HEADER OXIDOREDUCTASE 07-AUG-12 4GH8 TITLE CRYSTAL STRUCTURE OF A 'HUMANIZED' E. COLI DIHYDROFOLATE REDUCTASE COMPND MOL_ID: 1; COMPND 2 MOLECULE: DIHYDROFOLATE REDUCTASE; COMPND 3 CHAIN: B, 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; SOURCE 5 GENE: FOLA, TMRA, B0048, JW0047; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS TETRAHYDROFOLATE, ENZYME CATALYSIS, EVOLUTION, DIHYDROFOLATE KEYWDS 2 REDUCTASE, OXIDOREDUCTASE EXPDTA X-RAY DIFFRACTION AUTHOR J.B.FRENCH,C.T.LIU,P.HANOIAN,T.H.PRINGLE,S.HAMMES-SCHIFFER, AUTHOR 2 S.J.BENKOVIC REVDAT 4 28-FEB-24 4GH8 1 REMARK LINK REVDAT 3 15-NOV-17 4GH8 1 REMARK REVDAT 2 03-JUL-13 4GH8 1 JRNL REVDAT 1 05-JUN-13 4GH8 0 JRNL AUTH C.T.LIU,P.HANOIAN,J.B.FRENCH,T.H.PRINGLE,S.HAMMES-SCHIFFER, JRNL AUTH 2 S.J.BENKOVIC JRNL TITL FUNCTIONAL SIGNIFICANCE OF EVOLVING PROTEIN SEQUENCE IN JRNL TITL 2 DIHYDROFOLATE REDUCTASE FROM BACTERIA TO HUMANS. JRNL REF PROC.NATL.ACAD.SCI.USA V. 110 10159 2013 JRNL REFN ISSN 0027-8424 JRNL PMID 23733948 JRNL DOI 10.1073/PNAS.1307130110 REMARK 2 REMARK 2 RESOLUTION. 1.85 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.5.0110 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) : 1.85 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 50.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 95.1 REMARK 3 NUMBER OF REFLECTIONS : 31872 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) : 0.205 REMARK 3 R VALUE (WORKING SET) : 0.203 REMARK 3 FREE R VALUE : 0.245 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.100 REMARK 3 FREE R VALUE TEST SET COUNT : 1631 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) : 1.85 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.90 REMARK 3 REFLECTION IN BIN (WORKING SET) : 1879 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 80.61 REMARK 3 BIN R VALUE (WORKING SET) : 0.2790 REMARK 3 BIN FREE R VALUE SET COUNT : 100 REMARK 3 BIN FREE R VALUE : 0.3850 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 2544 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 165 REMARK 3 SOLVENT ATOMS : 169 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 22.28 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -2.32000 REMARK 3 B22 (A**2) : 3.67000 REMARK 3 B33 (A**2) : -1.76000 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : -0.71000 REMARK 3 B23 (A**2) : 0.00000 REMARK 3 REMARK 3 ESTIMATED OVERALL COORDINATE ERROR. REMARK 3 ESU BASED ON R VALUE (A): 0.152 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.145 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.106 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 3.629 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.956 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.934 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 2792 ; 0.018 ; 0.022 REMARK 3 BOND LENGTHS OTHERS (A): 1823 ; 0.004 ; 0.020 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 3832 ; 1.816 ; 2.017 REMARK 3 BOND ANGLES OTHERS (DEGREES): 4443 ; 1.141 ; 3.018 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 