HEADER OXIDOREDUCTASE 09-FEB-06 2FZJ TITLE NEW INSIGHTS INTO DHFR INTERACTIONS: ANALYSIS OF PNEUMOCYSTIS CARINII TITLE 2 AND MOUSE DHFR COMPLEXES WITH NADPH AND TWO HIGHLY POTENT TITLE 3 TRIMETHOPRIM DERIVATIVES COMPND MOL_ID: 1; COMPND 2 MOLECULE: DIHYDROFOLATE REDUCTASE; COMPND 3 CHAIN: A; COMPND 4 EC: 1.5.1.3; COMPND 5 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: MUS MUSCULUS; SOURCE 3 ORGANISM_COMMON: HOUSE MOUSE; SOURCE 4 ORGANISM_TAXID: 10090; SOURCE 5 GENE: DHFR; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 8 EXPRESSION_SYSTEM_STRAIN: JM109; SOURCE 9 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 10 EXPRESSION_SYSTEM_PLASMID: PPH70D KEYWDS DIHYDROFOLATE REDUCTASE, TRIMETHOPRIM DERIVATIVES, RING STACKING KEYWDS 2 INTERACTIONS, OXIDOREDUCTASE EXPDTA X-RAY DIFFRACTION AUTHOR V.CODY,J.PACE,K.CHISUM,A.ROSOWSKY REVDAT 4 30-AUG-23 2FZJ 1 REMARK REVDAT 3 20-NOV-13 2FZJ 1 FORMUL HET HETATM HETNAM REVDAT 3 2 1 HETSYN VERSN REVDAT 2 24-FEB-09 2FZJ 1 VERSN REVDAT 1 26-DEC-06 2FZJ 0 JRNL AUTH V.CODY,J.PACE,K.CHISUM,A.ROSOWSKY JRNL TITL NEW INSIGHTS INTO DHFR INTERACTIONS: ANALYSIS OF JRNL TITL 2 PNEUMOCYSTIS CARINII AND MOUSE DHFR COMPLEXES WITH NADPH AND JRNL TITL 3 TWO HIGHLY POTENT 5-(OMEGA-CARBOXY(ALKYLOXY) TRIMETHOPRIM JRNL TITL 4 DERIVATIVES REVEALS CONFORMATIONAL CORRELATIONS WITH JRNL TITL 5 ACTIVITY AND NOVEL PARALLEL RING STACKING INTERACTIONS. JRNL REF PROTEINS V. 65 959 2006 JRNL REFN ISSN 0887-3585 JRNL PMID 17019704 JRNL DOI 10.1002/PROT.21131 REMARK 2 REMARK 2 RESOLUTION. 2.00 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : CNS REMARK 3 AUTHORS : BRUNGER,ADAMS,CLORE,DELANO,GROS,GROSSE- REMARK 3 : KUNSTLEVE,JIANG,KUSZEWSKI,NILGES,PANNU, REMARK 3 : READ,RICE,SIMONSON,WARREN REMARK 3 REMARK 3 REFINEMENT TARGET : ENGH & HUBER REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.00 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 27.86 REMARK 3 DATA CUTOFF (SIGMA(F)) : 2.000 REMARK 3 DATA CUTOFF HIGH (ABS(F)) : NULL REMARK 3 DATA CUTOFF LOW (ABS(F)) : NULL REMARK 3 COMPLETENESS (WORKING+TEST) (%) : 84.4 REMARK 3 NUMBER OF REFLECTIONS : 12441 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 SET) : 0.234 REMARK 3 FREE R VALUE : 0.294 REMARK 3 FREE R VALUE TEST SET SIZE (%) : NULL REMARK 3 FREE R VALUE TEST SET COUNT : 1276 REMARK 3 ESTIMATED ERROR OF FREE R VALUE : NULL REMARK 3 REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN. REMARK 3 TOTAL NUMBER OF BINS USED : NULL REMARK 3 BIN RESOLUTION RANGE HIGH (A) : NULL REMARK 3 BIN RESOLUTION RANGE LOW (A) : NULL REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : