPHATE HETNAM XCF 5-[[(2R)-2-CYCLOPROPYL-7,8-DIMETHOXY-2H-CHROMEN-5- HETNAM 2 XCF YL]METHYL]PYRIMIDINE-2,4-DIAMINE FORMUL 2 NDP C21 H30 N7 O17 P3 FORMUL 3 XCF C19 H22 N4 O3 FORMUL 4 HOH *157(H2 O) HELIX 1 1 LEU X 24 THR X 36 1 13 HELIX 2 2 ARG X 44 GLY X 51 1 8 HELIX 3 3 SER X 78 LEU X 85 5 8 HELIX 4 4 GLY X 94 ILE X 102 1 9 SHEET 1 A 8 ASP X 74 ILE X 76 0 SHEET 2 A 8 ARG X 58 LEU X 62 1 N ASN X 59 O ASP X 74 SHEET 3 A 8 THR X 39 GLY X 43 1 N LEU X 40 O ARG X 58 SHEET 4 A 8 VAL X 89 GLY X 93 1 O PHE X 90 N THR X 39 SHEET 5 A 8 LEU X 2 ASP X 9 1 N SER X 3 O ILE X 91 SHEET 6 A 8 ASP X 107 ILE X 113 1 O TYR X 109 N ILE X 4 SHEET 7 A 8 HIS X 149 ARG X 156 -1 O LEU X 154 N MET X 108 SHEET 8 A 8 TRP X 131 GLU X 138 -1 N GLU X 132 O ILE X 155 SHEET 1 B 2 VAL X 13 GLY X 15 0 SHEET 2 B 2 THR X 121 PHE X 122 -1 O THR X 121 N ILE X 14 CISPEP 1 GLY X 93 GLY X 94 0 17.23 SITE 1 AC1 30 VAL X 6 ALA X 7 ILE X 14 GLY X 15 SITE 2 AC1 30 ASN X 18 GLN X 19 LEU X 20 GLY X 43 SITE 3 AC1 30 ARG X 44 LYS X 45 THR X 46 LEU X 62 SITE 4 AC1 30 THR X 63 SER X 64 HIS X 77 ILE X 79 SITE 5 AC1 30 PHE X 92 GLY X 93 GLY X 94 GLN X 95 SITE 6 AC1 30 THR X 96 LEU X 97 TYR X 98 GLU X 100 SITE 7 AC1 30 THR X 121 HOH X 163 HOH X 191 HOH X 202 SITE 8 AC1 30 XCF X 300 HOH X 302 SITE 1 AC2 11 LEU X 5 VAL X 6 ALA X 7 ASP X 27 SITE 2 AC2 11 LEU X 28 VAL X 31 LEU X 54 PHE X 92 SITE 3 AC2 11 HOH X 181 HOH X 182 NDP X 301 CRYST1 79.567 79.567 108.958 90.00 90.00 120.00 P 61 2 2 12 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 0.012568 0.007256 0.000000 0.00000 SCALE2 0.000000 0.014512 0.000000 0.00000 SCALE3 0.000000 0.000000 0.009178 0.00000