322 ; 5.867 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 120 ;36.613 ;24.167 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 407 ;13.102 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 15 ;16.301 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 410 ; 0.110 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 3041 ; 0.009 ; 0.021 REMARK 3 GENERAL PLANES OTHERS (A): 544 ; 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): 1638 ; 0.913 ; 1.500 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): 642 ; 0.238 ; 1.500 REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 2655 ; 1.663 ; 2.000 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 1154 ; 2.584 ; 3.000 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 1177 ; 3.866 ; 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 : 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 RIDING REMARK 3 POSITIONS U VALUES : REFINED INDIVIDUALLY REMARK 4 REMARK 4 4GH8 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 20-AUG-12. REMARK 100 THE DEPOSITION ID IS D_1000074179. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 24-JUN-12 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 6.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : CHESS REMARK 200 BEAMLINE : A1 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.987 REMARK 200 MONOCHROMATOR : SI(111) REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 210 REMARK 200 INTENSITY-INTEGRATION SOFTWARE : DENZO REMARK 200 DATA SCALING SOFTWARE : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 31876 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.850 REMARK 200 RESOLUTION RANGE LOW (A) : 50.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 95.2 REMARK 200 DATA REDUNDANCY : 2.600 REMARK 200 R MERGE (I) : 0.07800 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 8.9000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.85 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.88 REMARK 200 COMPLETENESS FOR SHELL (%) : 80.5 REMARK 200 DATA REDUNDANCY IN SHELL : 2.60 REMARK 200 R MERGE FOR SHELL (I) : 0.32700 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: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: MOLREP REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 54.65 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.71 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 200 MM CALCIUM ACETATE 38% PEG 400, PH REMARK 280 6.5, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 293K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 1 21 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,Y+1/2,-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 SMTRY1 2 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 2 0.000000 1.000000 0.000000 31.88650 REMARK 290 SMTRY3 2 0.000000 0.000000 -1.000000 0.00000 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: MONOMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: MONOMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 APPLY THE FOLLOWING TO CHAINS: 