HEADER OXIDOREDUCTASE 01-JUL-15 5CC9 TITLE L28F E.COLI DIHYDROFOLATE REDUCTASE COMPLEXED WITH 5,10- TITLE 2 DIDEAZATETRAHYDROFOLATE AND OXIDIZED NICOTINAMIDE ADENINE TITLE 3 DINUCLEOTIDE PHOSPHATE COMPND MOL_ID: 1; COMPND 2 MOLECULE: DIHYDROFOLATE REDUCTASE; COMPND 3 CHAIN: A; COMPND 4 EC: 1.5.1.3; COMPND 5 ENGINEERED: YES; COMPND 6 MUTATION: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: ESCHERICHIA COLI; SOURCE 3 ORGANISM_TAXID: 562; SOURCE 4 GENE: FOLA; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 7 EXPRESSION_SYSTEM_STRAIN: BL21(DE3); SOURCE 8 EXPRESSION_SYSTEM_VARIANT: DNAY; SOURCE 9 EXPRESSION_SYSTEM_PLASMID: PET22B KEYWDS FOLATE METABOLISM, OXIDOREDUCTASE EXPDTA X-RAY DIFFRACTION AUTHOR D.OYEN,P.E.WRIGHT REVDAT 5 27-SEP-23 5CC9 1 REMARK REVDAT 4 25-DEC-19 5CC9 1 REMARK REVDAT 3 27-SEP-17 5CC9 1 REMARK REVDAT 2 12-AUG-15 5CC9 1 JRNL REVDAT 1 05-AUG-15 5CC9 0 JRNL AUTH D.OYEN,R.B.FENWICK,R.L.STANFIELD,H.J.DYSON,P.E.WRIGHT JRNL TITL COFACTOR-MEDIATED CONFORMATIONAL DYNAMICS PROMOTE PRODUCT JRNL TITL 2 RELEASE FROM ESCHERICHIA COLI DIHYDROFOLATE REDUCTASE VIA AN JRNL TITL 3 ALLOSTERIC PATHWAY. JRNL REF J.AM.CHEM.SOC. V. 137 9459 2015 JRNL REFN ESSN 1520-5126 JRNL PMID 26147643 JRNL DOI 10.1021/JACS.5B05707 REMARK 2 REMARK 2 RESOLUTION. 1.20 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.9_1692 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) : 1.20 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 46.96 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.340 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.2 REMARK 3 NUMBER OF REFLECTIONS : 50619 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.157 REMARK 3 R VALUE (WORKING SET) : 0.155 REMARK 3 FREE R VALUE : 0.196 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.090 REMARK 3 FREE R VALUE TEST SET COUNT : 2574 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 46.9952 - 3.1416 0.99 2837 164 0.1489 0.2000 REMARK 3 2 3.1416 - 2.4936 0.99 2732 152 0.1611 0.2035 REMARK 3 3 2.4936 - 2.1784 0.99 2706 154 0.1465 0.1636 REMARK 3 4 2.1784 - 1.9792 1.00 2731 139 0.1443 0.1739 REMARK 3 5 1.9792 - 1.8374 1.00 2693 137 0.1437 0.1777 REMARK 3 6 1.8374 - 1.7290 0.99 2651 137 0.1451 0.1761 REMARK 3 7 1.7290 - 1.6424 1.00 2680 145 0.1416 0.1997 REMARK 3 8 1.6424 - 1.5709 0.99 2663 138 0.1359 0.2018 REMARK 3 9 1.5709 - 1.5104 1.00 2700 124 0.1395 0.1947 REMARK 3 10 1.5104 - 1.4583 0.99 2669 138 0.1471 0.1933 REMARK 3 11 1.4583 - 1.4127 0.99 2614 149 0.1532 0.1839 REMARK 3 12 1.4127 - 1.3723 1.00 2636 162 0.1684 0.1927 REMARK 3 13 1.3723 - 1.3362 0.99 2631 144 0.1791 0.2304 REMARK 3 14 1.3362 - 1.3036 0.99 2646 141 0.1949 0.2465 REMARK 3 15 1.3036 - 1.2740 0.99 2605 152 0.2043 0.2090 REMARK 3 16 1.2740 - 1.2469 0.99 2669 130 0.2247 0.2503 REMARK 3 17 1.2469 - 1.2219 0.99 2630 130 0.2525 0.2762 REMARK 3 18 1.2219 - 1.1988 0.97 2552 138 0.2823 0.3436 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) : 0.130 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 19.850 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 14.30 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 : 0.009 1591 REMARK 3 ANGLE : 1.319 2213 REMARK 3 CHIRALITY : 0.075 228 REMARK 3 PLANARITY : 0.007 281 REMARK 3 DIHEDRAL : 13.187 663 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 5CC9 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 22-JUL-15. REMARK 100 THE DEPOSITION ID IS D_1000211342. