HEADER OXIDOREDUCTASE 29-OCT-93 1DHI
TITLE LONG-RANGE STRUCTURAL EFFECTS IN A SECOND-SITE REVERTANT OF A MUTANT
TITLE 2 DIHYDROFOLATE REDUCTASE
COMPND MOL_ID: 1;
COMPND 2 MOLECULE: DIHYDROFOLATE REDUCTASE;
COMPND 3 CHAIN: A, B;
COMPND 4 EC: 1.5.1.3;
COMPND 5 ENGINEERED: YES
SOURCE MOL_ID: 1;
SOURCE 2 ORGANISM_SCIENTIFIC: ESCHERICHIA COLI;
SOURCE 3 ORGANISM_TAXID: 562
KEYWDS OXIDOREDUCTASE
EXPDTA X-RAY DIFFRACTION
AUTHOR S.J.OATLEY,J.E.VILLAFRANCA,K.A.BROWN,J.KRAUT
REVDAT 4 07-FEB-24 1DHI 1 REMARK SEQADV LINK
REVDAT 3 29-NOV-17 1DHI 1 HELIX
REVDAT 2 24-FEB-09 1DHI 1 VERSN
REVDAT 1 31-JAN-94 1DHI 0
JRNL AUTH K.A.BROWN,E.E.HOWELL,J.KRAUT
JRNL TITL LONG-RANGE STRUCTURAL EFFECTS IN A SECOND-SITE REVERTANT OF
JRNL TITL 2 A MUTANT DIHYDROFOLATE REDUCTASE.
JRNL REF PROC.NATL.ACAD.SCI.USA V. 90 11753 1993
JRNL REFN ISSN 0027-8424
JRNL PMID 8265622
JRNL DOI 10.1073/PNAS.90.24.11753
REMARK 1
REMARK 1 REFERENCE 1
REMARK 1 AUTH A.DION,C.E.LINN,T.D.BRADRICK,S.GEORGHIOU,E.E.HOWELL
REMARK 1 TITL HOW DO MUTATION AT PHENYLALANINE-153 AND ISOLEUCINE-155
REMARK 1 TITL 2 PARTIALLY SUPPRESS THE EFFECTS OF THE ASPARTATE-27-> SERINE
REMARK 1 TITL 3 MUTATION IN ESCHERICHIA COLI DIHYDROFOLATE REDUCTASE
REMARK 1 REF BIOCHEMISTRY V. 32 3479 1993
REMARK 1 REFN ISSN 0006-2960
REMARK 1 REFERENCE 2
REMARK 1 AUTH J.R.APPLEMAN,E.E.HOWELL,J.KRAUT,R.L.BLAKELY
REMARK 1 TITL ROLE OF ASPARTATE 27 OF DIHYDROFOLATE REDUCTASE FROM
REMARK 1 TITL 2 ESCHERICHIA COLI IN INTERCONVERSION OF ACTIVE AND INACTIVE
REMARK 1 TITL 3 ENZYME CONFORMERS AND THE BINDING OF NADPH
REMARK 1 REF J.BIOL.CHEM. V. 265 5579 1990
REMARK 1 REFN ISSN 0021-9258
REMARK 1 REFERENCE 3
REMARK 1 AUTH E.E.HOWELL,C.BOOTH,M.FARNUM,J.KRAUT,M.S.WARREN
REMARK 1 TITL A SECOND-SITE MUTATION AT PHENYLALANINE-137 THAT INCREASES
REMARK 1 TITL 2 CATALYTIC EFFICIENCY IN THE MUTANT ASPARTATE-27-> SERINE
REMARK 1 TITL 3 ESCHERICHIA COLI DIHYDROFOLATE REDUCTASE
REMARK 1 REF BIOCHEMISTRY V. 29 8561 1990
REMARK 1 REFN ISSN 0006-2960
REMARK 1 REFERENCE 4
REMARK 1 AUTH S.M.DUNN,T.M.LANIGAN,E.E.HOWELL
REMARK 1 TITL DIHYDROFOLATE REDUCTASE FROM ESCHERICHIA COLI: PROBING THE
REMARK 1 TITL 2 ROLE OF ASPARTATE-27 AND PHENYLALANINE-137 IN ENZYME
REMARK 1 TITL 3 CONFORMATION AND THE BINDING OF NADPH
REMARK 1 REF BIOCHEMISTRY V. 29 8569 1990
REMARK 1 REFN ISSN 0006-2960
REMARK 1 REFERENCE 5
REMARK 1 AUTH E.E.HOWELL,J.E.VILLAFRANCA,M.S.WAREN,S.J.OATLEY,J.KRAUT
REMARK 1 TITL FUNCTIONAL ROLE OF ASPARTIC ACID-27 IN DIHYDROFOLATE
REMARK 1 TITL 2 REDUCTASE REVEALED BY MUTAGENESIS
REMARK 1 REF SCIENCE V. 231 1123 1986
REMARK 1 REFN ISSN 0036-8075
REMARK 1 REFERENCE 6
REMARK 1 AUTH J.T.BOLIN,D.J.FILMAN,D.A.MATTHEWS,R.C.HAMLIN,J.KRAUT
REMARK 1 TITL CRYSTAL STRUCTURES OF ESCHERICHIA COLI AND LACTOBACILLUS
REMARK 1 TITL 2 CASEI DIHYDROFOLATE REDUCTASE AT 1.7 ANGSTROMS RESOLUTION.
