HEADER OXIDOREDUCTASE 17-DEC-10 3Q1H TITLE CRYSTAL STRUCTURE OF DIHYDROFOLATE REDUCTASE FROM YERSINIA PESTIS COMPND MOL_ID: 1; COMPND 2 MOLECULE: DIHYDROFOLATE REDUCTASE; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: DIHYDROFOLATE REDUCTASE TYPE I; COMPND 5 EC: 1.5.1.3; COMPND 6 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: YERSINIA PESTIS; SOURCE 3 ORGANISM_TAXID: 214092; SOURCE 4 STRAIN: CO92; SOURCE 5 GENE: FOLA, Y3688, YPO0486, YP_3693; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 8 EXPRESSION_SYSTEM_STRAIN: KRXPGRO7; SOURCE 9 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 10 EXPRESSION_SYSTEM_PLASMID: PMCSG7 KEYWDS STRUCTURAL GENOMICS, CENTER FOR STRUCTURAL GENOMICS OF INFECTIOUS KEYWDS 2 DISEASES, CSGID, ALPHA BETA FOLD, CYTOSOL, OXIDOREDUCTASE EXPDTA X-RAY DIFFRACTION AUTHOR N.MALTSEVA,Y.KIM,M.MAKOWSKA-GRZYSKA,R.MULLIGAN,L.PAPAZISI, AUTHOR 2 W.F.ANDERSON,A.JOACHIMIAK,CENTER FOR STRUCTURAL GENOMICS OF AUTHOR 3 INFECTIOUS DISEASES (CSGID) REVDAT 2 13-SEP-23 3Q1H 1 REMARK SEQADV REVDAT 1 12-JAN-11 3Q1H 0 JRNL AUTH N.MALTSEVA,Y.KIM,M.MAKOWSKA-GRZYSKA,R.MULLIGAN,L.PAPAZISI, JRNL AUTH 2 W.F.ANDERSON,A.JOACHIMIAK, JRNL AUTH 3 CENTER FOR STRUCTURAL GENOMICS OF INFECTIOUS DISEASES JRNL AUTH 4 (CSGID) JRNL TITL CRYSTAL STRUCTURE OF DIHYDROFOLATE REDUCTASE FROM YERSINIA JRNL TITL 2 PESTIS JRNL REF TO BE PUBLISHED JRNL REFN REMARK 2 REMARK 2 RESOLUTION. 1.80 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX (PHENIX.REFINE: 1.6.4_486) 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) : 1.80 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 33.76 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 98.9 REMARK 3 NUMBER OF REFLECTIONS : 14493 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.167 REMARK 3 R VALUE (WORKING SET) : 0.166 REMARK 3 FREE R VALUE : 0.200 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.040 REMARK 3 FREE R VALUE TEST SET COUNT : 730 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 33.7646 - 3.0841 1.00 2905 139 0.1583 0.1623 REMARK 3 2 3.0841 - 2.4481 1.00 2795 144 0.1732 0.2253 REMARK 3 3 2.4481 - 2.1387 1.00 2762 134 0.1641 0.2163 REMARK 3 4 2.1387 - 1.9432 1.00 2722 163 0.1600 0.2364 REMARK 3 5 1.9432 - 1.8039 0.95 2579 150 0.1944 0.2290 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : FLAT BULK SOLVENT MODEL REMARK 3 SOLVENT RADIUS : 1.10 REMARK 3 SHRINKAGE RADIUS : 0.83 REMARK 3 K_SOL : 0.35 REMARK 3 B_SOL : 30.42 REMARK 3 REMARK 3 ERROR ESTIMATES. REMARK 3 COORDINATE ERROR (MAXIMUM-LIKELIHOOD BASED) : 0.180 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : NULL REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 18.10 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 21.70 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -1.47100 REMARK 3 B22 (A**2) : 0.12350 REMARK 3 B33 (A**2) : 1.34750 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : 0.00000 REMARK 3 B23 (A**2) : 0.00000 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 : 0.007 1362 REMARK 3 ANGLE : 1.057 1854 REMARK 3 CHIRALITY : 0.079 194 REMARK 3 PLANARITY : 0.004 246 REMARK 3 DIHEDRAL : 12.934 499 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : 1 REMARK 3 TLS GROUP : 1 REMARK 3 SELECTION: CHAIN A REMARK 3 ORIGIN FOR THE GROUP (A): 15.8425 -12.2798 13.0938 REMARK 3 T TENSOR REMARK 3 T11: 0.0666 T22: 