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 09-JUL-14 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 7.0 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : SSRL REMARK 200 BEAMLINE : BL11-1 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.97945 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS PILATUS 6M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 50682 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.200 REMARK 200 RESOLUTION RANGE LOW (A) : 46.960 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : -3.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.2 REMARK 200 DATA REDUNDANCY : 12.20 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : 0.04600 REMARK 200 FOR THE DATA SET : 43.8000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.20 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.22 REMARK 200 COMPLETENESS FOR SHELL (%) : 98.6 REMARK 200 DATA REDUNDANCY IN SHELL : 12.20 REMARK 200 R MERGE FOR SHELL (I) : 1.00000 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 2.000 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: PHASER REMARK 200 STARTING MODEL: 1RX6 REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 44.37 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.19 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.1M TRIS(HYDROXYMETHYL)AMINOMETHANE, REMARK 280 20% W/V PEG3350, 0.2M CALCIUM ACETATE, PH 7.0, VAPOR DIFFUSION, REMARK 280 SITTING DROP, TEMPERATURE 277K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 21 21 21 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X+1/2,-Y,Z+1/2 REMARK 290 3555 -X,Y+1/2,-Z+1/2 REMARK 290 4555 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 17.26800 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 39.68850 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 29.12250 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 39.68850 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 17.26800 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 29.12250 REMARK 290 SMTRY3 4 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 470 REMARK 470 MISSING ATOM REMARK 470 THE FOLLOWING RESIDUES HAVE MISSING ATOMS (M=MODEL NUMBER; REMARK 470 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; REMARK 470 I=INSERTION CODE): REMARK 470 M RES CSSEQI ATOMS REMARK 470 ASP A 127 CG OD1 OD2 REMARK 470 ARG A 159 CG CD NE CZ NH1 NH2 REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CLOSE CONTACTS IN SAME ASYMMETRIC UNIT REMARK 500 REMARK 500 THE FOLLOWING ATOMS ARE IN CLOSE CONTACT. REMARK 500 REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI DISTANCE REMARK 500 O HOH A 477 O HOH A 491 2.14 REMARK 500 O HOH A 321 O HOH A 452 2.17 REMARK 500 OD2 ASP A 70 O HOH A 301 2.18 REMARK 500 O HOH A 323 O HOH A 475 2.19 