HEADER OXIDOREDUCTASE/OXIDOREDUCTASE INHIBITOR 11-FEB-14 4OR7 TITLE KLEBSIELLA PNEUMONIAE DIHYDROFOLATE REDUCTASE COMPLEXED WITH NADPH AND TITLE 2 6-ETHYL-5-{3-[3-(PYRIMIDIN-5-YL)PHENYL]PROP-1-YN-1-YL}PYRIMIDINE-2,4- TITLE 3 DIAMINE 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: KLEBSIELLA PNEUMONIAE CG43; SOURCE 3 ORGANISM_TAXID: 1244085; SOURCE 4 GENE: FOLA, D364_00170; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS 5, 6, 7, 8-TETRAHYDROFOLATE; 7, 8-DIHYDROFOLATE, HYDRIDE SHIFT, KEYWDS 2 OXIDOREDUCTASE-OXIDOREDUCTASE INHIBITOR COMPLEX EXPDTA X-RAY DIFFRACTION AUTHOR K.M.LAMB,A.C.ANDERSON REVDAT 3 28-FEB-24 4OR7 1 REMARK SEQADV REVDAT 2 17-DEC-14 4OR7 1 REMARK REVDAT 1 03-DEC-14 4OR7 0 JRNL AUTH K.M.LAMB,M.N.LOMBARDO,J.ALVERSON,N.D.PRIESTLEY,D.L.WRIGHT, JRNL AUTH 2 A.C.ANDERSON JRNL TITL CRYSTAL STRUCTURES OF KLEBSIELLA PNEUMONIAE DIHYDROFOLATE JRNL TITL 2 REDUCTASE BOUND TO PROPARGYL-LINKED ANTIFOLATES REVEAL JRNL TITL 3 FEATURES FOR POTENCY AND SELECTIVITY. JRNL REF ANTIMICROB.AGENTS CHEMOTHER. V. 58 7484 2014 JRNL REFN ISSN 0066-4804 JRNL PMID 25288083 JRNL DOI 10.1128/AAC.03555-14 REMARK 2 REMARK 2 RESOLUTION. 1.76 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX (PHENIX.REFINE: 1.8.2_1309) REMARK 3 AUTHORS : PAUL ADAMS,PAVEL AFONINE,VINCENT CHEN,IAN REMARK 3 : DAVIS,KRESHNA GOPAL,RALF GROSSE-KUNSTLEVE, REMARK 3 : LI-WEI HUNG,ROBERT IMMORMINO,TOM IOERGER, REMARK 3 : AIRLIE MCCOY,ERIK MCKEE,NIGEL MORIARTY, REMARK 3 : REETAL PAI,RANDY READ,JANE RICHARDSON, REMARK 3 : DAVID RICHARDSON,TOD ROMO,JIM SACCHETTINI, REMARK 3 : NICHOLAS SAUTER,JACOB SMITH,LAURENT REMARK 3 : STORONI,TOM TERWILLIGER,PETER ZWART REMARK 3 REMARK 3 REFINEMENT TARGET : ML REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.76 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 37.36 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.340 REMARK 3 COMPLETENESS FOR RANGE (%) : 100.0 REMARK 3 NUMBER OF REFLECTIONS : 23264 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.213 REMARK 3 R VALUE (WORKING SET) : 0.210 REMARK 3 FREE R VALUE : 0.250 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 7.810 REMARK 3 FREE R VALUE TEST SET COUNT : 1817 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT (IN BINS). REMARK 3 BIN RESOLUTION RANGE COMPL. NWORK NFREE RWORK RFREE REMARK 3 1 37.3716 - 4.1367 1.00 1775 154 0.1632 0.1840 REMARK 3 2 4.1367 - 3.2840 1.00 1691 145 0.1726 0.2077 REMARK 3 3 3.2840 - 2.8691 1.00 1671 141 0.2044 0.2367 REMARK 3 4 2.8691 - 2.6068 1.00 1650 139 0.2133 0.2472 REMARK 3 5 2.6068 - 2.4200 1.00 1646 138 0.2276 0.2918 REMARK 3 6 2.4200 - 2.2774 1.00 1627 137 0.2212 0.2944 REMARK 3 7 2.2774 - 2.1633 1.00 1645 137 0.2262 0.3114 REMARK 3 8 2.1633 - 2.0692 1.00 1638 138 0.2421 0.2638 REMARK 3 9 2.0692 - 1.9895 1.00 1618 136 0.2417 0.2770 REMARK 3 10 1.9895 - 1.9209 1.00 1637 137 0.2471 0.3038 REMARK 3 11 1.9209 - 1.8608 1.00 1610 136 0.2528 0.3026 REMARK 3 12 1.8608 - 1.8076 1.00 1629 140 0.2583 0.2815 REMARK 3 13 1.8076 - 1.7600 1.00 1610 139 0.2753 0.3088 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : FLAT BULK SOLVENT MODEL REMARK 3 SOLVENT RADIUS : 1.11 REMARK 3 SHRINKAGE RADIUS : 0.90 REMARK 3 K_SOL : NULL REMARK 3 B_SOL : NULL REMARK 3 REMARK 3 ERROR ESTIMATES. REMARK 