0.0725 REMARK 3 T33: 0.0476 T12: -0.0052 REMARK 3 T13: 0.0004 T23: -0.0016 REMARK 3 L TENSOR REMARK 3 L11: 0.2296 L22: 0.7127 REMARK 3 L33: 0.1208 L12: 0.2034 REMARK 3 L13: -0.0271 L23: 0.1526 REMARK 3 S TENSOR REMARK 3 S11: -0.0277 S12: 0.0599 S13: 0.0016 REMARK 3 S21: -0.0576 S22: 0.0350 S23: 0.0359 REMARK 3 S31: 0.0050 S32: -0.0435 S33: -0.0043 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 3Q1H COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 04-JAN-11. REMARK 100 THE DEPOSITION ID IS D_1000063075. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 15-DEC-10 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 5.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : APS REMARK 200 BEAMLINE : 19-ID REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.9793 REMARK 200 MONOCHROMATOR : DOUBLE CRYSTAL MONOCHROMATOR REMARK 200 OPTICS : MIRRORS REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 315R REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-3000 REMARK 200 DATA SCALING SOFTWARE : HKL-3000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 14518 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.800 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 (%) : 99.0 REMARK 200 DATA REDUNDANCY : 7.600 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : 0.07000 REMARK 200 FOR THE DATA SET : 12.6000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.80 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.83 REMARK 200 COMPLETENESS FOR SHELL (%) : 89.0 REMARK 200 DATA REDUNDANCY IN SHELL : 4.00 REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : 0.39300 REMARK 200 FOR SHELL : 2.880 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: BALBES REMARK 200 STARTING MODEL: PDBID 1DDS REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 41.68 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.11 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.2M LITHIUM SULFATE, 0.1M BIS-TRIS REMARK 280 PH5.5, 25% PEG 3350, VAPOR DIFFUSION, SITTING DROP, TEMPERATURE REMARK 280 289K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: C 2 2 21 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,-Y,Z+1/2 REMARK 290 3555 -X,Y,-Z+1/2 REMARK 290 4555 X,-Y,-Z REMARK 290 5555 X+1/2,Y+1/2,Z REMARK 290 6555 -X+1/2,-Y+1/2,Z+1/2 REMARK 290 7555 -X+1/2,Y+1/2,-Z+1/2 REMARK 290 8555 X+1/2,-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 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 32.34250 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 32.34250 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 0.00000 REMARK 290 SMTRY1 5 1.000000 0.000000 0.000000 30.23850 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 39.57600 REMARK 290 SMTRY3 5 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 6 -1.000000 0.000000 0.000000 30.23850 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 39.57600 REMARK 290 SMTRY3 6 0.000000 0.000000 1.000000 32.34250 REMARK 290 SMTRY1 7 -1.000000 0.000000 0.000000 30.23850 REMARK 290 SMTRY2 7 0.000000 1.000000 0.000000 39.57600 REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 32.34250 REMARK 290 SMTRY1 8 1.000000 0.000000 0.000000 30.23850 REMARK 290 SMTRY2 8 0.000000 -1.000000 0.000000 39.57600 REMARK 290 SMTRY3 8 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 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 