REMARK 1 TITL 3 I. GENERAL FEATURES AND BINDING OF METHOTREXATE
REMARK 1 REF BIOCHEMISTRY V. 257 13650 1982
REMARK 1 REFN ISSN 0006-2960
REMARK 1 REFERENCE 7
REMARK 1 AUTH D.J.FILMAN,J.T.BOLIN,D.A.MATTHEWS,J.KRAUT
REMARK 1 TITL CRYSTAL STRUCTURES OF ESCHERICHIA COLI AND LACTOBACILLUS
REMARK 1 TITL 2 CASEI DIHYDROFOLATE REDUCTASE AT 1.7 ANGSTROMS RESOLUTION.
REMARK 1 TITL 3 II. ENVIRONMENT OF BOUND NADPH AND IMPLICATIONS FOR
REMARK 1 TITL 4 CATALYSIS
REMARK 1 REF J.BIOL.CHEM. V. 257 13663 1982
REMARK 1 REFN ISSN 0021-9258
REMARK 2
REMARK 2 RESOLUTION. 1.90 ANGSTROMS.
REMARK 3
REMARK 3 REFINEMENT.
REMARK 3 PROGRAM : TNT
REMARK 3 AUTHORS : TRONRUD,TEN EYCK,MATTHEWS
REMARK 3
REMARK 3 DATA USED IN REFINEMENT.
REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.90
REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : NULL
REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL
REMARK 3 COMPLETENESS FOR RANGE (%) : NULL
REMARK 3 NUMBER OF REFLECTIONS : NULL
REMARK 3
REMARK 3 USING DATA ABOVE SIGMA CUTOFF.
REMARK 3 CROSS-VALIDATION METHOD : NULL
REMARK 3 FREE R VALUE TEST SET SELECTION : NULL
REMARK 3 R VALUE (WORKING + TEST SET) : 0.155
REMARK 3 R VALUE (WORKING SET) : NULL
REMARK 3 FREE R VALUE : NULL
REMARK 3 FREE R VALUE TEST SET SIZE (%) : NULL
REMARK 3 FREE R VALUE TEST SET COUNT : NULL
REMARK 3
REMARK 3 USING ALL DATA, NO SIGMA CUTOFF.
REMARK 3 R VALUE (WORKING + TEST SET, NO CUTOFF) : NULL
REMARK 3 R VALUE (WORKING SET, NO CUTOFF) : NULL
REMARK 3 FREE R VALUE (NO CUTOFF) : NULL
REMARK 3 FREE R VALUE TEST SET SIZE (%, NO CUTOFF) : NULL
REMARK 3 FREE R VALUE TEST SET COUNT (NO CUTOFF) : NULL
REMARK 3 TOTAL NUMBER OF REFLECTIONS (NO CUTOFF) : NULL
REMARK 3
REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT.
