HEADER OXIDOREDUCTASE 16-JUN-20 6XG4 TITLE X-RAY STRUCTURE OF ESCHERICHIA COLI DIHYDROFOLATE REDUCTASE L28R TITLE 2 MUTANT IN COMPLEX WITH TRIMETHOPRIM COMPND MOL_ID: 1; COMPND 2 MOLECULE: DIHYDROFOLATE REDUCTASE; COMPND 3 CHAIN: A; COMPND 4 EC: 1.5.1.3; COMPND 5 ENGINEERED: YES; COMPND 6 MUTATION: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: ESCHERICHIA COLI; SOURCE 3 ORGANISM_TAXID: 83333; SOURCE 4 STRAIN: K12 MG1655; SOURCE 5 GENE: FOLA, TMRA, B0048, JW0047; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 511693; SOURCE 8 EXPRESSION_SYSTEM_STRAIN: BL21; SOURCE 9 EXPRESSION_SYSTEM_VECTOR_TYPE: PET24A KEYWDS DIHYDROFOLATE REDUCTASE, DHFR, MUTANT, COMPLEX, TRIMETHOPRIM, KEYWDS 2 OXIDOREDUCTASE EXPDTA X-RAY DIFFRACTION AUTHOR I.K.GASZEK,M.S.MANNA,D.BOREK,E.TOPRAK REVDAT 3 03-APR-24 6XG4 1 REMARK REVDAT 2 06-OCT-21 6XG4 1 JRNL REVDAT 1 24-MAR-21 6XG4 0 JRNL AUTH M.S.MANNA,Y.T.TAMER,I.GASZEK,N.POULIDES,A.AHMED,X.WANG, JRNL AUTH 2 F.C.R.TOPRAK,D.R.WOODARD,A.Y.KOH,N.S.WILLIAMS,D.BOREK, JRNL AUTH 3 A.R.ATILGAN,J.D.HULLEMAN,C.ATILGAN,U.TAMBAR,E.TOPRAK JRNL TITL A TRIMETHOPRIM DERIVATIVE IMPEDES ANTIBIOTIC RESISTANCE JRNL TITL 2 EVOLUTION. JRNL REF NAT COMMUN V. 12 2949 2021 JRNL REFN ESSN 2041-1723 JRNL PMID 34011959 JRNL DOI 10.1038/S41467-021-23191-Z REMARK 2 REMARK 2 RESOLUTION. 2.10 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.8.0267 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) : 37.37 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 71.0 REMARK 3 NUMBER OF REFLECTIONS : 9837 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 CROSS-VALIDATION METHOD : THROUGHOUT REMARK 3 FREE R VALUE TEST SET SELECTION : FULL CROSS VALIDATION REMARK 3 R VALUE (WORKING + TEST SET) : 0.249 REMARK 3 R VALUE (WORKING SET) : 0.249 REMARK 3 FREE R VALUE : 0.278 REMARK 3 FREE R VALUE TEST SET SIZE (%) : NULL REMARK 3 FREE R VALUE TEST SET COUNT : NULL 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) : 2.16 REMARK 3 REFLECTION IN BIN (WORKING SET) : 212 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 21.72 REMARK 3 BIN R VALUE (WORKING SET) : 0.3390 REMARK 3 BIN FREE R VALUE SET COUNT : NULL REMARK 3 BIN FREE R VALUE : NULL REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 1270 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 76 REMARK 3 SOLVENT ATOMS : 131 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 35.20 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -0.11000 REMARK 3 B22 (A**2) : -0.11000 REMARK 3 B33 (A**2) : 0.35000 REMARK 3 B12 (A**2) : -0.05000 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): 0.369 REMARK 3 ESU BASED ON FREE R VALUE (A): NULL REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.160 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 10.763 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.908 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : NULL REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 1413 ; 0.006 ; 0.013 REMARK 3 BOND LENGTHS OTHERS (A): 1274 ; 0.001 ; 0.017 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 