3 COORDINATE ERROR (MAXIMUM-LIKELIHOOD BASED) : 0.200 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 24.160 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 TWINNING INFORMATION. REMARK 3 FRACTION: NULL REMARK 3 OPERATOR: NULL REMARK 3 REMARK 3 DEVIATIONS FROM IDEAL VALUES. REMARK 3 RMSD COUNT REMARK 3 BOND : 0.006 1534 REMARK 3 ANGLE : 1.101 2109 REMARK 3 CHIRALITY : 0.075 215 REMARK 3 PLANARITY : 0.004 275 REMARK 3 DIHEDRAL : 15.263 567 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : NULL REMARK 3 REMARK 3 NCS DETAILS REMARK 3 NUMBER OF NCS GROUPS : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 4OR7 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 12-FEB-14. REMARK 100 THE DEPOSITION ID IS D_1000084848. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : NULL REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 7.4 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : NSLS REMARK 200 BEAMLINE : X4A REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.9789 REMARK 200 MONOCHROMATOR : KOHZU DOUBLE CRYSTAL REMARK 200 MONOCHROMATOR REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 4R REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : D*TREK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 25725 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.760 REMARK 200 RESOLUTION RANGE LOW (A) : 37.360 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 13.280 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 100.0 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) : 1.76 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.79 REMARK 200 COMPLETENESS FOR SHELL (%) : 100.0 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: PHASER FOR MR REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 59.35 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 3.03 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 100 MM CACODYLATE, 125 MM SODIUM REMARK 280 ACETATE, 25% (W/V) PEG 8000, 11 MM CALCIUM CHLORIDE, 11 MM REMARK 280 BENTAINE HYDROCHLORIDE, PH 7.4, VAPOR DIFFUSION, SITTING DROP, REMARK 280 TEMPERATURE 277K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 32 2 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -Y,X-Y,Z+2/3 REMARK 290 3555 -X+Y,-X,Z+1/3 REMARK 290 4555 Y,X,-Z REMARK 290 5555 X-Y,-Y,-Z+1/3 REMARK 290 6555 -X,-X+Y,-Z+2/3 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 70.28400 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 35.14200 REMARK 290 SMTRY1 4 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 4 0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 4 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 5 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 5 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 5 0.000000 0.000000 -1.000000 35.14200 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 70.28400 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 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 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 A 21 42.49 -75.56 REMARK 500 ASP A 69 114.53 -163.51 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 NAP A 201 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE 25U A 202 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 