REMARK 3 PROTEIN ATOMS : 2498
REMARK 3 NUCLEIC ACID ATOMS : 0
REMARK 3 HETEROGEN ATOMS : 69
REMARK 3 SOLVENT ATOMS : 385
REMARK 3
REMARK 3 WILSON B VALUE (FROM FCALC, A**2) : NULL
REMARK 3
REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES. RMS WEIGHT COUNT
REMARK 3 BOND LENGTHS (A) : 0.020 ; NULL ; NULL
REMARK 3 BOND ANGLES (DEGREES) : 2.900 ; NULL ; NULL
REMARK 3 TORSION ANGLES (DEGREES) : NULL ; NULL ; NULL
REMARK 3 PSEUDOROTATION ANGLES (DEGREES) : NULL ; NULL ; NULL
REMARK 3 TRIGONAL CARBON PLANES (A) : NULL ; NULL ; NULL
REMARK 3 GENERAL PLANES (A) : NULL ; NULL ; NULL
REMARK 3 ISOTROPIC THERMAL FACTORS (A**2) : NULL ; NULL ; NULL
REMARK 3 NON-BONDED CONTACTS (A) : NULL ; NULL ; NULL
REMARK 3
REMARK 3 INCORRECT CHIRAL-CENTERS (COUNT) : NULL
REMARK 3
REMARK 3 BULK SOLVENT MODELING.
REMARK 3 METHOD USED : NULL
REMARK 3 KSOL : NULL
REMARK 3 BSOL : NULL
REMARK 3
REMARK 3 RESTRAINT LIBRARIES.
REMARK 3 STEREOCHEMISTRY : NULL
REMARK 3 ISOTROPIC THERMAL FACTOR RESTRAINTS : NULL
REMARK 3
REMARK 3 OTHER REFINEMENT REMARKS: NULL
REMARK 4
REMARK 4 1DHI COMPLIES WITH FORMAT V. 3.30, 13-JUL-11
REMARK 100
REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY BNL.
REMARK 100 THE DEPOSITION ID IS D_1000172782.
REMARK 200
REMARK 200 EXPERIMENTAL DETAILS
REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION
REMARK 200 DATE OF DATA COLLECTION : NULL
REMARK 200 TEMPERATURE (KELVIN) : NULL
REMARK 200 PH : NULL
REMARK 200 NUMBER OF CRYSTALS USED : NULL
REMARK 200
REMARK 200 SYNCHROTRON (Y/N) : NULL
REMARK 200 RADIATION SOURCE : NULL
REMARK 200 BEAMLINE : NULL
REMARK 200 X-RAY GENERATOR MODEL : NULL
REMARK 200 MONOCHROMATIC OR LAUE (M/L) : NULL
REMARK 200 WAVELENGTH OR RANGE (A) : NULL
REMARK 200 MONOCHROMATOR : NULL
REMARK 200 OPTICS : NULL
REMARK 200
REMARK 200 DETECTOR TYPE : NULL
REMARK 200 DETECTOR MANUFACTURER : NULL
REMARK 200 INTENSITY-INTEGRATION SOFTWARE : NULL
REMARK 200 DATA SCALING SOFTWARE : NULL
REMARK 200
REMARK 200 NUMBER OF UNIQUE REFLECTIONS : NULL
REMARK 200 RESOLUTION RANGE HIGH (A) : NULL
REMARK 200 RESOLUTION RANGE LOW (A) : NULL
REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL
REMARK 200
REMARK 200 OVERALL.
REMARK 200 COMPLETENESS FOR RANGE (%) : NULL
REMARK 200 DATA REDUNDANCY : NULL
REMARK 200 R MERGE (I) : NULL
REMARK 200 R SYM (I) : NULL
REMARK 200 <I/SIGMA(I)> 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 <I/SIGMA(I)> FOR SHELL : NULL
REMARK 200
REMARK 200 DIFFRACTION PROTOCOL: NULL
REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: NULL
REMARK 200 SOFTWARE USED: NULL
REMARK 200 STARTING MODEL: NULL
REMARK 200
REMARK 200 REMARK: NULL
REMARK 280
REMARK 280 CRYSTAL
REMARK 280 SOLVENT CONTENT, VS (%): 52.20
REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.57
REMARK 280
REMARK 280 CRYSTALLIZATION CONDITIONS: NULL
REMARK 290
REMARK 290 CRYSTALLOGRAPHIC SYMMETRY
REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 61
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
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 24.64000
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 49.28000
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 36.96000
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 61.60000
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 12.32000
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 TRANSFORMATION PRESENTED ON *MTRIX* RECORDS BELOW WILL
REMARK 300 YIELD APPROXIMATE COORDINATES FOR CHAIN *A* WHEN APPLIED TO
REMARK 300 CHAIN *B*.