1934 ; 1.417 ; 1.651 REMARK 3 BOND ANGLES OTHERS (DEGREES): 2933 ; 1.112 ; 1.583 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 164 ; 7.560 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 77 ;33.498 ;21.688 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 219 ;18.538 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 11 ;13.371 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 181 ; 0.054 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 1601 ; 0.006 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): 330 ; 0.001 ; 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): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): NULL ; NULL ; NULL 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): 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 : 1 REMARK 3 REMARK 3 TLS GROUP : 1 REMARK 3 NUMBER OF COMPONENTS GROUP : 2 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : A 1 A 159 REMARK 3 RESIDUE RANGE : A 301 A 303 REMARK 3 ORIGIN FOR THE GROUP (A): -11.393 22.809 16.417 REMARK 3 T TENSOR REMARK 3 T11: 0.0775 T22: 0.2198 REMARK 3 T33: 0.1881 T12: -0.0178 REMARK 3 T13: -0.0459 T23: -0.0707 REMARK 3 L TENSOR REMARK 3 L11: 2.6213 L22: 2.2049 REMARK 3 L33: 7.7022 L12: -0.1271 REMARK 3 L13: -0.4206 L23: -0.7783 REMARK 3 S TENSOR REMARK 3 S11: 0.2513 S12: 0.3186 S13: -0.2622 REMARK 3 S21: -0.1330 S22: -0.0206 S23: 0.1122 REMARK 3 S31: 0.4726 S32: 0.0346 S33: -0.2307 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: REMARK 3 HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REMARK 3 WITH TLS ADDED. REMARK 3 REMARK 3 DUE TO ANISOTROPIC LACK OF COMPLETENESS, THE MODEL WAS FIRST REMARK 3 REFINED AGAINST ALL DATA, AND THE RESULTING MODEL WAS REFINED REMARK 3 TWENTY TIMES IN PARALLEL, WITH EACH SET OF REFINEMENTS USING A REMARK 3 DIFFERENT TEST SET, UNTIL THE TWENTY MODELS CONVERGED. THE R-FREE REMARK 3 REPORTED IS THE AVERAGE OF THE TWENTY R-FREE VALUES. REMARK 4 REMARK 4 6XG4 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 30-JUN-20. REMARK 100 THE DEPOSITION ID IS D_1000250089. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 12-JUL-18 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 5.6 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : APS REMARK 200 BEAMLINE : 19-ID REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.97919 REMARK 200 MONOCHROMATOR : SI(111) REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS PILATUS 6M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-3000 REMARK 200 DATA SCALING SOFTWARE : HKL-3000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 13880 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.100 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 (%) : 99.9 REMARK 200 DATA REDUNDANCY : 9.300 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 37.5000 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) : 2.12 REMARK 200 COMPLETENESS FOR SHELL (%) : 100.0 REMARK 200 DATA REDUNDANCY IN SHELL : 8.80 REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 0.700 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: