HEADER OXIDOREDUCTASE 29-OCT-93 1DHJ 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 K.A.BROWN,J.KRAUT REVDAT 4 07-FEB-24 1DHJ 1 REMARK SEQADV LINK REVDAT 3 29-NOV-17 1DHJ 1 HELIX REVDAT 2 24-FEB-09 1DHJ 1 VERSN REVDAT 1 31-JAN-94 1DHJ 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. 1.80 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) : 1.80 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) : 0.167 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 : 2494 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 69 REMARK 3 SOLVENT ATOMS : 404 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) : 3.000 ; 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 1DHJ 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_1000172783. 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 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: 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 (%): 51.51 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.54 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 24.57333 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 49.14667 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 36.86000 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 61.43333 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 12.28667 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 LYS A 76 CG CD CE NZ REMARK 470 LYS A 106 CE NZ REMARK 470 GLU A 129 CD OE1 OE2 REMARK 470 ASP A 131 CG OD1 OD2 REMARK 470 ARG A 159 CD NE CZ NH1 NH2 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 A 410 O HOH A 585 2.15 REMARK 500 O PRO A 130 O TRP A 133 2.16 REMARK 500 O HOH B 635 O HOH B 800 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 OD2 ASP B 70 O HOH B 789 5564 2.04 REMARK 500 O HOH A 569 O HOH B 728 3564 2.09 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 0.067 REMARK 500 GLU A 118 CD GLU A 118 OE2 0.092 REMARK 500 GLU A 120 CD GLU A 120 OE2 0.079 REMARK 500 GLU A 134 CD GLU A 134 OE2 0.082 REMARK 500 GLU A 139 CD GLU A 139 OE1 0.084 REMARK 500 SER B 27 CB SER B 27 OG -0.085 REMARK 500 GLU B 48 CD GLU B 48 OE2 0.077 REMARK 500 GLU B 80 CD GLU B 80 OE2 0.077 REMARK 500 GLU B 101 CD GLU B 101 OE2 0.101 REMARK 500 GLU B 118 CD GLU B 118 OE2 0.095 REMARK 500 GLU B 134 CD GLU B 134 OE2 0.072 REMARK 500 SER B 150 CB SER B 150 OG -0.097 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. = 5.7 DEGREES REMARK 500 ASP A 11 CB - CG - OD2 ANGL. DEV. = -7.4 DEGREES REMARK 500 ARG A 12 NE - CZ - NH1 ANGL. DEV. = 3.4 DEGREES REMARK 500 ARG A 12 NE - CZ - NH2 ANGL. DEV. = -3.2 DEGREES REMARK 500 ARG A 33 NE - CZ - NH1 ANGL. DEV. = 3.6 DEGREES REMARK 500 ARG A 33 NE - CZ - NH2 ANGL. DEV. = -3.1 DEGREES REMARK 500 ARG A 57 NE - CZ - NH1 ANGL. DEV. = 3.1 