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 APPLY THE FOLLOWING TO CHAINS: A, 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 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 PRO A 66 CB CG CD
REMARK 470 THR A 68 OG1 CG2
REMARK 470 ASP A 70 OD1 OD2
REMARK 470 LYS A 76 CG CD CE NZ
REMARK 470 LYS A 106 CE NZ
REMARK 470 GLU A 129 CD OE1 OE2
REMARK 470 PRO A 130 O
REMARK 470 ASP A 131 CB CG OD1 OD2
REMARK 470 ARG A 159 CD NE CZ NH1 NH2
REMARK 470 ASP B 87 OD2
REMARK 470 ASP B 127 OD2
REMARK 470 GLU B 129 CD OE1 OE2
REMARK 470 ASP B 131 CG OD1 OD2
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 HOH B 680 O HOH B 724 2.10
REMARK 500 O HOH A 412 O HOH A 569 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 OD2 ASP B 70 O HOH B 777 5564 1.88
REMARK 500 CB PRO A 130 O HOH A 462 6655 1.91
REMARK 500 O HOH A 463 O HOH B 723 3564 2.11
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 GLU A 48 CD GLU A 48 OE2 0.081
REMARK 500 GLU A 80 CD GLU A 80 OE2 0.079
REMARK 500 GLU A 90 CD GLU A 90 OE2 0.070
REMARK 500 GLU A 118 CD GLU A 118 OE2 0.079
REMARK 500 GLU A 120 CD GLU A 120 OE2 0.072
REMARK 500 GLU A 134 CD GLU A 134 OE2 0.082
REMARK 500 GLU A 157 CD GLU A 157 OE2 0.075
REMARK 500 GLU B 17 CD GLU B 17 OE2 0.098
REMARK 500 GLU B 48 CD GLU B 48 OE2 0.066
REMARK 500 GLU B 80 CD GLU B 80 OE2 0.087
REMARK 500 GLU B 90 CD GLU B 90 OE1 -0.066
REMARK 500 GLU B 101 CD GLU B 101 OE2 0.079
REMARK 500 GLU B 118 CD GLU B 118 OE2 0.086
REMARK 500 GLU B 120 CD GLU B 120 OE2 0.080
REMARK 500 GLU B 139 CD GLU B 139 OE1 0.067
REMARK 500 GLU B 157 CD GLU B 157 OE2 0.084
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 ASP A 11 CB - CG - OD1 ANGL. DEV. = 5.9 DEGREES
REMARK 500 ARG A 12 NE - CZ - NH1 ANGL. DEV. = 4.9 DEGREES
REMARK 500 GLN A 65 CB - CA - C ANGL. DEV. = 13.7 DEGREES
REMARK 500 ASP A 69 CB - CG - OD1 ANGL. DEV. = 5.8 DEGREES
REMARK 500 ASP A 69 CB - CG - OD2 ANGL. DEV. = -8.1 DEGREES
REMARK 500 ASP A 79 CB - CG - OD1 ANGL. DEV. = 6.1 DEGREES
REMARK 500 ASP A 87 CB - CG - OD1 ANGL. DEV. = -5.5 DEGREES
REMARK 500 ARG A 98 CG - CD - NE ANGL. DEV. = -17.1 DEGREES
REMARK 500 ARG A 98 CD - NE - CZ ANGL. DEV. = 11.5 DEGREES
REMARK 500 ARG A 98 NE - CZ - NH1 ANGL. DEV. = 5.0 DEGREES
REMARK 500 ARG A 98 NE - CZ - NH2 ANGL. DEV. = -6.9 DEGREES
REMARK 500 GLU A 101 CG - CD - OE2 ANGL. DEV. = -12.2 DEGREES
REMARK 500 TYR A 111 CB - CG - CD2 ANGL. DEV. = -4.2 DEGREES