375 REMARK 375 SPECIAL POSITION REMARK 375 THE FOLLOWING ATOMS ARE FOUND TO BE WITHIN 0.15 ANGSTROMS REMARK 375 OF A SYMMETRY RELATED ATOM AND ARE ASSUMED TO BE ON SPECIAL REMARK 375 POSITIONS. REMARK 375 REMARK 375 ATOM RES CSSEQI REMARK 375 HOH A 298 LIES ON A SPECIAL POSITION. REMARK 375 HOH A 318 LIES ON A SPECIAL POSITION. REMARK 375 HOH A 319 LIES ON A SPECIAL POSITION. REMARK 465 REMARK 465 MISSING RESIDUES REMARK 465 THE FOLLOWING RESIDUES WERE NOT LOCATED IN THE REMARK 465 EXPERIMENT. (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 465 IDENTIFIER; SSSEQ=SEQUENCE NUMBER; I=INSERTION CODE.) REMARK 465 REMARK 465 M RES C SSSEQI REMARK 465 SER A -2 REMARK 465 ASN A -1 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 ALA A 11 -122.50 56.80 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 SO4 A 170 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SO4 A 171 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: IDP90544 RELATED DB: TARGETDB DBREF 3Q1H A 1 160 UNP Q7CG83 Q7CG83_YERPE 1 160 SEQADV 3Q1H SER A -2 UNP Q7CG83 EXPRESSION TAG SEQADV 3Q1H ASN A -1 UNP Q7CG83 EXPRESSION TAG SEQADV 3Q1H ALA A 0 UNP Q7CG83 EXPRESSION TAG SEQRES 1 A 163 SER ASN ALA MET ILE ILE SER LEU ILE ALA ALA LEU ALA SEQRES 2 A 163 ALA ASP ARG VAL ILE GLY MET GLU ASN ALA MET PRO TRP SEQRES 3 A 163 HIS LEU PRO ALA ASP LEU ALA TRP PHE LYS ARG ASN THR SEQRES 4 A 163 LEU ASN LYS PRO VAL ILE MET GLY ARG LYS THR PHE GLU SEQRES 5 A 163 SER ILE GLY ARG PRO LEU PRO GLY ARG LEU ASN ILE VAL SEQRES 6 A 163 ILE SER SER GLN PRO GLY THR ASP GLU ARG VAL THR TRP SEQRES 7 A 163 ALA ALA SER ILE GLU GLU ALA LEU ALA PHE ALA GLY ASN SEQRES 8 A 163 ALA GLU GLU VAL MET VAL MET GLY GLY GLY ARG VAL TYR SEQRES 9 A 163 LYS GLN PHE LEU ASP ARG ALA ASN ARG MET TYR LEU THR SEQRES 10 A 163 HIS ILE ASP ALA GLU VAL GLY GLY ASP THR HIS PHE PRO SEQRES 11 A 163 ASP TYR GLU PRO ASP GLU TRP GLU SER VAL PHE SER GLU SEQRES 12 A 163 PHE HIS ASP ALA ASP GLU ALA ASN SER HIS SER TYR CYS SEQRES 13 A 163 PHE GLU ILE LEU GLU ARG ARG HET SO4 A 170 5 HET SO4 A 171 5 HETNAM SO4 SULFATE ION FORMUL 2 SO4 2(O4 S 2-) FORMUL 4 HOH *163(H2 O) HELIX 1 1 PRO A 26 ASP A 28 5 3 HELIX 2 2 LEU A 29 LEU A 37 1 9 HELIX 3 3 ARG A 45 GLY A 52 1 8 HELIX 4 4 SER A 78 ALA A 86 1 9 HELIX 5 5 GLY A 97 LEU A 105 1 9 HELIX 6 6 GLU A 130 ASP A 132 5 3 SHEET 1 A 6 ARG A 13 VAL A 14 0 SHEET 2 A 6 ILE A 2 ALA A 10 -1 N ALA A 10 O ARG A 13 SHEET 3 A 6 GLU A 91 VAL A 94 1 O VAL A 94 N SER A 4 SHEET 4 A 6 VAL A 41 GLY A 44 1 N ILE A 42 O MET A 93 SHEET 5 A 6 ASN A 60 ILE A 63 1 O ILE A 61 N VAL A 41 SHEET 6 A 6 THR A 74 ALA A 76 1 O THR A 74 N ASN A 60 SHEET 1 B 5 ARG A 13 VAL A 14 0 SHEET 2 B 5 ILE A 2 ALA A 10 -1 N ALA A 10 O ARG A 13 SHEET 3 B 5 ARG A 110 HIS A 115 1 O TYR A 112 N LEU A 5 SHEET 4 B 5 TYR A 152 ARG A 159 -1 O CYS A 153 N HIS A 115 SHEET 5 B 5 TRP A 134 HIS A 142 -1 N GLU A 135 O GLU A 158 CISPEP 1 GLY A 96 GLY A 97 0 -0.58 SITE 1 AC1 9 GLY A 44 ARG A 45 LYS A 46 THR A 47 SITE 2 AC1 9 GLY A 97 ARG A 99 VAL A 100 HOH A 163 SITE 3 AC1 9 HOH A 301 SITE 1 AC2 4 ARG A 45 SER A 64 SER A 65 ARG A 99 CRYST1 60.477 79.152 64.685 90.00 90.00 90.00 C 2 2 21 8 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 0.016535 0.000000 0.000000 0.00000 SCALE2 0.000000 0.012634 0.000000 0.00000 SCALE3 0.000000 0.000000 0.015460 0.00000