HEADER OXIDOREDUCTASE 14-JAN-04 1S3Y TITLE STRUCTURE DETERMINATION OF TETRAHYDROQUINAZOLINE ANTIFOLATES IN TITLE 2 COMPLEX WITH HUMAN AND PNEUMOCYSTIS CARINII DIHYDROFOLATE REDUCTASE: TITLE 3 CORRELATIONS OF ENZYME SELECTIVITY AND STEREOCHEMISTRY 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: PNEUMOCYSTIS CARINII; SOURCE 3 ORGANISM_TAXID: 4754; SOURCE 4 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 5 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS PNEUMOCYSTIS CARINII DIHYDROFOLATE REDUCTASE, INHIBITORS, KEYWDS 2 STEREOCHEMISTRY, OXIDOREDUCTASE EXPDTA X-RAY DIFFRACTION AUTHOR V.CODY,J.R.LUFT,W.PANGBORN,A.GANGJEE,S.F.QUEENER REVDAT 3 14-FEB-24 1S3Y 1 REMARK REVDAT 2 24-FEB-09 1S3Y 1 VERSN REVDAT 1 30-MAR-04 1S3Y 0 JRNL AUTH V.CODY,J.R.LUFT,W.PANGBORN,A.GANGJEE,S.F.QUEENER JRNL TITL STRUCTURE DETERMINATION OF TETRAHYDROQUINAZOLINE ANTIFOLATES JRNL TITL 2 IN COMPLEX WITH HUMAN AND PNEUMOCYSTIS CARINII DIHYDROFOLATE JRNL TITL 3 REDUCTASE: CORRELATIONS BETWEEN ENZYME SELECTIVITY AND JRNL TITL 4 STEREOCHEMISTRY. JRNL REF ACTA CRYSTALLOGR.,SECT.D V. 60 646 2004 JRNL REFN ISSN 0907-4449 JRNL PMID 15039552 JRNL DOI 10.1107/S0907444904002094 REMARK 2 REMARK 2 RESOLUTION. 2.25 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) : 2.25 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 50.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 DATA CUTOFF HIGH (ABS(F)) : NULL REMARK 3 DATA CUTOFF LOW (ABS(F)) : NULL REMARK 3 COMPLETENESS (WORKING+TEST) (%) : NULL REMARK 3 NUMBER OF REFLECTIONS : 6996 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) : 0.233 REMARK 3 FREE R VALUE : 0.289 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 10.000 REMARK 3 FREE R VALUE TEST SET COUNT : 764 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 : 1685 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 70 REMARK 3 SOLVENT ATOMS : 23 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : NULL 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) : 1.220 REMARK 3 DIHEDRAL ANGLES (DEGREES) : 1.680 REMARK 3 IMPROPER ANGLES (DEGREES) : 2.810 REMARK 3 REMARK 3 ISOTROPIC THERMAL MODEL : NULL REMARK 3 REMARK 3 ISOTROPIC THERMAL FACTOR RESTRAINTS. RMS SIGMA REMARK 3 MAIN-CHAIN BOND (A**2) : NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE (A**2) : NULL ; 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 : NULL REMARK 3 TOPOLOGY FILE 1 : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 1S3Y COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 20-JAN-04. REMARK 100 THE DEPOSITION ID IS D_1000021336. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 29-JAN-98 REMARK 200 TEMPERATURE (KELVIN) : 298 REMARK 200 PH : 6.0 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) : 1.5418,1.5621,1.7321 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 : 6996 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.250 REMARK 200 RESOLUTION RANGE LOW (A) : 50.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 0.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 73.9 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) : 2.25 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.33 REMARK 200 COMPLETENESS FOR SHELL (%) : 76.7 REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : 0.17700 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: FOURIER SYNTHESIS REMARK 200 SOFTWARE USED: CNS REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 40.52 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.07 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 50 MM MES, 100 MM KCL, PH 6.0, THERMAL REMARK 280 GRADIENT, 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 21.64300 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: 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 PRO A 26 C - N - CA ANGL. DEV. = 10.7 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 SER A 22 67.76 14.63 REMARK 500 ASN A 23 -64.64 73.14 REMARK 500 SER A 24 -86.98 -1.60 REMARK 500 LEU A 25 76.86 107.91 REMARK 500 PRO A 26 -4.69 -36.65 REMARK 500 ASP A 47 39.82 -96.59 REMARK 500 GLU A 50 -41.82 -131.13 REMARK 500 THR A 81 141.37 -172.31 REMARK 500 SER A 85 -105.58 -98.63 REMARK 500 LEU A 88 -128.35 -80.44 REMARK 500 ASN A 90 -30.90 -159.86 REMARK 500 ASN A 118 -62.30 -109.55 REMARK 500 ILE A 150 -169.86 -76.69 REMARK 500 VAL A 168 -65.40 -95.59 REMARK 500 REMARK 500 REMARK: NULL REMARK 615 REMARK 615 ZERO OCCUPANCY ATOM REMARK 615 THE FOLLOWING RESIDUES HAVE ATOMS MODELED WITH ZERO REMARK 615 OCCUPANCY. THE LOCATION AND PROPERTIES OF THESE ATOMS REMARK 615 MAY NOT BE RELIABLE. (M=MODEL NUMBER; RES=RESIDUE NAME; REMARK 615 C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE): REMARK 615 M RES C SSEQI REMARK 615 NAP A 207 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE NAP A 207 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE TQT A 208 DBREF 1S3Y A 1 206 UNP P16184 DYR_PNECA 1 206 SEQRES 1 A 206 MET ASN GLN GLN LYS SER LEU THR LEU ILE VAL ALA LEU SEQRES 2 A 206 THR THR SER TYR GLY ILE GLY ARG SER ASN SER LEU PRO SEQRES 3 A 206 TRP LYS LEU LYS LYS GLU ILE SER TYR PHE LYS ARG VAL SEQRES 4 A 206 THR SER PHE VAL PRO THR PHE ASP SER PHE GLU SER MET SEQRES 5 A 206 ASN VAL VAL LEU MET GLY ARG LYS THR TRP GLU SER ILE SEQRES 6 A 206 PRO LEU GLN PHE ARG PRO LEU LYS GLY ARG ILE ASN VAL SEQRES 7 A 206 VAL ILE THR ARG ASN GLU SER LEU ASP LEU GLY ASN GLY SEQRES 8 A 206 ILE HIS SER ALA LYS SER LEU ASP HIS ALA LEU GLU LEU SEQRES 9 A 206 LEU TYR ARG THR TYR GLY SER GLU SER SER VAL GLN ILE SEQRES 10 A 206 ASN ARG ILE PHE VAL ILE GLY GLY ALA GLN LEU TYR LYS SEQRES 11 A 206 ALA ALA MET ASP HIS PRO LYS LEU ASP ARG ILE MET ALA SEQRES 12 A 206 THR ILE ILE TYR LYS ASP ILE HIS CYS ASP VAL PHE PHE SEQRES 13 A 206 PRO LEU LYS PHE ARG ASP LYS GLU TRP SER SER VAL TRP SEQRES 14 A 206 LYS LYS GLU LYS HIS SER ASP LEU GLU SER TRP VAL GLY SEQRES 15 A 206 THR LYS VAL PRO HIS GLY LYS ILE ASN GLU ASP GLY PHE SEQRES 16 A 206 ASP TYR GLU PHE GLU MET TRP THR ARG ASP LEU HET NAP A 207 48 HET TQT A 208 22 HETNAM NAP NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE HETNAM TQT 6-(OCTAHYDRO-1H-INDOL-1-YLMETHYL)DECAHYDROQUINAZOLINE- HETNAM 2 TQT 2,4-DIAMINE HETSYN NAP 2'-MONOPHOSPHOADENOSINE 5'-DIPHOSPHORIBOSE FORMUL 2 NAP C21 H28 N7 O17 P3 FORMUL 3 TQT C17 H33 N5 FORMUL 4 HOH *23(H2 O) HELIX 1 1 LEU A 29 PHE A 42 1 14 HELIX 2 2 THR A 45 PHE A 49 5 5 HELIX 3 3 ARG A 59 ILE A 65 1 7 HELIX 4 4 PRO A 66 ARG A 70 5 5 HELIX 5 5 SER A 97 TYR A 109 1 13 HELIX 6 6 GLY A 125 ASP A 134 1 10 HELIX 7 7 ASP A 162 SER A 166 5 5 HELIX 8 8 LYS A 173 VAL A 181 1 9 SHEET 1 A 8 HIS A 93 ALA A 95 0 SHEET 2 A 8 ARG A 75 ILE A 80 1 N VAL A 79 O HIS A 93 SHEET 3 A 8 MET A 52 GLY A 58 1 N VAL A 55 O ILE A 76 SHEET 4 A 8 ILE A 117 GLY A 124 1 O ARG A 119 N VAL A 54 SHEET 5 A 8 LEU A 7 THR A 14 1 N THR A 8 O VAL A 122 SHEET 6 A 8 LEU A 138 ILE A 146 1 O MET A 142 N LEU A 9 SHEET 7 A 8 PHE A 195 THR A 203 -1 O TRP A 202 N ILE A 141 SHEET 8 A 8 LYS A 170 LYS A 171 -1 N LYS A 170 O THR A 203 SHEET 1 B 8 HIS A 93 ALA A 95 0 SHEET 2 B 8 ARG A 75 ILE A 80 1 N VAL A 79 O HIS A 93 SHEET 3 B 8 MET A 52 GLY A 58 1 N VAL A 55 O ILE A 76 SHEET 4 B 8 ILE A 117 GLY A 124 1 O ARG A 119 N VAL A 54 SHEET 5 B 8 LEU A 7 THR A 14 1 N THR A 8 O VAL A 122 SHEET 6 B 8 LEU A 138 ILE A 146 1 O MET A 142 N LEU A 9 SHEET 7 B 8 PHE A 195 THR A 203 -1 O TRP A 202 N ILE A 141 SHEET 8 B 8 ILE A 190 GLU A 192 -1 N ILE A 190 O TYR A 197 SHEET 1 C 2 GLY A 18 GLY A 20 0 SHEET 2 C 2 VAL A 154 PHE A 155 -1 N VAL A 154 O GLY A 20 CISPEP 1 ARG A 70 PRO A 71 0 0.18 SITE 1 AC1 11 GLY A 58 ARG A 59 LYS A 60 THR A 61 SITE 2 AC1 11 ILE A 80 THR A 81 ARG A 82 LYS A 96 SITE 3 AC1 11 GLY A 125 ALA A 126 GLN A 127 SITE 1 AC2 11 ILE A 10 VAL A 11 LEU A 25 GLU A 32 SITE 2 AC2 11 ILE A 33 PHE A 36 SER A 64 PRO A 66 SITE 3 AC2 11 ILE A 123 TYR A 129 THR A 144 CRYST1 37.359 43.286 61.397 90.00 94.65 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 0.026767 0.000000 0.002177 0.00000 SCALE2 0.000000 0.023102 0.000000 0.00000 SCALE3 0.000000 0.000000 0.016341 0.00000