REMARK 500 ASP A 132 CB - CG - OD2 ANGL. DEV. = -7.0 DEGREES
REMARK 500 ASP A 142 CB - CG - OD2 ANGL. DEV. = -6.5 DEGREES
REMARK 500 ASP A 144 CB - CG - OD2 ANGL. DEV. = -5.8 DEGREES
REMARK 500 ASP B 11 CB - CG - OD1 ANGL. DEV. = 7.1 DEGREES
REMARK 500 ASP B 11 CB - CG - OD2 ANGL. DEV. = -6.1 DEGREES
REMARK 500 ARG B 12 CG - CD - NE ANGL. DEV. = -12.8 DEGREES
REMARK 500 ARG B 12 CD - NE - CZ ANGL. DEV. = 19.3 DEGREES
REMARK 500 ARG B 12 NE - CZ - NH1 ANGL. DEV. = 5.9 DEGREES
REMARK 500 ARG B 12 NE - CZ - NH2 ANGL. DEV. = -6.3 DEGREES
REMARK 500 ARG B 33 NE - CZ - NH1 ANGL. DEV. = 4.0 DEGREES
REMARK 500 ASP B 37 CB - CG - OD1 ANGL. DEV. = 7.2 DEGREES
REMARK 500 ASP B 37 CB - CG - OD2 ANGL. DEV. = -6.1 DEGREES
REMARK 500 ARG B 52 NE - CZ - NH1 ANGL. DEV. = 4.8 DEGREES
REMARK 500 ASP B 69 CB - CG - OD1 ANGL. DEV. = 8.8 DEGREES
REMARK 500 ASP B 69 CB - CG - OD2 ANGL. DEV. = -5.8 DEGREES
REMARK 500 ASP B 79 CB - CG - OD1 ANGL. DEV. = 9.1 DEGREES
REMARK 500 ASP B 87 CB - CG - OD1 ANGL. DEV. = 5.5 DEGREES
REMARK 500 ASP B 116 CB - CG - OD1 ANGL. DEV. = 6.3 DEGREES
REMARK 500 ASP B 122 CB - CG - OD2 ANGL. DEV. = -6.5 DEGREES
REMARK 500 ASP B 127 CB - CG - OD1 ANGL. DEV. = 6.4 DEGREES
REMARK 500 ASP B 142 CB - CG - OD1 ANGL. DEV. = 6.7 DEGREES
REMARK 500 ASP B 142 CB - CG - OD2 ANGL. DEV. = -5.9 DEGREES
REMARK 500 ASP B 144 CB - CG - OD1 ANGL. DEV. = 9.2 DEGREES
REMARK 500 ASP B 144 CB - CG - OD2 ANGL. DEV. = -7.0 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 A 17 -58.80 -146.66
REMARK 500 PRO A 130 11.97 -54.34
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 620 CA
REMARK 620 N RES CSSEQI ATOM
REMARK 620 1 HOH A 483 O
REMARK 620 2 SER B 135 O 92.3
REMARK 620 3 HOH B 658 O 87.0 91.3
REMARK 620 4 HOH B 659 O 92.6 173.2 84.2
REMARK 620 5 HOH B 661 O 177.7 89.7 91.9 85.3
REMARK 620 6 HOH B 673 O 89.9 95.9 172.2 88.8 90.9
REMARK 620 N 1 2 3 4 5
REMARK 800
REMARK 800 SITE
REMARK 800 SITE_IDENTIFIER: APT
REMARK 800 EVIDENCE_CODE: AUTHOR
REMARK 800 SITE_DESCRIPTION: RESIDUES INTERACTING WITH THE PTERIDINE OF THE
REMARK 800 METHOTREXATE INHIBITOR IN CHAIN A
REMARK 800
REMARK 800 SITE_IDENTIFIER: ANM
REMARK 800 EVIDENCE_CODE: AUTHOR
REMARK 800 SITE_DESCRIPTION: RESIDUES INTERACTING WITH THE N(10) METHYL OF
REMARK 800 THE METHOTREXATE INHIBITOR IN CHAIN A
REMARK 800
REMARK 800 SITE_IDENTIFIER: AAB
REMARK 800 EVIDENCE_CODE: AUTHOR
REMARK 800 SITE_DESCRIPTION: RESIDUES INTERACTING WITH THE P-AMINO BENZOYL OF