NULL REMARK 3 REFLECTIONS IN BIN (WORKING SET) : NULL REMARK 3 BIN R VALUE (WORKING SET) : NULL REMARK 3 BIN FREE R VALUE : NULL REMARK 3 BIN FREE R VALUE TEST SET SIZE (%) : NULL REMARK 3 BIN FREE R VALUE TEST SET COUNT : NULL REMARK 3 ESTIMATED ERROR OF BIN FREE R VALUE : NULL REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 1513 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 75 REMARK 3 SOLVENT ATOMS : 123 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 15.00 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 54.60 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : NULL REMARK 3 B22 (A**2) : NULL REMARK 3 B33 (A**2) : NULL REMARK 3 B12 (A**2) : NULL REMARK 3 B13 (A**2) : NULL REMARK 3 B23 (A**2) : NULL REMARK 3 REMARK 3 ESTIMATED COORDINATE ERROR. REMARK 3 ESD FROM LUZZATI PLOT (A) : NULL REMARK 3 ESD FROM SIGMAA (A) : NULL REMARK 3 LOW RESOLUTION CUTOFF (A) : NULL REMARK 3 REMARK 3 CROSS-VALIDATED ESTIMATED COORDINATE ERROR. REMARK 3 ESD FROM C-V LUZZATI PLOT (A) : NULL REMARK 3 ESD FROM C-V SIGMAA (A) : NULL REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES. REMARK 3 BOND LENGTHS (A) : 0.008 REMARK 3 BOND ANGLES (DEGREES) : 1.230 REMARK 3 DIHEDRAL ANGLES (DEGREES) : NULL REMARK 3 IMPROPER ANGLES (DEGREES) : NULL REMARK 3 REMARK 3 ISOTROPIC THERMAL MODEL : ISOTROPIC REMARK 3 REMARK 3 ISOTROPIC THERMAL FACTOR RESTRAINTS. RMS SIGMA REMARK 3 MAIN-CHAIN BOND (A**2) : 1.460 ; NULL REMARK 3 MAIN-CHAIN ANGLE (A**2) : 2.350 ; NULL REMARK 3 SIDE-CHAIN BOND (A**2) : NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE (A**2) : NULL ; 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 NCS MODEL : NULL REMARK 3 REMARK 3 NCS RESTRAINTS. RMS SIGMA/WEIGHT REMARK 3 GROUP 1 POSITIONAL (A) : NULL ; NULL REMARK 3 GROUP 1 B-FACTOR (A**2) : NULL ; NULL REMARK 3 REMARK 3 PARAMETER FILE 1 : PROTEIN_REP.PARAM REMARK 3 PARAMETER FILE 2 : COE-M221.PARAM REMARK 3 PARAMETER FILE 3 : WATER_REP.PARAM REMARK 3 PARAMETER FILE 4 : ION.PARAM REMARK 3 PARAMETER FILE 5 : DHF-M221.PARAM REMARK 3 PARAMETER FILE 6 : NULL REMARK 3 TOPOLOGY FILE 1 : PROTEIN.TOP REMARK 3 TOPOLOGY FILE 2 : COE-M221.TOP REMARK 3 TOPOLOGY FILE 3 : WATER.TOP REMARK 3 TOPOLOGY FILE 4 : ION.TOP REMARK 3 TOPOLOGY FILE 5 : DHF-M221.TOP REMARK 3 TOPOLOGY FILE 6 : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 2FZJ COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 16-FEB-06. REMARK 100 THE DEPOSITION ID IS D_1000036499. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 17-DEC-04 REMARK 200 TEMPERATURE (KELVIN) : 200 REMARK 200 PH : 6.