HEADER OXIDOREDUCTASE 16-OCT-07 2RK1 TITLE DHFR R67 COMPLEXED WITH NADP AND DIHYDROFOLATE COMPND MOL_ID: 1; COMPND 2 MOLECULE: DIHYDROFOLATE REDUCTASE TYPE 2; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: DIHYDROFOLATE REDUCTASE TYPE II; COMPND 5 EC: 1.5.1.3 SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: ESCHERICHIA COLI; SOURCE 3 STRAIN: TMP-RESISTANT, CONTAINING R67 DHFR OVERPRODUCING SOURCE 4 PLASMID PLZ1 KEYWDS OXIDOREDUCTASE, NADP, DIHYDROFOLATE, ASYMMETRIC LIGAND KEYWDS 2 BINDING, ANTIBIOTIC RESISTANCE, METHOTREXATE RESISTANCE, KEYWDS 3 ONE-CARBON METABOLISM, PLASMID, TRIMETHOPRIM RESISTANCE EXPDTA X-RAY DIFFRACTION AUTHOR J.M.KRAHN,R.E.LONDON REVDAT 2 24-FEB-09 2RK1 1 VERSN REVDAT 1 03-JUN-08 2RK1 0 JRNL AUTH J.M.KRAHN,M.R.JACKSON,E.F.DEROSE,E.E.HOWELL, JRNL AUTH 2 R.E.LONDON JRNL TITL CRYSTAL STRUCTURE OF A TYPE II DIHYDROFOLATE JRNL TITL 2 REDUCTASE CATALYTIC TERNARY COMPLEX. JRNL REF BIOCHEMISTRY V. 46 14878 2007 JRNL REFN ISSN 0006-2960 JRNL PMID 18052202 JRNL DOI 10.1021/BI701532R REMARK 1 REMARK 2 REMARK 2 RESOLUTION. 1.26 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.2.0019 REMARK 3 AUTHORS : MURSHUDOV,VAGIN,DODSON REMARK 3 REMARK 3 REFINEMENT TARGET : MAXIMUM LIKELIHOOD REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.26 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 26.22 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 99.7 REMARK 3 NUMBER OF REFLECTIONS : 15838 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, PRESERVED FROM 2RH2 REMARK 3 R VALUE (WORKING + TEST SET) : 0.124 REMARK 3 R VALUE (WORKING SET) : 0.123 REMARK 3 FREE R VALUE : 0.152 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.100 REMARK 3 FREE R VALUE TEST SET COUNT : 854 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) : 1.26 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.29 REMARK 3 REFLECTION IN BIN (WORKING SET) : 1096 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 95.36 REMARK 3 BIN R VALUE (WORKING SET) : 0.3060 REMARK 3 BIN FREE R VALUE SET COUNT : 54 REMARK 3 BIN FREE R VALUE : 0.3760 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 1034 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 85 REMARK 3 SOLVENT ATOMS : 122 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 14.40 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 0.00000 REMARK 3 B22 (A**2) : 0.00000 REMARK 3 B33 (A**2) : 0.00000 REMARK 3 B12 (A**2) : 0.00000 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): 0.045 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.042 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.021 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 1.057 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.974 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.967 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 649 ; 0.016 ; 0.021 REMARK 3 BOND LENGTHS OTHERS (A): 497 ; 0.001 ; 0.020 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 913 ; 2.121 ; 2.080 REMARK 3 BOND ANGLES OTHERS (DEGREES): 1139 ; 0.870 ; 3.000 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 78 ; 6.219 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 26 ;34.012 ;24.231 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 83 ;12.569 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 3 ;11.459 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 89 ; 0.102 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 740 ; 0.009 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): 139 ; 0.002 ; 0.020 REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): 121 ; 0.298 ; NULL REMARK 3 NON-BONDED CONTACTS OTHERS (A): 520 ; 0.245 ; NULL REMARK 3 NON-BONDED TORSION REFINED