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 PRO A 21 56.73 -101.66 REMARK 500 ASP A 69 117.30 -167.72 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 DDF A 202 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 5CCC RELATED DB: PDB DBREF 5CC9 A 1 159 UNP P0ABQ5 DYR_ECOL6 1 159 SEQADV 5CC9 PHE A 28 UNP P0ABQ5 LEU 28 ENGINEERED MUTATION SEQRES 1 A 159 MET ILE SER LEU ILE ALA ALA LEU ALA VAL ASP ARG VAL SEQRES 2 A 159 ILE GLY MET GLU ASN ALA MET PRO TRP ASN LEU PRO ALA SEQRES 3 A 159 ASP PHE ALA TRP PHE LYS ARG ASN THR LEU ASN LYS PRO SEQRES 4 A 159 VAL ILE MET GLY ARG HIS THR TRP GLU SER ILE GLY ARG SEQRES 5 A 159 PRO LEU PRO GLY ARG LYS ASN ILE ILE LEU SER SER GLN SEQRES 6 A 159 PRO GLY THR ASP ASP ARG VAL THR TRP VAL LYS SER VAL SEQRES 7 A 159 ASP GLU ALA ILE ALA ALA CYS GLY ASP VAL PRO GLU ILE SEQRES 8 A 159 MET VAL ILE GLY GLY GLY ARG VAL TYR GLU GLN PHE LEU SEQRES 9 A 159 PRO LYS ALA GLN LYS LEU TYR LEU THR HIS ILE ASP ALA SEQRES 10 A 159 GLU VAL GLU GLY ASP THR HIS PHE PRO ASP TYR GLU PRO SEQRES 11 A 159 ASP ASP TRP GLU SER VAL PHE SER GLU PHE HIS ASP ALA SEQRES 12 A 159 ASP ALA GLN ASN SER HIS SER TYR CYS PHE GLU ILE LEU SEQRES 13 A 159 GLU ARG ARG HET NAP A 201 146 HET DDF A 202 55 HETNAM NAP NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE HETNAM DDF 5,10-DIDEAZATETRAHYDROFOLIC ACID HETSYN NAP 2'-MONOPHOSPHOADENOSINE 5'-DIPHOSPHORIBOSE FORMUL 2 NAP C21 H28 N7 O17 P3 FORMUL 3 DDF C21 H25 N5 O6 FORMUL 4 HOH *239(H2 O) HELIX 1 AA1 ALA A 9 VAL A 13 5 5 HELIX 2 AA2 MET A 16 MET A 20 5 5 HELIX 3 AA3 LEU A 24 LEU A 36 1 13 HELIX 4 AA4 ARG A 44 GLY A 51 1 8 HELIX 5 AA5 SER A 77 CYS A 85 1 9 HELIX 6 AA6 GLY A 96 LEU A 104 1 9 HELIX 7 AA7 PRO A 105 ALA A 107 5 3 HELIX 8 AA8 GLU A 129 ASP A 131 5 3 SHEET 1 AA1 8 THR A 73 VAL A 75 0 SHEET 2 AA1 8 ASN A 59 LEU A 62 1 N ILE A 61 O THR A 73 SHEET 3 AA1 8 VAL A 40 GLY A 43 1 N VAL A 40 O ILE A 60 SHEET 4 AA1 8 ILE A 91 VAL A 93 1 O MET A 92 N ILE A 41 SHEET 5 AA1 8 ILE A 2 LEU A 8 1 N SER A 3 O VAL A 93 SHEET 6 AA1 8 LYS A 109 ILE A 115 1 O ILE A 115 N LEU A 8 SHEET 7 AA1 8 TYR A 151 ARG A 158 -1 O CYS A 152 N HIS A 114 SHEET 8 AA1 8 TRP A 133 HIS A 141 -1 N HIS A 141 O TYR A 151 CISPEP 1 GLY A 95 GLY A 96 0 6.75 SITE 1 AC1 31 MET A 16 GLY A 43 ARG A 44 HIS A 45 SITE 2 AC1 31 THR A 46 LEU A 62 SER A 63 SER A 64 SITE 3 AC1 31 LYS A 76 GLY A 96 GLY A 97 ARG A 98 SITE 4 AC1 31 VAL A 99 GLN A 102 ASP A 122 THR A 123 SITE 5 AC1 31 GLU A 134 SER A 135 VAL A 136 HOH A 314 SITE 6 AC1 31 HOH A 320 HOH A 322 HOH A 325 HOH A 326 SITE 7 AC1 31 HOH A 337 HOH A 340 HOH A 347 HOH A 366 SITE 8 AC1 31 HOH A 409 HOH A 428 HOH A 429 SITE 1 AC2 20 ILE A 5 ALA A 6 ALA A 7 ASP A 27 SITE 2 AC2 20 PHE A 28 PHE A 31 LYS A 32 ILE A 50 SITE 3 AC2 20 LEU A 54 ARG A 57 ILE A 94 TYR A 100 SITE 4 AC2 20 THR A 113 HOH A 316 HOH A 328 HOH A 343 SITE 5 AC2 20 HOH A 350 HOH A 375 HOH A 390 HOH A 408 CRYST1 34.536 58.245 79.377 90.00 90.00 90.00 P 21 21 21 4 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 0.028955 0.000000 0.000000 0.00000 SCALE2 0.000000 0.017169 0.000000 0.00000 SCALE3 0.000000 0.000000 0.012598 0.00000