REMARK 800 THE METHOTREXATE INHIBITOR IN CHAIN A
REMARK 800
REMARK 800 SITE_IDENTIFIER: AGL
REMARK 800 EVIDENCE_CODE: AUTHOR
REMARK 800 SITE_DESCRIPTION: RESIDUES INTERACTING WITH THE GLUTAMATE OF THE
REMARK 800 METHOTREXATE INHIBITOR IN CHAIN A
REMARK 800
REMARK 800 SITE_IDENTIFIER: BPT
REMARK 800 EVIDENCE_CODE: AUTHOR
REMARK 800 SITE_DESCRIPTION: RESIDUES INTERACTING WITH THE PTERIDINE OF THE
REMARK 800 METHOTREXATE INHIBITOR IN CHAIN B
REMARK 800
REMARK 800 SITE_IDENTIFIER: BNM
REMARK 800 EVIDENCE_CODE: AUTHOR
REMARK 800 SITE_DESCRIPTION: RESIDUES INTERACTING WITH THE N(10) METHYL OF
REMARK 800 THE METHOTREXATE INHIBITOR IN CHAIN B
REMARK 800
REMARK 800 SITE_IDENTIFIER: BAB
REMARK 800 EVIDENCE_CODE: AUTHOR
REMARK 800 SITE_DESCRIPTION: RESIDUES INTERACTING WITH THE P-AMINO BENZOYL OF
REMARK 800 THE METHOTREXATE INHIBITOR IN CHAIN B
REMARK 800
REMARK 800 SITE_IDENTIFIER: BGL
REMARK 800 EVIDENCE_CODE: AUTHOR
REMARK 800 SITE_DESCRIPTION: RESIDUES INTERACTING WITH THE GLUTAMATE OF THE
REMARK 800 METHOTREXATE INHIBITOR IN CHAIN B
REMARK 800
REMARK 800 SITE_IDENTIFIER: AC1
REMARK 800 EVIDENCE_CODE: SOFTWARE
REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CL A 401
REMARK 800
REMARK 800 SITE_IDENTIFIER: AC2
REMARK 800 EVIDENCE_CODE: SOFTWARE
REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CL B 605
REMARK 800
REMARK 800 SITE_IDENTIFIER: AC3
REMARK 800 EVIDENCE_CODE: SOFTWARE
REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CA B 620
REMARK 800
REMARK 800 SITE_IDENTIFIER: AC4
REMARK 800 EVIDENCE_CODE: SOFTWARE
REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MTX A 161
REMARK 800
REMARK 800 SITE_IDENTIFIER: AC5
REMARK 800 EVIDENCE_CODE: SOFTWARE
REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MTX B 361
REMARK 999
REMARK 999 SEQUENCE
REMARK 999 SEQUENCE ADVISORY NOTICE:
REMARK 999 DIFFERENCE BETWEEN SWISS-PROT AND PDB SEQUENCE.
REMARK 999
REMARK 999 SWISS-PROT ENTRY NAME: DYRA_ECOLI
REMARK 999
REMARK 999 SWISS-PROT RESIDUE PDB SEQRES
REMARK 999 NAME NUMBER NAME CHAIN SEQ/INSERT CODE
REMARK 999 ASN 37 ASP A 37
REMARK 999 ASN 37 ASP B 37
DBREF 1DHI A 1 159 UNP P0ABQ4 DYR_ECOLI 1 159
DBREF 1DHI B 1 159 UNP P0ABQ4 DYR_ECOLI 1 159
SEQADV 1DHI SER A 27 UNP P0ABQ4 ASP 27 CONFLICT
SEQADV 1DHI ASP A 37 UNP P0ABQ4 ASN 37 CONFLICT
SEQADV 1DHI SER B 27 UNP P0ABQ4 ASP 27 CONFLICT
SEQADV 1DHI ASP B 37 UNP P0ABQ4 ASN 37 CONFLICT
SEQRES 1 A 159 MET ILE SER LEU ILE ALA ALA LEU ALA VAL ASP ARG VAL