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : N REMARK 200 RADIATION SOURCE : ROTATING ANODE REMARK 200 BEAMLINE : NULL REMARK 200 X-RAY GENERATOR MODEL : RIGAKU RU200 REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.5418 REMARK 200 MONOCHROMATOR : GRAPHITE REMARK 200 OPTICS : MIRRORS REMARK 200 REMARK 200 DETECTOR TYPE : IMAGE PLATE REMARK 200 DETECTOR MANUFACTURER : RIGAKU RAXIS IV REMARK 200 INTENSITY-INTEGRATION SOFTWARE : DENZO REMARK 200 DATA SCALING SOFTWARE : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 12442 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.000 REMARK 200 RESOLUTION RANGE LOW (A) : 27.860 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 2.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 97.9 REMARK 200 DATA REDUNDANCY : 6.000 REMARK 200 R MERGE (I) : 0.03700 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: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: CNS REMARK 200 STARTING MODEL: PDB ENTRY 1U70 REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 45.46 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.26 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.17 M NA ACETATE, 0.085 MM NA REMARK 280 CACODYLATE, 25.5% PEG 4K, PH 6.5, VAPOR DIFFUSION, HANGING DROP, REMARK 280 TEMPERATURE 298K 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 30.51700 REMARK 290 SMTRY3 2 0.000000 0.000000 -1.000000 0.00000 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 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 ASN A 13 31.44 -85.02 REMARK 500 ASN A 19 28.43 48.44 REMARK 500 ASP A 110 -93.57 -111.75 REMARK 500 PRO A 128 170.43 -59.94 REMARK 500 MET A 139 53.64 -69.71 REMARK 500 REMARK 500 REMARK: NULL 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 187 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE DH3 A 188 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 1U70 RELATED DB: PDB REMARK 900 MOUSE DHFR DBREF 2FZJ A 1 186 UNP P00375 DYR_MOUSE 1 186 SEQRES 1 A 186 VAL ARG PRO LEU ASN CYS ILE VAL ALA VAL SER GLN ASN SEQRES 2 A 186 MET GLY ILE GLY LYS ASN GLY ASP LEU PRO TRP PRO PRO SEQRES 3 A 186 LEU ARG ASN GLU PHE LYS TYR PHE GLN ARG MET THR THR SEQRES 4 A 186 THR SER SER VAL GLU GLY LYS GLN ASN LEU VAL ILE MET SEQRES 5 A 186 GLY ARG LYS THR TRP PHE SER ILE PRO GLU LYS ASN ARG SEQRES 6 A 186 PRO LEU LYS ASP ARG ILE ASN ILE VAL LEU SER ARG GLU SEQRES 7 A 186 LEU LYS GLU PRO PRO ARG GLY ALA HIS PHE LEU ALA LYS SEQRES 8 A 186 SER LEU ASP ASP ALA LEU ARG LEU ILE GLU GLN PRO GLU SEQRES 9 A 186 LEU ALA SER LYS VAL ASP MET VAL TRP ILE VAL GLY GLY SEQRES 10 A 186 SER SER VAL TYR GLN GLU ALA MET