4OSG RELATED DB: PDB DBREF 4OR7 A 1 159 UNP U5M636 U5M636_KLEPN 1 159 SEQADV 4OR7 HIS A 160 UNP U5M636 EXPRESSION TAG SEQADV 4OR7 HIS A 161 UNP U5M636 EXPRESSION TAG SEQADV 4OR7 HIS A 162 UNP U5M636 EXPRESSION TAG SEQADV 4OR7 HIS A 163 UNP U5M636 EXPRESSION TAG SEQADV 4OR7 HIS A 164 UNP U5M636 EXPRESSION TAG SEQADV 4OR7 HIS A 165 UNP U5M636 EXPRESSION TAG SEQRES 1 A 165 MET ILE SER LEU ILE ALA ALA LEU ALA VAL ASP ARG VAL SEQRES 2 A 165 ILE GLY MET GLU ASN ALA MET PRO TRP ASN LEU PRO ALA SEQRES 3 A 165 ASP LEU ALA TRP PHE LYS ARG ASN THR LEU ASN LYS PRO SEQRES 4 A 165 VAL VAL MET GLY ARG LEU THR TRP GLU SER ILE GLY ARG SEQRES 5 A 165 PRO LEU PRO GLY ARG LYS ASN ILE VAL ILE SER SER LYS SEQRES 6 A 165 PRO GLY SER ASP ASP ARG VAL GLN TRP VAL SER SER VAL SEQRES 7 A 165 GLU GLU ALA ILE ALA ALA CYS GLY ASP VAL GLU GLU ILE SEQRES 8 A 165 MET VAL ILE GLY GLY GLY ARG VAL TYR GLU GLN PHE LEU SEQRES 9 A 165 PRO LYS ALA GLN LYS LEU TYR LEU THR HIS ILE ASP ALA SEQRES 10 A 165 GLU VAL GLU GLY ASP THR HIS PHE PRO ASP TYR ASP PRO SEQRES 11 A 165 ASP GLU TRP GLU SER VAL PHE SER GLU PHE HIS ASP ALA SEQRES 12 A 165 ASP ALA GLN ASN SER HIS SER TYR CYS PHE GLU ILE LEU SEQRES 13 A 165 GLU ARG ARG HIS HIS HIS HIS HIS HIS HET NAP A 201 48 HET 25U A 202 25 HETNAM NAP NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE HETNAM 25U 6-ETHYL-5-{3-[3-(PYRIMIDIN-5-YL)PHENYL]PROP-1-YN-1- HETNAM 2 25U YL}PYRIMIDINE-2,4-DIAMINE HETSYN NAP 2'-MONOPHOSPHOADENOSINE 5'-DIPHOSPHORIBOSE FORMUL 2 NAP C21 H28 N7 O17 P3 FORMUL 3 25U C19 H18 N6 FORMUL 4 HOH *233(H2 O) HELIX 1 1 ALA A 9 ASP A 11 5 3 HELIX 2 2 LEU A 24 LEU A 36 1 13 HELIX 3 3 ARG A 44 GLY A 51 1 8 HELIX 4 4 SER A 77 GLY A 86 1 10 HELIX 5 5 GLY A 96 LEU A 104 1 9 HELIX 6 6 PRO A 105 ALA A 107 5 3 HELIX 7 7 ASP A 129 ASP A 131 5 3 SHEET 1 A 8 GLN A 73 VAL A 75 0 SHEET 2 A 8 ASN A 59 ILE A 62 1 N VAL A 61 O VAL A 75 SHEET 3 A 8 VAL A 40 GLY A 43 1 N VAL A 40 O ILE A 60 SHEET 4 A 8 ILE A 91 GLY A 95 1 O ILE A 94 N VAL A 41 SHEET 5 A 8 ILE A 2 LEU A 8 1 N SER A 3 O VAL A 93 SHEET 6 A 8 LYS A 109 ILE A 115 1 O ILE A 115 N LEU A 8 SHEET 7 A 8 TYR A 151 ARG A 158 -1 O GLU A 154 N LEU A 112 SHEET 8 A 8 TRP A 133 HIS A 141 -1 N VAL A 136 O ILE A 155 SHEET 1 B 2 VAL A 13 GLY A 15 0 SHEET 2 B 2 THR A 123 HIS A 124 -1 O THR A 123 N ILE A 14 CISPEP 1 GLY A 95 GLY A 96 0 0.82 SITE 1 AC1 37 ALA A 6 ALA A 7 ILE A 14 GLY A 15 SITE 2 AC1 37 MET A 16 ASN A 18 ALA A 19 MET A 20 SITE 3 AC1 37 TRP A 22 GLY A 43 ARG A 44 LEU A 45 SITE 4 AC1 37 THR A 46 ILE A 62 SER A 63 SER A 64 SITE 5 AC1 37 SER A 76 ILE A 94 GLY A 96 GLY A 97 SITE 6 AC1 37 ARG A 98 VAL A 99 TYR A 100 GLN A 102 SITE 7 AC1 37 25U A 202 HOH A 305 HOH A 313 HOH A 326 SITE 8 AC1 37 HOH A 327 HOH A 341 HOH A 352 HOH A 380 SITE 9 AC1 37 HOH A 408 HOH A 409 HOH A 429 HOH A 433 SITE 10 AC1 37 HOH A 446 SITE 1 AC2 15 ILE A 5 ALA A 6 MET A 20 ASP A 27 SITE 2 AC2 15 LEU A 28 PHE A 31 SER A 49 ILE A 50 SITE 3 AC2 15 ARG A 52 LEU A 54 ILE A 94 TYR A 100 SITE 4 AC2 15 THR A 113 NAP A 201 HOH A 301 CRYST1 61.161 61.161 105.426 90.00 90.00 120.00 P 32 2 1 6 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 0.016350 0.009440 0.000000 0.00000 SCALE2 0.000000 0.018880 0.000000 0.00000 SCALE3 0.000000 0.000000 0.009485 0.00000