SEQRES 2 A 159 ILE GLY MET GLU ASN ALA MET PRO TRP ASN LEU PRO ALA
SEQRES 3 A 159 SER LEU ALA TRP PHE LYS ARG ASN THR LEU ASP LYS PRO
SEQRES 4 A 159 VAL ILE MET GLY ARG HIS THR TRP GLU SER ILE GLY ARG
SEQRES 5 A 159 PRO LEU PRO GLY ARG LYS ASN ILE ILE LEU SER SER GLN
SEQRES 6 A 159 PRO GLY THR ASP ASP ARG VAL THR TRP VAL LYS SER VAL
SEQRES 7 A 159 ASP GLU ALA ILE ALA ALA CYS GLY ASP VAL PRO GLU ILE
SEQRES 8 A 159 MET VAL ILE GLY GLY GLY ARG VAL TYR GLU GLN PHE LEU
SEQRES 9 A 159 PRO LYS ALA GLN LYS LEU TYR LEU THR HIS ILE ASP ALA
SEQRES 10 A 159 GLU VAL GLU GLY ASP THR HIS PHE PRO ASP TYR GLU PRO
SEQRES 11 A 159 ASP ASP TRP GLU SER VAL PHE SER GLU PHE HIS ASP ALA
SEQRES 12 A 159 ASP ALA GLN ASN SER HIS SER TYR CYS PHE GLU ILE LEU
SEQRES 13 A 159 GLU ARG ARG
SEQRES 1 B 159 MET ILE SER LEU ILE ALA ALA LEU ALA VAL ASP ARG VAL
SEQRES 2 B 159 ILE GLY MET GLU ASN ALA MET PRO TRP ASN LEU PRO ALA
SEQRES 3 B 159 SER LEU ALA TRP PHE LYS ARG ASN THR LEU ASP LYS PRO
SEQRES 4 B 159 VAL ILE MET GLY ARG HIS THR TRP GLU SER ILE GLY ARG
SEQRES 5 B 159 PRO LEU PRO GLY ARG LYS ASN ILE ILE LEU SER SER GLN
SEQRES 6 B 159 PRO GLY THR ASP ASP ARG VAL THR TRP VAL LYS SER VAL
SEQRES 7 B 159 ASP GLU ALA ILE ALA ALA CYS GLY ASP VAL PRO GLU ILE
SEQRES 8 B 159 MET VAL ILE GLY GLY GLY ARG VAL TYR GLU GLN PHE LEU
SEQRES 9 B 159 PRO LYS ALA GLN LYS LEU TYR LEU THR HIS ILE ASP ALA
SEQRES 10 B 159 GLU VAL GLU GLY ASP THR HIS PHE PRO ASP TYR GLU PRO
SEQRES 11 B 159 ASP ASP TRP GLU SER VAL PHE SER GLU PHE HIS ASP ALA
SEQRES 12 B 159 ASP ALA GLN ASN SER HIS SER TYR CYS PHE GLU ILE LEU
SEQRES 13 B 159 GLU ARG ARG
HET CL A 401 1
HET MTX A 161 33
HET CL B 605 1
HET CA B 620 1
HET MTX B 361 33
HETNAM CL CHLORIDE ION
HETNAM MTX METHOTREXATE
HETNAM CA CALCIUM ION
FORMUL 3 CL 2(CL 1-)
FORMUL 4 MTX 2(C20 H22 N8 O5)
FORMUL 6 CA CA 2+
FORMUL 8 HOH *385(H2 O)
HELIX 1 HBA LEU A 24 THR A 35 1 12
HELIX 2 HCA GLY A 43 ILE A 50 1 8
HELIX 3 HEA SER A 77 GLY A 86 1 10
HELIX 4 HFA GLY A 96 LEU A 104 1 9
HELIX 5 HBB LEU B 24 THR B 35 1 12
HELIX 6 HCB GLY B 43 ILE B 50 1 8
HELIX 7 HEB SER B 77 GLY B 86 1 10
HELIX 8 HFB GLY B 96 LEU B 104 1 9
SHEET 1 S1A 8 THR A 73 VAL A 75 0
SHEET 2 S1A 8 LYS A 58 SER A 63 1 O ASN A 59 N THR A 73
SHEET 3 S1A 8 PRO A 39 GLY A 43 1 N VAL A 40 O LYS A 58
SHEET 4 S1A 8 ILE A 91 GLY A 95 1 N MET A 92 O PRO A 39
SHEET 5 S1A 8 MET A 1 LEU A 8 1 O MET A 1 N ILE A 91
SHEET 6 S1A 8 GLN A 108 ASP A 116 1 O LYS A 109 N LEU A 4