ATOMS (A): 311 ; 0.225 ; 0.500 REMARK 3 NON-BONDED TORSION OTHERS (A): 387 ; 0.106 ; 0.500 REMARK 3 H-BOND (X...Y) REFINED ATOMS (A): 113 ; 0.293 ;99.999 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): 17 ; 0.163 ; NULL REMARK 3 SYMMETRY VDW OTHERS (A): 72 ; 0.326 ; NULL REMARK 3 SYMMETRY H-BOND REFINED ATOMS (A): 35 ; 0.141 ;99.999 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): 364 ; 2.499 ; 2.000 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): 137 ; 1.359 ; 2.000 REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 575 ; 3.166 ; 3.000 REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 371 ; 4.852 ; 5.000 REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 338 ; 6.560 ;10.000 REMARK 3 REMARK 3 ANISOTROPIC THERMAL FACTOR RESTRAINTS. COUNT RMS WEIGHT REMARK 3 RIGID-BOND RESTRAINTS (A**2): 714 ; 2.563 ; 3.000 REMARK 3 SPHERICITY; FREE ATOMS (A**2): 122 ;20.897 ; 8.000 REMARK 3 SPHERICITY; BONDED ATOMS (A**2): 598 ; 6.865 ; 8.000 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 : 1.40 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 REMARK 3 RIDING POSITIONS REMARK 4 REMARK 4 2RK1 COMPLIES WITH FORMAT V. 3.15, 01-DEC-08 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 29-NOV-07. REMARK 100 THE RCSB ID CODE IS RCSB044953. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 17-MAR-05 REMARK 200 TEMPERATURE (KELVIN) : 100.0 REMARK 200 PH : 8.00 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : N REMARK 200 RADIATION SOURCE : ROTATING ANODE REMARK 200 BEAMLINE : NULL REMARK 200 X-RAY GENERATOR MODEL : RIGAKU MICROMAX-007 HF REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.5418 REMARK 200 MONOCHROMATOR : CONFOCAL MIRRORS (VARIMAX HF) REMARK 200 OPTICS : VARIMAX HF, CONFOCAL MIRRORS REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : RIGAKU SATURN 92 REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : HKL-2000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 15838 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.260 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 (%) : 99.6 REMARK 200 DATA REDUNDANCY : 12.400 REMARK 200 R MERGE (I) : 0.07200 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 14.1000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.26 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.29 REMARK 200 COMPLETENESS FOR SHELL (%) : 96.5 REMARK 200 DATA REDUNDANCY IN SHELL : 5.40 REMARK 200 R MERGE FOR SHELL (I) : 0.49900 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 3.000 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: CNS REMARK 200 STARTING MODEL: 2RH2 REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 44.79 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.23 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 50% 2-METHYL-2,4-PENTANEDIOL (MPD), REMARK 280 100 MM TRIS, PH 8.0, VAPOR DIFFUSION, HANGING DROP, REMARK 280 TEMPERATURE 277K, PH 8.00 REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: I 41 2 2 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X+1/2,-Y+1/2,Z+1/2 REMARK 290 3555 -Y,X+1/2,Z+1/4 REMARK 290 4555 Y+1/2,-X,Z+3/4 REMARK 290 5555 -X+1/2,Y,-Z+3/4 REMARK 290 6555 X,-Y+1/2,-Z+1/4 REMARK 290 7555 Y+1/2,X+1/2,-Z+1/2 REMARK 290 8555 -Y,-X,-Z REMARK 290 9555 X+1/2,Y+1/2,Z+1/2 REMARK 290 10555 -X,-Y,Z REMARK 290 11555 -Y+1/2,X,Z+3/4 REMARK 290 12555 Y,-X+1/2,Z+1/4 REMARK 290 13555 -X,Y+1/2,-Z+1/4 REMARK 290 14555 X+1/2,-Y,-Z+3/4 REMARK 290 15555 Y,X,-Z REMARK 290 16555 -Y+1/2,-X+1/2,-Z+1/2 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 33.90200 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 33.90200 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 26.10050 REMARK 290 