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: MONOMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: MONOMERIC REMARK 350 SOFTWARE USED: PISA 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 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 LYS B 54 CG CD CE NZ REMARK 470 ARG B 102 CG CD NE CZ NH1 NH2 REMARK 470 GLU B 105 CG CD OE1 OE2 REMARK 470 GLU B 124 CG CD OE1 OE2 REMARK 470 ASP B 136 CG OD1 OD2 REMARK 470 LYS A 54 CG CD CE NZ REMARK 470 ASP A 74 CG OD1 OD2 REMARK 470 GLU A 84 CD OE1 OE2 REMARK 470 ASP A 120 CG OD1 OD2 REMARK 470 GLU A 138 CG CD OE1 OE2 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 A 45 NE - CZ - NH1 ANGL. DEV. = -3.5 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 PRO B 21 38.29 -91.60 REMARK 500 ASP B 135 -159.17 -79.66 REMARK 500 ASP B 136 44.73 -103.08 REMARK 500 PRO A 21 35.77 -81.04 REMARK 500 REMARK 500 REMARK: NULL REMARK 620 REMARK 620 METAL COORDINATION REMARK 620 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 620 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE): REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 CA B 203 CA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 GLU B 53 O REMARK 620 2 GLU B 53 OE1 80.9 REMARK 620 3 ARG B 56 O 89.1 84.7 REMARK 620 4 HOH B 365 O 91.0 162.7 79.9 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 CA A 204 CA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 GLU A 53 O REMARK 620 2 GLU A 53 OE1 82.2 REMARK 620 3 ARG A 56 O 88.2 81.4 REMARK 620 4 HOH A 370 O 99.2 163.0 81.6 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 CA A 203 CA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP A 131 OD1 REMARK 620 2 ASP A 131 OD2 53.3 REMARK 620 3 GLU A 133 OE1 91.4 75.0 REMARK 620 4 HOH A 354 O 71.4 124.3 102.0 REMARK 620 5 HOH A 355 O 128.5 78.0 90.9 156.4 REMARK 620 N 1 2 3 4 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MTX B 201 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE NDP B 202 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CA B 203 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MTX A 201 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE NDP A 202 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CA A 203 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC7 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CA A 204 REMARK 999 REMARK 999 SEQUENCE REMARK 999 TWO INSERTIONS COMPARING TO UNP P0ABQ4 SEQUENCE, RESIDUE ASN 23 WAS REMARK 999 REPLACED BY TWO AMINO ACIDS (PRO PRO) AND RESIDUES GLY 51 WAS REMARK 999 REPLACED BY FOUR AMINO ACIDS (PRO GLU LYS ASN). DBREF 4GH8 B 1 162 UNP P0ABQ4 DYR_ECOLI 1 158 DBREF 4GH8 A 1 162 UNP P0ABQ4 DYR_ECOLI 1 158 SEQADV 4GH8 PRO B 23 UNP P0ABQ4 ASN 23 SEE REMARK 999 SEQADV 4GH8 PRO B 24 UNP P0ABQ4 ASN 23 SEE REMARK 999 SEQADV 4GH8 PRO B 52 UNP P0ABQ4 GLY 51 SEE REMARK 999 SEQADV 4GH8 GLU B 53 UNP P0ABQ4 GLY 51 SEE REMARK 999 SEQADV 4GH8 LYS B 54 UNP P0ABQ4 GLY 51 SEE REMARK 999 SEQADV 4GH8 ASN B 55 UNP P0ABQ4 GLY 51 SEE REMARK 999 SEQADV 4GH8 PRO A 23 UNP P0ABQ4 ASN 23 SEE