HEADER OXIDOREDUCTASE 29-MAY-23 8SZD TITLE CRYSTAL STRUCTURE OF YERSINIA PESTIS DIHYDROFOLATE REDUCTASE AT 1.25-A TITLE 2 RESOLUTION 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: YERSINIA PESTIS; SOURCE 3 ORGANISM_TAXID: 632; SOURCE 4 GENE: FOLA, TMRA, YPO0486; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS DHFR, OXIDOREDUCTASE EXPDTA X-RAY DIFFRACTION AUTHOR G.X.SHAW,S.CHERRY,J.E.TROPEA,D.S.WAUGH,X.JI REVDAT 2 22-MAY-24 8SZD 1 REMARK REVDAT 1 07-JUN-23 8SZD 0 JRNL AUTH G.X.SHAW,S.CHERRY,J.E.TROPEA,D.S.WAUGH,X.JI JRNL TITL CRYSTAL STRUCTURE OF YERSINIA PESTIS DIHYDROFOLATE REDUCTASE JRNL TITL 2 AT 1.25-A RESOLUTION JRNL REF TO BE PUBLISHED JRNL REFN REMARK 2 REMARK 2 RESOLUTION. 1.25 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX (1.20.1_4487: ???) 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) : 1.25 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 27.29 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.360 REMARK 3 COMPLETENESS FOR RANGE (%) : 95.0 REMARK 3 NUMBER OF REFLECTIONS : 40578 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.198 REMARK 3 R VALUE (WORKING SET) : 0.197 REMARK 3 FREE R VALUE : 0.221 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.930 REMARK 3 FREE R VALUE TEST SET COUNT : 2000 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 27.2900 - 3.0200 0.94 2871 149 0.1804 0.1998 REMARK 3 2 3.0100 - 2.3900 1.00 2947 153 0.1952 0.2268 REMARK 3 3 2.3900 - 2.0900 1.00 2923 152 0.1861 0.2034 REMARK 3 4 2.0900 - 1.9000 1.00 2902 150 0.1840 0.2093 REMARK 3 5 1.9000 - 1.7600 1.00 2899 149 0.1936 0.2207 REMARK 3 6 1.7600 - 1.6600 1.00 2871 149 0.1971 0.1925 REMARK 3 7 1.6600 - 1.5800 1.00 2915 152 0.2018 0.2409 REMARK 3 8 1.5800 - 1.5100 1.00 2869 148 0.2067 0.2136 REMARK 3 9 1.5100 - 1.4500 1.00 2884 150 0.2107 0.2527 REMARK 3 10 1.4500 - 1.4000 1.00 2854 148 0.2317 0.2507 REMARK 3 11 1.4000 - 1.3600 0.98 2830 146 0.2744 0.3066 REMARK 3 12 1.3600 - 1.3200 0.90 2586 135 0.2812 0.3362 REMARK 3 13 1.3200 - 1.2800 0.79 2288 119 0.2834 0.3423 REMARK 3 14 1.2800 - 1.2500 0.68 1939 100 0.3103 0.3298 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 : 0.90 REMARK 3 K_SOL : NULL REMARK 3 B_SOL : NULL REMARK 3 REMARK 3 ERROR ESTIMATES. REMARK 3 COORDINATE ERROR (MAXIMUM-LIKELIHOOD BASED) : 0.160 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 23.420 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 : 0.010 1491 REMARK 3 ANGLE : 1.169 2044 REMARK 3 CHIRALITY : 0.102 208 REMARK 3 PLANARITY : 0.010 281 REMARK 3 DIHEDRAL : 13.588 558 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 8SZD COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 30-MAY-23. REMARK 100 THE DEPOSITION ID IS D_1000274859. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 14-OCT-06 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 6.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : APS REMARK 200 BEAMLINE : 22-ID REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.0000 REMARK 200 MONOCHROMATOR : DOUBLE CRYSTAL REMARK 200 OPTICS : DOUBLE CRYSTAL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : MARMOSAIC 300 MM CCD REMARK 200 INTENSITY-INTEGRATION SOFTWARE : DENZO REMARK 200 DATA SCALING SOFTWARE : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 40606 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.250 REMARK 200 RESOLUTION RANGE LOW (A) : 30.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 95.0 REMARK 200 DATA REDUNDANCY : 5.100 REMARK 200 R MERGE (I) : 0.06200 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 18.0000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.25 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.29 REMARK 200 COMPLETENESS FOR SHELL (%) : 70.4 REMARK 200 DATA REDUNDANCY IN SHELL : 2.00 REMARK 200 R MERGE FOR SHELL (I) : 0.44700 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: AMORE REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 41.21 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.09 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: AMMONIUM SULFATE, CITRATE, PH 6.5, REMARK 280 VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 293K 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 32.17350 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 32.17350 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 