SMTRY1 3 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 1.000000 0.000000 0.000000 33.90200 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 13.05025 REMARK 290 SMTRY1 4 0.000000 1.000000 0.000000 33.90200 REMARK 290 SMTRY2 4 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 39.15075 REMARK 290 SMTRY1 5 -1.000000 0.000000 0.000000 33.90200 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 5 0.000000 0.000000 -1.000000 39.15075 REMARK 290 SMTRY1 6 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 33.90200 REMARK 290 SMTRY3 6 0.000000 0.000000 -1.000000 13.05025 REMARK 290 SMTRY1 7 0.000000 1.000000 0.000000 33.90200 REMARK 290 SMTRY2 7 1.000000 0.000000 0.000000 33.90200 REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 26.10050 REMARK 290 SMTRY1 8 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY2 8 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 8 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 9 1.000000 0.000000 0.000000 33.90200 REMARK 290 SMTRY2 9 0.000000 1.000000 0.000000 33.90200 REMARK 290 SMTRY3 9 0.000000 0.000000 1.000000 26.10050 REMARK 290 SMTRY1 10 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 10 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 10 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 11 0.000000 -1.000000 0.000000 33.90200 REMARK 290 SMTRY2 11 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 11 0.000000 0.000000 1.000000 39.15075 REMARK 290 SMTRY1 12 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY2 12 -1.000000 0.000000 0.000000 33.90200 REMARK 290 SMTRY3 12 0.000000 0.000000 1.000000 13.05025 REMARK 290 SMTRY1 13 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 13 0.000000 1.000000 0.000000 33.90200 REMARK 290 SMTRY3 13 0.000000 0.000000 -1.000000 13.05025 REMARK 290 SMTRY1 14 1.000000 0.000000 0.000000 33.90200 REMARK 290 SMTRY2 14 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 14 0.000000 0.000000 -1.000000 39.15075 REMARK 290 SMTRY1 15 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY2 15 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 15 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 16 0.000000 -1.000000 0.000000 33.90200 REMARK 290 SMTRY2 16 -1.000000 0.000000 0.000000 33.90200 REMARK 290 SMTRY3 16 0.000000 0.000000 -1.000000 26.10050 REMARK 290 REMARK 290 REMARK: NULL REMARK 300 REMARK 300 BIOMOLECULE: 1 REMARK 300 SEE REMARK 350 FOR THE AUTHOR PROVIDED AND/OR PROGRAM REMARK 300 GENERATED ASSEMBLY INFORMATION FOR THE STRUCTURE IN REMARK 300 THIS ENTRY. THE REMARK MAY ALSO PROVIDE INFORMATION ON REMARK 300 BURIED SURFACE AREA. REMARK 300 REMARK: THE BIOLOGICAL ASSEMBLY IS A TETRAMER GENERATED FROM THE REMARK 300 MONOMER IN THE ASYMMETRIC UNIT WITH THE SYMMETRY OPERATIONS: X, REMARK 300 Y, Z; Y, X, -Z; -X, -Y, Z; -Y, -X, -Z; THE NADP AND REMARK 300 DIHYDROFOLATE LIGANDS SHOULD BE INCLUDED ONLY FOR THE IDENTITY REMARK 300 OPERATOR, AND ASSIGNED FULL OCCUPANCY. WATER MOLECULES THAT REMARK 300 CLASH WITH NADP OR DIHYDROFOLATE SHOULD THEN BE REMOVED TO REMARK 300 OBTAIN THE SET OF WATERS THAT ARE VALID FOR THE TETRAMER. TYR69 REMARK 300 AND GLN67 ARE ALSO ASYMMETRIC, BUT THE CORRELATION OF THEIR REMARK 300 ALTERNATE CONFORMATIONS TO THE ASYMMETRIC LIGAND BINDING HAS NOT REMARK 300 BEEN CONCLUSIVELY DETERMINED. 