MOLREP REMARK 200 STARTING MODEL: WT DHFR SOLVED IN THE SAME SPACE GROUP REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 59.39 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 3.03 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.1 M SODIUM CITRATE TRIBASIC REMARK 280 DIHYDRATE (PH 5.6), 0.15 M AMMONIUM ACETATE AND 17.5% OR 20% PEG REMARK 280 4000; 10 MM NADPH, 2 MM TMP WAS INCUBATED WITH THE L28R VARIANT REMARK 280 OF DHFR OVERNIGHT AT 293 K, VAPOR DIFFUSION, HANGING DROP REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 32 2 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -Y,X-Y,Z+2/3 REMARK 290 3555 -X+Y,-X,Z+1/3 REMARK 290 4555 Y,X,-Z REMARK 290 5555 X-Y,-Y,-Z+1/3 REMARK 290 6555 -X,-X+Y,-Z+2/3 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 69.77400 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 34.88700 REMARK 290 SMTRY1 4 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 4 0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 4 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 5 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 5 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 5 0.000000 0.000000 -1.000000 34.88700 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 69.77400 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 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 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 465 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 HIS A 160 REMARK 465 HIS A 161 REMARK 465 HIS A 162 REMARK 465 HIS A 163 REMARK 465 HIS A 164 REMARK 465 HIS A 165 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 OD1 ASP A 11 O HOH A 401 2.05 REMARK 500 OD1 ASP A 142 O HOH A 402 2.13 REMARK 500 OD2 ASP A 70 O HOH A 403 2.18 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 A 494 O HOH A 510 5565 2.17 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 THR A 68 19.53 -142.41 REMARK 500 THR A 68 24.41 -145.47 REMARK 500 ASP A 116 70.03 -68.61 REMARK 500 ALA A 143 155.60 -49.65 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 530 DISTANCE = 5.81 ANGSTROMS REMARK 525 HOH A 531 DISTANCE = 6.01 ANGSTROMS REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue NDP A 301 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue GOL A 302 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue TOP A 303 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue CL A 304 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 1DRH RELATED DB: PDB REMARK 900 DHFR IN THE SAME, RARE, CRYSTAL FORM REMARK 900 RELATED ID: 7DFR RELATED DB: PDB REMARK 900 DHFR IN THE SAME, RARE, CRYSTAL FORM REMARK 900 RELATED ID: 1DRE RELATED DB: PDB REMARK 900 DHFR IN THE SAME, RARE, CRYSTAL FORM REMARK 900 RELATED ID: 1RH3 RELATED DB: PDB REMARK 900 DHFR IN THE SAME, RARE, CRYSTAL FORM DBREF 6XG4 A 1 159 UNP P0ABQ4 DYR_ECOLI 1 159 SEQADV 6XG4 ARG A 28 UNP P0ABQ4 LEU 28 ENGINEERED MUTATION SEQADV 6XG4 HIS A 160 UNP P0ABQ4 EXPRESSION TAG SEQADV 6XG4 HIS A 161 UNP P0ABQ4 EXPRESSION TAG SEQADV 6XG4 HIS A 162 UNP P0ABQ4 EXPRESSION TAG SEQADV 6XG4 