DEGREES REMARK 500 ARG A 57 NE - CZ - NH2 ANGL. DEV. = -3.1 DEGREES REMARK 500 ASP A 69 CB - CG - OD2 ANGL. DEV. = -8.0 DEGREES REMARK 500 ARG A 98 NE - CZ - NH1 ANGL. DEV. = 3.4 DEGREES REMARK 500 ARG A 98 NE - CZ - NH2 ANGL. DEV. = -4.2 DEGREES REMARK 500 ASP A 116 CB - CG - OD1 ANGL. DEV. = 7.4 DEGREES REMARK 500 ASP A 122 CB - CG - OD2 ANGL. DEV. = -6.6 DEGREES REMARK 500 ASP A 132 CB - CG - OD2 ANGL. DEV. = -6.0 DEGREES REMARK 500 SER A 138 CB - CA - C ANGL. DEV. = 12.9 DEGREES REMARK 500 ASP A 142 CB - CG - OD1 ANGL. DEV. = 7.8 DEGREES REMARK 500 ASP A 142 CB - CG - OD2 ANGL. DEV. = -7.3 DEGREES REMARK 500 ARG A 158 NE - CZ - NH1 ANGL. DEV. = 4.8 DEGREES REMARK 500 ARG A 158 NE - CZ - NH2 ANGL. DEV. = -4.2 DEGREES REMARK 500 ASP B 11 CB - CG - OD1 ANGL. DEV. = 6.1 DEGREES REMARK 500 ASP B 11 CB - CG - OD2 ANGL. DEV. = -5.7 DEGREES REMARK 500 ARG B 12 NE - CZ - NH1 ANGL. DEV. = 6.0 DEGREES REMARK 500 ARG B 12 NE - CZ - NH2 ANGL. DEV. = -5.7 DEGREES REMARK 500 SER B 27 N - CA - CB ANGL. DEV. = 15.0 DEGREES REMARK 500 ASP B 37 CB - CG - OD1 ANGL. DEV. = 7.3 DEGREES REMARK 500 ASP B 37 CB - CG - OD2 ANGL. DEV. = -9.8 DEGREES REMARK 500 ARG B 44 NE - CZ - NH1 ANGL. DEV. = 3.3 DEGREES REMARK 500 ARG B 52 NE - CZ - NH1 ANGL. DEV. = 6.8 DEGREES REMARK 500 ASP B 69 CB - CG - OD1 ANGL. DEV. = 7.1 DEGREES REMARK 500 ASP B 70 CB - CG - OD1 ANGL. DEV. = 6.5 DEGREES REMARK 500 ASP B 79 CB - CG - OD1 ANGL. DEV. = 6.2 DEGREES REMARK 500 ASP B 79 CB - CG - OD2 ANGL. DEV. = -5.9 DEGREES REMARK 500 ASP B 87 CB - CG - OD1 ANGL. DEV. = 6.1 DEGREES REMARK 500 ASP B 87 CB - CG - OD2 ANGL. DEV. = -6.8 DEGREES REMARK 500 ASP B 116 CB - CG - OD2 ANGL. DEV. = -5.4 DEGREES REMARK 500 ASP B 122 CB - CG - OD2 ANGL. DEV. = -6.0 DEGREES REMARK 500 HIS B 124 N - CA - CB ANGL. DEV. = -12.3 DEGREES REMARK 500 ASP B 127 CB - CG - OD2 ANGL. DEV. = -6.4 DEGREES REMARK 500 ASP B 132 CB - CG - OD2 ANGL. DEV. = -6.3 DEGREES REMARK 500 SER B 137 CB - CA - C ANGL. DEV. = -12.4 DEGREES REMARK 500 ASP B 144 CB - CG - OD1 ANGL. DEV. = 6.6 DEGREES REMARK 500 ASP B 144 CB - CG - OD2 ANGL. DEV. = -6.0 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 -53.25 -123.69 REMARK 500 PRO A 130 1.66 -53.81 REMARK 500 PRO B 130 0.43 -62.88 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: PLANAR GROUPS REMARK 500 REMARK 500 PLANAR GROUPS IN THE FOLLOWING RESIDUES HAVE A TOTAL REMARK 500 RMS DISTANCE OF ALL ATOMS FROM THE BEST-FIT PLANE REMARK 500 BY MORE THAN AN EXPECTED VALUE OF 6*RMSD, WITH AN REMARK 500 RMSD 0.02 ANGSTROMS, OR AT LEAST ONE ATOM HAS REMARK 500 AN RMSD GREATER THAN THIS VALUE REMARK 500 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 500 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 M RES CSSEQI RMS TYPE REMARK 500 