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: TETRAMERIC 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 0.000000 -1.000000 0.000000 0.00000 REMARK 350 BIOMT2 2 -1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT3 2 0.000000 0.000000 -1.000000 0.00000 REMARK 350 BIOMT1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT2 3 0.000000 -1.000000 0.000000 0.00000 REMARK 350 BIOMT3 3 0.000000 0.000000 1.000000 0.00000 REMARK 350 BIOMT1 4 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT2 4 1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT3 4 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 VAL A 17 REMARK 465 PHE A 18 REMARK 465 PRO A 19 REMARK 465 SER A 20 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 ASN A 21 N CB CG OD1 ND2 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 SER A 34 CB SER A 34 OG -0.087 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 509 DISTANCE = 6.21 ANGSTROMS REMARK 525 HOH A 608 DISTANCE = 5.84 ANGSTROMS REMARK 610 REMARK 610 MISSING HETEROATOM REMARK 610 THE FOLLOWING RESIDUES HAVE MISSING ATOMS (M=MODEL NUMBER; REMARK 610 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; REMARK 610 I=INSERTION CODE): REMARK 610 M RES C SSEQI REMARK 610 DHF A 0 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE DHF A 0 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE NAP A 1 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MRD A 500 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MRD A 501 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MRD A 502 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 2P4T RELATED DB: PDB REMARK 900 A MUTANT FORM OF THE SAME PROTEIN (Q67H) COMPLEXED WITH REMARK 900 NADP. THE MUTANT HAS A HIGHER AFFINITY FOR NADP, BUT REMARK 900 APPEARS TO BIND DIFFERENTLY. REMARK 900 RELATED ID: 2RH2 RELATED DB: PDB REMARK 900 HIGH RESOLUTION STRUCTURE OF THE SAME PROTEIN WITH NO REMARK 900 LIGANDS, USED AS A STARTING MODEL FOR THIS STRUCTURE. DBREF 2RK1 A 17 78 UNP P00383 DYR21_ECOLX 17 78 SEQRES 1 A 62 VAL PHE PRO SER ASN ALA THR PHE GLY MET GLY ASP ARG SEQRES 2 A 62 VAL ARG LYS LYS SER GLY ALA ALA TRP GLN GLY GLN ILE SEQRES 3 A 62 VAL GLY TRP TYR CYS THR ASN LEU THR PRO GLU GLY TYR SEQRES 4 A 62 ALA VAL GLU SER GLU ALA HIS PRO GLY SER VAL GLN ILE SEQRES 5 A 62 TYR PRO VAL ALA ALA LEU GLU ARG ILE ASN HET DHF A 0 13 HET NAP A 1 48 HET MRD A 500 8 HET MRD A 501 8 HET MRD A 502 8 HETNAM DHF DIHYDROFOLIC ACID HETNAM NAP NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE HETNAM MRD (4R)-2-METHYLPENTANE-2,4-DIOL HETSYN NAP 2'-MONOPHOSPHOADENOSINE 5'-DIPHOSPHORIBOSE FORMUL 2 DHF C19 H21 N7 O6 FORMUL 3 NAP C21 H28 N7 O17 P3 FORMUL 4 MRD 3(C6 H14 O2) FORMUL 7 HOH *109(H2 O) SHEET 1 A 5 VAL A 66 PRO A 70 0 SHEET 2 A 5 GLY A 54 SER A 59 -1 N TYR A 55 O TYR A 69 SHEET 3 A 5 GLN A 39 TYR A 46 -1 N VAL A 43 O ALA A 56 SHEET 4 A 5 ARG A 29 LYS A 32 -1 N VAL A 30 O GLY A 40 SHEET 5 A 5 LEU A 74 ARG A 76 -1 O GLU A 75 N ARG A 31 SITE 1 AC1 11 GLN A 67 ILE A 68 TYR A 69 HOH A 547 SITE 2 AC1 11 HOH A 550 HOH A 575 HOH A 581 HOH A 596 SITE 3 AC1 11 HOH A 603 HOH A 605 HOH A 608 SITE 1 AC2 35 LYS A 32 SER A 34 GLY A 35 ALA A 36 SITE 2 AC2 35 LEU A 50 GLY A 64 SER A 65 GLN A 67 SITE 3 AC2 35 ILE A 68 TYR A 69 PRO A 70 ALA A 72 SITE 4 AC2 35 ALA A 73 HOH A 503 HOH A 504 HOH A 506 SITE 5 AC2 35 HOH A 508 HOH A 509 HOH A 510 HOH A 527 SITE 6 AC2 35 HOH A 538 HOH A 547 HOH A 550 HOH A 565 SITE 7 AC2 35 HOH A 567 HOH A 575 HOH A 578 HOH A 581 SITE 8 AC2 35 HOH A 590 HOH A 591 HOH A 592 HOH A 596 SITE 9 AC2 35 HOH A 597 HOH A 605 HOH A 608 SITE 1 AC3 9 ALA A 22 GLY A 25 ARG A 76 ILE A 77 SITE 2 AC3 9 ASN A 78 HOH A 559 HOH A 580 HOH A 595 SITE 3 AC3 9 HOH A 600 SITE 1 AC4 5 GLY A 35 ASN A 49 LEU A 50 PRO A 52 SITE 2 AC4 5 HOH A 570 SITE 1 AC5 4 PHE A 24 GLY A 25 TRP A 45 HOH A 600 CRYST1 67.804 67.804 52.201 90.00 90.00 90.00 I 41 2 2 16 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 0.014748 0.000000 0.000000 0.00000 SCALE2 0.000000 0.014748 0.000000 0.00000 SCALE3 0.000000 0.000000 0.019157 0.00000 MASTER 381 0 5 0 5 0 18 6 0 0 0 5 END