ASN GLN PRO GLY HIS SEQRES 11 A 186 LEU ARG LEU PHE VAL THR ARG ILE MET GLN GLU PHE GLU SEQRES 12 A 186 SER ASP THR PHE PHE PRO GLU ILE ASP LEU GLY LYS TYR SEQRES 13 A 186 LYS LEU LEU PRO GLU TYR PRO GLY VAL LEU SER GLU VAL SEQRES 14 A 186 GLN GLU GLU LYS GLY ILE LYS TYR LYS PHE GLU VAL TYR SEQRES 15 A 186 GLU LYS LYS ASP HET NDP A 187 48 HET DH3 A 188 27 HETNAM NDP NADPH DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDE HETNAM 2 NDP PHOSPHATE HETNAM DH3 2,4-DIAMINO-5-[3',4'-DIMETHOXY-5'-(5-CARBOXYL-1- HETNAM 2 DH3 PENTYNYL)]BENZYL PYRIMIDINE FORMUL 2 NDP C21 H30 N7 O17 P3 FORMUL 3 DH3 C19 H22 N4 O4 FORMUL 4 HOH *123(H2 O) HELIX 1 1 LEU A 27 THR A 40 1 14 HELIX 2 2 ARG A 54 ILE A 60 1 7 HELIX 3 3 PRO A 61 ARG A 65 5 5 HELIX 4 4 SER A 92 GLU A 101 1 10 HELIX 5 5 GLN A 102 SER A 107 1 6 HELIX 6 6 GLY A 117 ASN A 126 1 10 SHEET 1 A 8 PHE A 88 ALA A 90 0 SHEET 2 A 8 ILE A 71 LEU A 75 1 N VAL A 74 O ALA A 90 SHEET 3 A 8 GLN A 47 GLY A 53 1 N VAL A 50 O ILE A 71 SHEET 4 A 8 VAL A 109 GLY A 116 1 O TRP A 113 N LEU A 49 SHEET 5 A 8 LEU A 4 SER A 11 1 N ILE A 7 O ILE A 114 SHEET 6 A 8 LEU A 131 ILE A 138 1 O PHE A 134 N CYS A 6 SHEET 7 A 8 ILE A 175 LYS A 184 -1 O LYS A 184 N LEU A 131 SHEET 8 A 8 LYS A 157 LEU A 158 -1 N LYS A 157 O GLU A 183 SHEET 1 B 8 PHE A 88 ALA A 90 0 SHEET 2 B 8 ILE A 71 LEU A 75 1 N VAL A 74 O ALA A 90 SHEET 3 B 8 GLN A 47 GLY A 53 1 N VAL A 50 O ILE A 71 SHEET 4 B 8 VAL A 109 GLY A 116 1 O TRP A 113 N LEU A 49 SHEET 5 B 8 LEU A 4 SER A 11 1 N ILE A 7 O ILE A 114 SHEET 6 B 8 LEU A 131 ILE A 138 1 O PHE A 134 N CYS A 6 SHEET 7 B 8 ILE A 175 LYS A 184 -1 O LYS A 184 N LEU A 131 SHEET 8 B 8 GLN A 170 GLU A 172 -1 N GLN A 170 O TYR A 177 SHEET 1 C 2 GLY A 15 ILE A 16 0 SHEET 2 C 2 THR A 146 PHE A 147 -1 O THR A 146 N ILE A 16 CISPEP 1 ARG A 65 PRO A 66 0 0.32 SITE 1 AC1 29 VAL A 8 ALA A 9 ILE A 16 GLY A 17 SITE 2 AC1 29 LYS A 18 GLY A 20 ASP A 21 TRP A 24 SITE 3 AC1 29 GLY A 53 ARG A 54 LYS A 55 THR A 56 SITE 4 AC1 29 LEU A 75 SER A 76 ARG A 77 GLU A 78 SITE 5 AC1 29 LYS A 91 SER A 92 VAL A 115 GLY A 116 SITE 6 AC1 29 GLY A 117 SER A 118 SER A 119 VAL A 120 SITE 7 AC1 29 GLU A 123 HOH A 240 HOH A 250 HOH A 274 SITE 8 AC1 29 HOH A 311 SITE 1 AC2 14 ILE A 7 VAL A 8 ALA A 9 LEU A 22 SITE 2 AC2 14 GLU A 30 PHE A 31 PHE A 34 GLN A 35 SITE 3 AC2 14 SER A 59 LYS A 68 ARG A 70 VAL A 115 SITE 4 AC2 14 TYR A 121 HOH A 255 CRYST1 41.806 61.034 43.080 90.00 118.00 90.00 P 1 21 1 2 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 0.023920 0.000000 0.012718 0.00000 SCALE2 0.000000 0.016384 0.000000 0.00000 SCALE3 0.000000 0.000000 0.026290 0.00000