REMARK 999 SEQADV 4GH8 PRO A 24 UNP P0ABQ4 ASN 23 SEE REMARK 999 SEQADV 4GH8 PRO A 52 UNP P0ABQ4 GLY 51 SEE REMARK 999 SEQADV 4GH8 GLU A 53 UNP P0ABQ4 GLY 51 SEE REMARK 999 SEQADV 4GH8 LYS A 54 UNP P0ABQ4 GLY 51 SEE REMARK 999 SEQADV 4GH8 ASN A 55 UNP P0ABQ4 GLY 51 SEE REMARK 999 SEQRES 1 B 162 MET ILE SER LEU ILE ALA ALA LEU ALA VAL ASP ARG VAL SEQRES 2 B 162 ILE GLY MET GLU ASN ALA MET PRO TRP PRO PRO LEU PRO SEQRES 3 B 162 ALA ASP LEU ALA TRP PHE LYS ARG ASN THR LEU ASN LYS SEQRES 4 B 162 PRO VAL ILE MET GLY ARG HIS THR TRP GLU SER ILE PRO SEQRES 5 B 162 GLU LYS ASN ARG PRO LEU PRO GLY ARG LYS ASN ILE ILE SEQRES 6 B 162 LEU SER SER GLN PRO GLY THR ASP ASP ARG VAL THR TRP SEQRES 7 B 162 VAL LYS SER VAL ASP GLU ALA ILE ALA ALA CYS GLY ASP SEQRES 8 B 162 VAL PRO GLU ILE MET VAL ILE GLY GLY GLY ARG VAL TYR SEQRES 9 B 162 GLU GLN PHE LEU PRO LYS ALA GLN LYS LEU TYR LEU THR SEQRES 10 B 162 HIS ILE ASP ALA GLU VAL GLU GLY ASP THR HIS PHE PRO SEQRES 11 B 162 ASP TYR GLU PRO ASP ASP TRP GLU SER VAL PHE SER GLU SEQRES 12 B 162 PHE HIS ASP ALA ASP ALA GLN ASN SER HIS SER TYR CYS SEQRES 13 B 162 PHE GLU ILE LEU GLU ARG SEQRES 1 A 162 MET ILE SER LEU ILE ALA ALA LEU ALA VAL ASP ARG VAL SEQRES 2 A 162 ILE GLY MET GLU ASN ALA MET PRO TRP PRO PRO LEU PRO SEQRES 3 A 162 ALA ASP LEU ALA TRP PHE LYS ARG ASN THR LEU ASN LYS SEQRES 4 A 162 PRO VAL ILE MET GLY ARG HIS THR TRP GLU SER ILE PRO SEQRES 5 A 162 GLU LYS ASN ARG PRO LEU PRO GLY ARG LYS ASN ILE ILE SEQRES 6 A 162 LEU SER SER GLN PRO GLY THR ASP ASP ARG VAL THR TRP SEQRES 7 A 162 VAL LYS SER VAL ASP GLU ALA ILE ALA ALA CYS GLY ASP SEQRES 8 A 162 VAL PRO GLU ILE MET VAL ILE GLY GLY GLY ARG VAL TYR SEQRES 9 A 162 GLU GLN PHE LEU PRO LYS ALA GLN LYS LEU TYR LEU THR SEQRES 10 A 162 HIS ILE ASP ALA GLU VAL GLU GLY ASP THR HIS PHE PRO SEQRES 11 A 162 ASP TYR GLU PRO ASP ASP TRP GLU SER VAL PHE SER GLU SEQRES 12 A 162 PHE HIS ASP ALA ASP ALA GLN ASN SER HIS SER TYR CYS SEQRES 13 A 162 PHE GLU ILE LEU GLU ARG HET MTX B 201 33 HET NDP B 202 48 HET CA B 203 1 HET MTX A 201 33 HET NDP A 202 48 HET CA A 203 1 HET CA A 204 1 HETNAM MTX METHOTREXATE HETNAM NDP NADPH DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDE HETNAM 2 NDP PHOSPHATE HETNAM CA CALCIUM ION FORMUL 3 MTX 2(C20 H22 N8 O5) FORMUL 4 NDP 2(C21 H30 N7 O17 P3) FORMUL 5 CA 3(CA 2+) FORMUL 10 HOH *169(H2 O) HELIX 1 1 ALA B 9 ASP B 11 5 3 HELIX 2 2 LEU B 25 LEU B 37 1 13 HELIX 3 3 ARG B 45 SER B 50 1 6 HELIX 4 4 ILE B 51 ARG B 56 5 6 HELIX 5 5 SER B 81 GLY B 90 1 10 HELIX 6 6 GLY B 100 LEU B 108 1 9 HELIX 7 7 PRO B 109 ALA B 111 5 3 HELIX 8 8 ALA A 9 ASP A 11 5 3 HELIX 9 9 LEU A 25 LEU A 37 1 13 HELIX 10 10 ARG A 45 ILE A 51 1 7 HELIX 11 11 PRO A 52 ARG A 56 5 5 HELIX 12 12 SER A 81 GLY A 90 1 10 HELIX 13 13 GLY A 100 LEU A 108 1 9 HELIX 14 14 PRO A 109 ALA A 111 5 3 SHEET 1 A 8 THR B 77 VAL B 79 0 SHEET 2 A 8 ASN B 63 LEU B 66 1 N ILE B 65 O THR B 77 SHEET 3 A 8 VAL B 41 GLY B 44 1 N MET B 43 O LEU B 66 SHEET 4 A 8 ILE B 95 VAL B 97 1 O MET B 96 N ILE B 42 SHEET 5 A 8 ILE B 2 LEU B 8 1 N SER B 3 O ILE