30.12850 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 39.57800 REMARK 290 SMTRY3 5 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 6 -1.000000 0.000000 0.000000 30.12850 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 39.57800 REMARK 290 SMTRY3 6 0.000000 0.000000 1.000000 32.17350 REMARK 290 SMTRY1 7 -1.000000 0.000000 0.000000 30.12850 REMARK 290 SMTRY2 7 0.000000 1.000000 0.000000 39.57800 REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 32.17350 REMARK 290 SMTRY1 8 1.000000 0.000000 0.000000 30.12850 REMARK 290 SMTRY2 8 0.000000 -1.000000 0.000000 39.57800 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 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 CL CL A 203 LIES ON A SPECIAL POSITION. REMARK 375 MG MG A 204 LIES ON A SPECIAL POSITION. REMARK 375 HOH A 393 LIES ON A SPECIAL POSITION. REMARK 375 HOH A 405 LIES ON A SPECIAL POSITION. REMARK 375 HOH A 408 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 -3 REMARK 465 GLY A -2 REMARK 465 GLY 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 -118.58 51.49 REMARK 500 ALA A 11 -120.49 51.49 REMARK 500 ARG A 53 145.47 -174.92 REMARK 500 MET A 95 -7.21 -142.59 REMARK 500 REMARK 500 REMARK: NULL REMARK 525 REMARK 525 SOLVENT REMARK 525 REMARK 525 THE SOLVENT MOLECULES HAVE CHAIN IDENTIFIERS THAT REMARK 525 INDICATE THE POLYMER CHAIN WITH WHICH THEY ARE MOST REMARK 525 CLOSELY ASSOCIATED. THE REMARK LISTS ALL THE SOLVENT REMARK 525 MOLECULES WHICH ARE MORE THAN 5A AWAY FROM THE REMARK 525 NEAREST POLYMER CHAIN (M = MODEL NUMBER; REMARK 525 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE REMARK 525 NUMBER; I=INSERTION CODE): REMARK 525 REMARK 525 M RES CSSEQI REMARK 525 HOH A 438 DISTANCE = 6.10 ANGSTROMS 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 MG A 204 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 GLU A 119 OE1 REMARK 620 2 GLU A 119 OE1 0.0 REMARK 620 N 1 DBREF1 8SZD A 1 160 UNP A0A3N4BLI0_YERPE DBREF2 8SZD A A0A3N4BLI0 1 160 SEQADV 8SZD SER A -3 UNP A0A3N4BLI EXPRESSION TAG SEQADV 8SZD GLY A -2 UNP A0A3N4BLI EXPRESSION TAG SEQADV 8SZD GLY A -1 UNP A0A3N4BLI EXPRESSION TAG SEQADV 8SZD GLY A 0 UNP A0A3N4BLI EXPRESSION TAG SEQRES 1 A 164 SER GLY GLY GLY MET ILE ILE SER LEU ILE ALA ALA LEU SEQRES 2 A 164 ALA ALA ASP ARG VAL ILE GLY MET GLU ASN ALA MET PRO SEQRES 3 A 164 TRP HIS LEU PRO ALA ASP LEU ALA TRP PHE LYS ARG ASN SEQRES 4 A 164 THR LEU ASN LYS PRO VAL ILE MET GLY ARG LYS THR PHE SEQRES 5 A 164 GLU SER ILE GLY ARG PRO LEU PRO GLY ARG LEU ASN ILE SEQRES 6 A 164 VAL ILE SER SER GLN PRO GLY THR ASP GLU ARG VAL THR SEQRES 7 A 164 TRP ALA ALA SER ILE GLU GLU ALA LEU ALA PHE ALA GLY SEQRES 8 A 164 ASN ALA GLU GLU VAL MET VAL MET GLY GLY GLY ARG VAL SEQRES 9 A 164 TYR LYS GLN PHE LEU ASP ARG ALA ASN ARG MET TYR LEU SEQRES 10 A 164 THR HIS ILE ASP ALA GLU VAL GLY GLY ASP THR HIS PHE SEQRES 11 A 164 PRO ASP TYR GLU PRO ASP GLU TRP GLU SER VAL PHE SER SEQRES 12 A 164 GLU PHE HIS ASP ALA ASP GLU ALA ASN SER HIS SER TYR SEQRES 13 A 164 CYS PHE GLU ILE LEU GLU ARG ARG HET SO4 A 201 5 HET SO4 A 202 5 HET CL A 203 1 HET MG A 204 1 HETNAM SO4 SULFATE ION HETNAM CL CHLORIDE ION HETNAM MG MAGNESIUM ION FORMUL 2 SO4 2(O4 S 2-) FORMUL 4 CL CL 1- FORMUL 5 MG MG 2+ FORMUL 6 HOH *138(H2 O) HELIX 1 AA1 PRO A 26 LEU A 29 5 4 HELIX 2 AA2 ALA A 30 LEU A 37 1 8 HELIX 3 AA3 ARG A 45 GLY A 52 1 8 HELIX 4 AA4 SER A 78 ALA A 86 1 9 HELIX 5 AA5 GLY A 97 LEU A 105 1 9 HELIX 6 AA6 GLU A 130 ASP A 132 5 3 SHEET 1 AA1 6 ARG A 13 VAL A 14 0 SHEET 2 AA1 6 ILE A 2 ALA A 10 -1 N ALA A 10 O ARG A 13 SHEET 3 AA1 6 GLU A 91 VAL A 94 1 O VAL A 94 N SER A 4 SHEET 4 AA1 6 VAL A 41 GLY A 44 1 N ILE A 42 O MET A 93 SHEET 5 AA1 6 ASN A 60 ILE A 63 1 O ILE A 63 N MET A 43 SHEET 6 AA1 6 THR A 74 ALA A 76 1 O THR A 74 N ASN A 60 SHEET 1 AA2 5 ARG A 13 VAL A 14 0 SHEET 2 AA2 5 ILE A 2 ALA A 10 -1 N ALA A 10 O ARG A 13 SHEET 3 AA2 5 ARG A 110 HIS A 115 1 O TYR A 112 N LEU A 5 SHEET 4 AA2 5 TYR A 152 ARG A 159 -1 O CYS A 153 N HIS A 115 SHEET 5 AA2 5 TRP A 134 HIS A 142 -1 N GLU A 135 O GLU A 158 LINK OE1 GLU A 119 MG MG A 204 1555 1555 2.05 LINK OE1 GLU A 119 MG MG A 204 1555 4555 2.05 CRYST1 60.257 79.156 64.347 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 0.016596 0.000000 0.000000 0.00000 SCALE2 0.000000 0.012633 0.000000 0.00000 SCALE3 0.000000 0.000000 0.015541 0.00000