SHEET 7 S1A 8 SER A 150 ARG A 159 -1 N ARG A 158 O GLN A 108
SHEET 8 S1A 8 ASP A 132 HIS A 141 -1 N GLU A 134 O GLU A 157
SHEET 1 S1B 8 THR B 73 VAL B 75 0
SHEET 2 S1B 8 LYS B 58 SER B 63 1 O ASN B 59 N THR B 73
SHEET 3 S1B 8 PRO B 39 GLY B 43 1 N VAL B 40 O LYS B 58
SHEET 4 S1B 8 PRO B 89 GLY B 95 1 N MET B 92 O PRO B 39
SHEET 5 S1B 8 MET B 1 LEU B 8 1 O MET B 1 N ILE B 91
SHEET 6 S1B 8 GLN B 108 ASP B 116 1 O LYS B 109 N LEU B 4
SHEET 7 S1B 8 SER B 150 ARG B 159 -1 N ARG B 158 O GLN B 108
SHEET 8 S1B 8 ASP B 132 HIS B 141 -1 N GLU B 134 O GLU B 157
LINK O HOH A 483 CA CA B 620 2665 1555 2.34
LINK O SER B 135 CA CA B 620 1555 1555 2.28
LINK CA CA B 620 O HOH B 658 1555 1555 2.31
LINK CA CA B 620 O HOH B 659 1555 2665 2.42
LINK CA CA B 620 O HOH B 661 1555 2665 2.49
LINK CA CA B 620 O HOH B 673 1555 1555 2.36
CISPEP 1 GLY A 95 GLY A 96 0 2.83
CISPEP 2 GLY B 95 GLY B 96 0 2.85
SITE 1 APT 11 ILE A 5 ALA A 6 ALA A 7 TRP A 22
SITE 2 APT 11 SER A 27 LEU A 28 PHE A 31 ILE A 94
SITE 3 APT 11 THR A 113 HOH A 404 HOH A 410
SITE 1 ANM 1 SER A 49
SITE 1 AAB 5 LEU A 28 PHE A 31 ILE A 50 ARG A 52
SITE 2 AAB 5 LEU A 54
SITE 1 AGL 5 LEU A 28 PHE A 31 LYS A 32 LEU A 54
SITE 2 AGL 5 ARG A 57
SITE 1 BPT 11 ILE B 5 ALA B 6 ALA B 7 TRP B 22
SITE 2 BPT 11 SER B 27 LEU B 28 PHE B 31 ILE B 94
SITE 3 BPT 11 THR B 113 HOH B 627 HOH B 656
SITE 1 BNM 1 SER B 49
SITE 1 BAB 5 LEU B 28 PHE B 31 ILE B 50 ARG B 52
SITE 2 BAB 5 LEU B 54
SITE 1 BGL 5 LEU B 28 PHE B 31 LYS B 32 LEU B 54
SITE 2 BGL 5 ARG B 57
SITE 1 AC1 5 GLY A 43 HIS A 45 THR A 46 GLY A 96
SITE 2 AC1 5 HOH A 464
SITE 1 AC2 4 GLY B 43 HIS B 45 THR B 46 GLY B 96
SITE 1 AC3 6 HOH A 483 SER B 135 HOH B 658 HOH B 659
SITE 2 AC3 6 HOH B 661 HOH B 673
SITE 1 AC4 13 ILE A 5 ALA A 6 PHE A 31 LYS A 32
SITE 2 AC4 13 SER A 49 ILE A 50 ARG A 52 ARG A 57
SITE 3 AC4 13 ILE A 94 TYR A 100 THR A 113 HOH A 496
SITE 4 AC4 13 HOH A 525
SITE 1 AC5 13 ILE B 5 ALA B 6 PHE B 31 LYS B 32
SITE 2 AC5 13 ILE B 50 ARG B 52 ARG B 57 ILE B 94
SITE 3 AC5 13 TYR B 100 THR B 113 HOH B 656 HOH B 696
SITE 4 AC5 13 HOH B 713
CRYST1 93.190 93.190 73.920 90.00 90.00 120.00 P 61 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 0.010731 0.006195 0.000000 0.00000
SCALE2 0.000000 0.012391 0.000000 0.00000
SCALE3 0.000000 0.000000 0.013528 0.00000
MTRIX1 1 -0.924500 -0.374890 0.069060 59.67269 1
MTRIX2 1 -0.333130 0.706490 -0.624410 46.60130 1
MTRIX3 1 0.185290 -0.600270 -0.778030 96.32106 1
(ATOM LINES ARE NOT SHOWN.)
END