HIS A 163 UNP P0ABQ4 EXPRESSION TAG SEQADV 6XG4 HIS A 164 UNP P0ABQ4 EXPRESSION TAG SEQADV 6XG4 HIS A 165 UNP P0ABQ4 EXPRESSION TAG SEQRES 1 A 165 MET ILE SER LEU ILE ALA ALA LEU ALA VAL ASP ARG VAL SEQRES 2 A 165 ILE GLY MET GLU ASN ALA MET PRO TRP ASN LEU PRO ALA SEQRES 3 A 165 ASP ARG ALA TRP PHE LYS ARG ASN THR LEU ASN LYS PRO SEQRES 4 A 165 VAL ILE MET GLY ARG HIS THR TRP GLU SER ILE GLY ARG SEQRES 5 A 165 PRO LEU PRO GLY ARG LYS ASN ILE ILE LEU SER SER GLN SEQRES 6 A 165 PRO GLY THR ASP ASP ARG VAL THR TRP VAL LYS SER VAL SEQRES 7 A 165 ASP GLU ALA ILE ALA ALA CYS GLY ASP VAL PRO GLU ILE SEQRES 8 A 165 MET VAL ILE GLY GLY GLY ARG VAL TYR GLU GLN PHE LEU SEQRES 9 A 165 PRO LYS ALA GLN LYS LEU TYR LEU THR HIS ILE ASP ALA SEQRES 10 A 165 GLU VAL GLU GLY ASP THR HIS PHE PRO ASP TYR GLU PRO SEQRES 11 A 165 ASP ASP TRP GLU SER VAL PHE SER GLU PHE HIS ASP ALA SEQRES 12 A 165 ASP ALA GLN ASN SER HIS SER TYR CYS PHE GLU ILE LEU SEQRES 13 A 165 GLU ARG ARG HIS HIS HIS HIS HIS HIS HET NDP A 301 48 HET GOL A 302 6 HET TOP A 303 21 HET CL A 304 1 HETNAM NDP NADPH DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDE HETNAM 2 NDP PHOSPHATE HETNAM GOL GLYCEROL HETNAM TOP TRIMETHOPRIM HETNAM CL CHLORIDE ION HETSYN GOL GLYCERIN; PROPANE-1,2,3-TRIOL FORMUL 2 NDP C21 H30 N7 O17 P3 FORMUL 3 GOL C3 H8 O3 FORMUL 4 TOP C14 H18 N4 O3 FORMUL 5 CL CL 1- FORMUL 6 HOH *131(H2 O) HELIX 1 AA1 LEU A 24 LEU A 36 1 13 HELIX 2 AA2 ARG A 44 GLY A 51 1 8 HELIX 3 AA3 SER A 77 GLY A 86 1 10 HELIX 4 AA4 GLY A 96 LEU A 104 1 9 HELIX 5 AA5 PRO A 105 ALA A 107 5 3 HELIX 6 AA6 GLU A 129 ASP A 131 5 3 SHEET 1 AA1 8 THR A 73 VAL A 75 0 SHEET 2 AA1 8 ASN A 59 LEU A 62 1 N ILE A 61 O THR A 73 SHEET 3 AA1 8 VAL A 40 GLY A 43 1 N VAL A 40 O ILE A 60 SHEET 4 AA1 8 ILE A 91 GLY A 95 1 O GLY A 95 N GLY A 43 SHEET 5 AA1 8 ILE A 2 LEU A 8 1 N SER A 3 O VAL A 93 SHEET 6 AA1 8 LYS A 109 ILE A 115 1 O ILE A 115 N LEU A 8 SHEET 7 AA1 8 TYR A 151 ARG A 158 -1 O GLU A 154 N LEU A 112 SHEET 8 AA1 8 TRP A 133 HIS A 141 -1 N HIS A 141 O TYR A 151 SHEET 1 AA2 2 VAL A 13 GLY A 15 0 SHEET 2 AA2 2 THR A 123 HIS A 124 -1 O THR A 123 N ILE A 14 CISPEP 1 GLY A 95 GLY A 96 0 -5.76 SITE 1 AC1 29 ALA A 6 ALA A 7 ILE A 14 GLY A 15 SITE 2 AC1 29 ASN A 18 ALA A 19 MET A 20 GLY A 43 SITE 3 AC1 29 ARG A 44 HIS A 45 THR A 46 LEU A 62 SITE 4 AC1 29 SER A 63 SER A 64 LYS A 76 VAL A 78 SITE 5 AC1 29 ILE A 94 GLY A 96 GLY A 97 ARG A 98 SITE 6 AC1 29 VAL A 99 TYR A 100 GLN A 102 TOP A 303 SITE 7 AC1 29 HOH A 407 HOH A 427 HOH A 432 HOH A 433 SITE 8 AC1 29 HOH A 446 SITE 1 AC2 7 VAL A 10 ASP A 116 SER A 148 HIS A 149 SITE 2 AC2 7 SER A 150 HOH A 408 HOH A 434 SITE 1 AC3 14 ILE A 5 ALA A 6 MET A 20 ASP A 27 SITE 2 AC3 14 PHE A 31 SER A 49 ILE A 50 ILE A 94 SITE 3 AC3 14 TYR A 100 NDP A 301 HOH A 409 HOH A 440 SITE 4 AC3 14 HOH A 470 HOH A 520 SITE 1 AC4 2 ARG A 98 GLN A 102 CRYST1 61.548 61.548 104.661 90.00 90.00 120.00 P 32 2 1 6 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 0.016247 0.009380 0.000000 0.00000 SCALE2 0.000000 0.018761 0.000000 0.00000 SCALE3 0.000000 0.000000 0.009555 0.00000