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 <I/SIGMA(I)> 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 <I/SIGMA(I)> 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
(ATOM LINES ARE NOT SHOWN.)
END