GLU A 17 0.07 SIDE CHAIN REMARK 500 ASN A 23 0.10 SIDE CHAIN REMARK 500 GLU A 80 0.08 SIDE CHAIN REMARK 500 ASN B 23 0.07 SIDE CHAIN 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 484 O REMARK 620 2 SER B 135 O 97.6 REMARK 620 3 HOH B 659 O 71.9 70.6 REMARK 620 4 HOH B 660 O 84.0 85.1 142.5 REMARK 620 5 HOH B 661 O 89.6 166.1 123.1 83.9 REMARK 620 6 HOH B 663 O 173.4 83.8 114.6 89.7 87.8 REMARK 620 7 HOH B 676 O 101.4 105.6 50.1 167.0 84.4 84.4 REMARK 620 N 1 2 3 4 5 6 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 1DHJ A 1 159 UNP P0ABQ4 DYR_ECOLI 1 159 DBREF 1DHJ B 1 159 UNP P0ABQ4 DYR_ECOLI 1 159 SEQADV 1DHJ SER A 27 UNP P0ABQ4 ASP 27 CONFLICT SEQADV 1DHJ ASP A 37 UNP P0ABQ4 ASN 37 CONFLICT SEQADV 1DHJ SER A 137 UNP P0ABQ4 PHE 137 CONFLICT SEQADV 1DHJ SER B 27 UNP P0ABQ4 ASP 27 CONFLICT SEQADV 1DHJ ASP B 37 UNP P0ABQ4 ASN 37 CONFLICT SEQADV 1DHJ SER B 137 UNP P0ABQ4 PHE 137 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 SER 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 SER 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 *404(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 484 CA CA B 620 2665 1555 2.36 LINK O SER B 135 CA CA B 620 1555 1555 2.24 LINK CA CA B 620 O HOH B 659 1555 1555 3.25 LINK CA CA B 620 O HOH B 660 1555 1555 2.42 LINK CA CA B 620 O HOH B 661 1555 2665 2.32 LINK CA CA B 620 O HOH B 663 1555 2665 2.59 LINK CA CA B 620 O HOH B 676 1555 1555 2.29 CISPEP 1 GLY A 95 GLY A 96 0 3.10 CISPEP 2 GLY B 95 GLY B 96 0 0.54 SITE 1 APT 10 ILE A 5 ALA A 6 ALA A 7 TRP A 22 SITE 2 APT 10 SER A 27 LEU A 28 PHE A 31 ILE A 94 SITE 3 APT 10 THR A 113 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 10 ILE B 5 ALA B 6 ALA B 7 TRP B 22 SITE 2 BPT 10 SER B 27 LEU B 28 PHE B 31 ILE B 94 SITE 3 BPT 10 THR B 113 HOH B 628 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 435 SITE 1 AC2 5 GLY B 43 HIS B 45 THR B 46 GLY B 96 SITE 2 AC2 5 HOH B 742 SITE 1 AC3 6 HOH A 484 SER B 135 HOH B 660 HOH B 661 SITE 2 AC3 6 HOH B 663 HOH B 676 SITE 1 AC4 17 ILE A 5 ALA A 6 ALA A 7 LEU A 28 SITE 2 AC4 17 PHE A 31 LYS A 32 SER A 49 ILE A 50 SITE 3 AC4 17 ARG A 52 ARG A 57 ILE A 94 TYR A 100 SITE 4 AC4 17 THR A 113 HOH A 497 HOH A 526 HOH A 529 SITE 5 AC4 17 HOH A 551 SITE 1 AC5 13 ILE B 5 ALA B 6 ALA B 7 PHE B 31 SITE 2 AC5 13 LYS B 32 ILE B 50 ARG B 52 ARG B 57 SITE 3 AC5 13 ILE B 94 TYR B 100 THR B 113 HOH B 699 SITE 4 AC5 13 HOH B 717 CRYST1 92.490 92.490 73.720 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 0.010812 0.006242 0.000000 0.00000 SCALE2 0.000000 0.012485 0.000000 0.00000 SCALE3 0.000000 0.000000 0.013565 0.00000 MTRIX1 1 -0.927240 -0.367390 0.072450 58.60026 1 MTRIX2 1 -0.329250 0.707700 -0.625100 46.49393 1 MTRIX3 1 0.178390 -0.603470 -0.777170 96.31854 1