B 95 SHEET 6 A 8 LYS B 113 ILE B 119 1 O ILE B 119 N LEU B 8 SHEET 7 A 8 TYR B 155 GLU B 161 -1 O CYS B 156 N HIS B 118 SHEET 8 A 8 GLU B 138 HIS B 145 -1 N VAL B 140 O ILE B 159 SHEET 1 B 2 VAL B 13 GLY B 15 0 SHEET 2 B 2 THR B 127 HIS B 128 -1 O THR B 127 N ILE B 14 SHEET 1 C 8 THR A 77 VAL A 79 0 SHEET 2 C 8 LYS A 62 LEU A 66 1 N ILE A 65 O THR A 77 SHEET 3 C 8 PRO A 40 GLY A 44 1 N VAL A 41 O LYS A 62 SHEET 4 C 8 ILE A 95 VAL A 97 1 O MET A 96 N ILE A 42 SHEET 5 C 8 ILE A 2 LEU A 8 1 N SER A 3 O ILE A 95 SHEET 6 C 8 LYS A 113 ILE A 119 1 O ILE A 119 N LEU A 8 SHEET 7 C 8 TYR A 155 GLU A 161 -1 O CYS A 156 N HIS A 118 SHEET 8 C 8 GLU A 138 HIS A 145 -1 N HIS A 145 O TYR A 155 SHEET 1 D 2 VAL A 13 GLY A 15 0 SHEET 2 D 2 THR A 127 HIS A 128 -1 O THR A 127 N ILE A 14 LINK O GLU B 53 CA CA B 203 1555 1555 2.31 LINK OE1 GLU B 53 CA CA B 203 1555 1555 2.49 LINK O ARG B 56 CA CA B 203 1555 1555 2.32 LINK CA CA B 203 O HOH B 365 1555 1555 2.21 LINK O GLU A 53 CA CA A 204 1555 1555 2.17 LINK OE1 GLU A 53 CA CA A 204 1555 1555 2.45 LINK O ARG A 56 CA CA A 204 1555 1555 2.33 LINK OD1 ASP A 131 CA CA A 203 1555 1555 2.42 LINK OD2 ASP A 131 CA CA A 203 1555 1555 2.45 LINK OE1 GLU A 133 CA CA A 203 1555 1555 2.46 LINK CA CA A 203 O HOH A 354 1555 1555 2.42 LINK CA CA A 203 O HOH A 355 1555 1555 2.32 LINK CA CA A 204 O HOH A 370 1555 1555 2.32 CISPEP 1 ARG B 56 PRO B 57 0 -6.64 CISPEP 2 GLY B 99 GLY B 100 0 8.42 CISPEP 3 ARG A 56 PRO A 57 0 -10.47 CISPEP 4 GLY A 99 GLY A 100 0 6.38 SITE 1 AC1 19 ILE B 5 ALA B 6 ALA B 7 MET B 20 SITE 2 AC1 19 ASP B 28 LEU B 29 PHE B 32 LYS B 33 SITE 3 AC1 19 SER B 50 ASN B 55 ARG B 61 ILE B 98 SITE 4 AC1 19 TYR B 104 THR B 117 NDP B 202 HOH B 303 SITE 5 AC1 19 HOH B 318 HOH B 330 HOH B 366 SITE 1 AC2 28 ALA B 6 ALA B 7 ILE B 14 GLY B 15 SITE 2 AC2 28 ASN B 18 ALA B 19 GLY B 44 ARG B 45 SITE 3 AC2 28 HIS B 46 THR B 47 LEU B 66 SER B 67 SITE 4 AC2 28 SER B 68 LYS B 80 ILE B 98 GLY B 100 SITE 5 AC2 28 GLY B 101 ARG B 102 VAL B 103 TYR B 104 SITE 6 AC2 28 GLN B 106 MTX B 201 HOH B 302 HOH B 312 SITE 7 AC2 28 HOH B 335 HOH B 339 HOH B 340 HOH B 353 SITE 1 AC3 3 GLU B 53 ARG B 56 HOH B 365 SITE 1 AC4 15 ILE A 5 ALA A 6 MET A 20 ASP A 28 SITE 2 AC4 15 PHE A 32 LYS A 33 ASN A 55 ARG A 61 SITE 3 AC4 15 ILE A 98 TYR A 104 THR A 117 NDP A 202 SITE 4 AC4 15 HOH A 305 HOH A 360 HOH A 395 SITE 1 AC5 29 ALA A 6 ALA A 7 ILE A 14 GLY A 15 SITE 2 AC5 29 ASN A 18 ALA A 19 GLY A 44 ARG A 45 SITE 3 AC5 29 HIS A 46 THR A 47 LEU A 66 SER A 67 SITE 4 AC5 29 SER A 68 LYS A 80 ILE A 98 GLY A 100 SITE 5 AC5 29 GLY A 101 ARG A 102 VAL A 103 TYR A 104 SITE 6 AC5 29 GLN A 106 MTX A 201 HOH A 303 HOH A 321 SITE 7 AC5 29 HOH A 330 HOH A 343 HOH A 357 HOH A 364 SITE 8 AC5 29 HOH A 384 SITE 1 AC6 4 ASP A 131 GLU A 133 HOH A 354 HOH A 355 SITE 1 AC7 3 GLU A 53 ARG A 56 HOH A 370 CRYST1 52.245 63.773 62.439 90.00 106.82 90.00 P 1 21 1 4 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 0.019141 0.000000 0.005786 0.00000 SCALE2 0.000000 0.015681 0.000000 0.00000 SCALE3 0.000000 0.000000 0.016731 0.00000