HEADER OXIDOREDUCTASE 10-FEB-23 8G4Z TITLE E. COLI DHFR COMPLEX WITH NADP+ AND FOLATE: EF-X OFF MODEL BY LAUE TITLE 2 DIFFRACTION (NO ELECTRIC FIELD) 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: ESCHERICHIA COLI; SOURCE 3 ORGANISM_TAXID: 83333; SOURCE 4 STRAIN: K-12; SOURCE 5 GENE: FOLA, TMRA, B0048, JW0047; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS DIHYDROFOLATE REDUCTASE, OXIDOREDUCTASE EXPDTA X-RAY DIFFRACTION AUTHOR J.B.GREISMAN,K.M.DALTON,D.E.BROOKNER,M.A.KLUREZA,D.R.HEKSTRA REVDAT 1 03-JAN-24 8G4Z 0 JRNL AUTH J.B.GREISMAN,K.M.DALTON,D.E.BROOKNER,M.A.KLUREZA,D.R.HEKSTRA JRNL TITL E. COLI DHFR COMPLEX WITH NADP+ AND FOLATE: EF-X OFF MODEL JRNL TITL 2 BY LAUE DIFFRACTION (NO ELECTRIC FIELD) JRNL REF TO BE PUBLISHED JRNL REFN REMARK 2 REMARK 2 RESOLUTION. 1.70 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.19.2_4158 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 : GEOSTD + MONOMER LIBRARY + CDL V1.2 REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.70 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 41.36 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.320 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.5 REMARK 3 NUMBER OF REFLECTIONS : 17637 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.150 REMARK 3 R VALUE (WORKING SET) : 0.147 REMARK 3 FREE R VALUE : 0.195 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT : 882 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 41.3600 - 3.0900 0.99 2943 155 0.1603 0.2085 REMARK 3 2 3.0900 - 2.4500 0.99 2805 148 0.1563 0.2106 REMARK 3 3 2.4500 - 2.1400 1.00 2777 146 0.1440 0.1814 REMARK 3 4 2.1400 - 1.9500 0.99 2755 145 0.1336 0.1724 REMARK 3 5 1.9500 - 1.8100 1.00 2734 144 0.1342 0.1982 REMARK 3 6 1.8100 - 1.7000 0.99 2741 144 0.1408 0.1890 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) : 0.133 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 18.217 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 1.27 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 8.53 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 : 0.004 1591 REMARK 3 ANGLE : 0.767 2197 REMARK 3 CHIRALITY : 0.053 220 REMARK 3 PLANARITY : 0.007 292 REMARK 3 DIHEDRAL : 13.222 589 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : 1 REMARK 3 TLS GROUP : 1 REMARK 3 SELECTION: ALL REMARK 3 ORIGIN FOR THE GROUP (A): 23.4680 21.3848 35.4668 REMARK 3 T TENSOR REMARK 3 T11: -0.0113 T22: -0.0138 REMARK 3 T33: -0.0132 T12: -0.0213 REMARK 3 T13: -0.0169 T23: -0.0236 REMARK 3 L TENSOR REMARK 3 L11: 0.0840 L22: 0.0305 REMARK 3 L33: 0.0184 L12: 0.0364 REMARK 3 L13: 0.0176 L23: -0.0065 REMARK 3 S TENSOR REMARK 3 S11: 0.0003 S12: 0.0313 S13: -0.0209 REMARK 3 S21: 0.0019 S22: 0.0135 S23: 0.0069 REMARK 3 S31: -0.0049 S32: -0.0049 S33: 0.1145 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 8G4Z COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 26-FEB-23. REMARK 100 THE DEPOSITION ID IS D_1000272178. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 02-APR-21 REMARK 200 TEMPERATURE (KELVIN) : 278 REMARK 200 PH : 5.4 - 5.8 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : APS REMARK 200 BEAMLINE : 14-ID-B REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : L REMARK 200 WAVELENGTH OR RANGE (A) : 1.02-1.18 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : RAYONIX MX340-HS REMARK 200 INTENSITY-INTEGRATION SOFTWARE : PRECOGNITION 5.2.2 REMARK 200 DATA SCALING SOFTWARE : CARELESS 0.2.0 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 17637 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.700 REMARK 200 RESOLUTION RANGE LOW (A) : 41.360 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.5 REMARK 200 DATA REDUNDANCY : 35.53 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 19.6800 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.70 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.76 REMARK 200 COMPLETENESS FOR SHELL (%) : 99.4 REMARK 200 DATA REDUNDANCY IN SHELL : 27.40 REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 9.760 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: LAUE REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: FOURIER SYNTHESIS REMARK 200 SOFTWARE USED: PHENIX 1.19.2_4158 REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 42.53 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.14 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 20 MM IMADAZOLE (PH 5.4-5.8), 15-20% REMARK 280 PEG 400, 125 MM MNCL2, VAPOR DIFFUSION, SITTING DROP, REMARK 280 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 17.14300 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 49.49750 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 22.76500 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 49.49750 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 17.14300 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 22.76500 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 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 ASP A 69 114.27 -170.05 REMARK 500 REMARK 500 REMARK: NULL 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 MN A 205 MN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP A 70 OD2 REMARK 620 2 ASP A 87 OD1 95.4 REMARK 620 N 1 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MN A 203 MN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP A 116 O REMARK 620 2 ASP A 116 O 4.8 REMARK 620 3 HIS A 149 ND1 89.8 94.4 REMARK 620 4 ARG A 159 O 11.5 13.3 91.2 REMARK 620 5 ARG A 159 O 12.0 14.1 90.4 1.0 REMARK 620 6 HOH A 353 O 89.9 85.2 174.3 89.6 90.5 REMARK 620 7 HOH A 392 O 82.8 83.5 100.7 71.3 70.9 85.0 REMARK 620 8 HOH A 417 O 164.1 164.7 91.3 152.7 152.1 90.6 81.4 REMARK 620 N 1 2 3 4 5 6 7 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MN A 207 MN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP A 127 OD1 REMARK 620 2 HOH A 326 O 168.6 REMARK 620 3 HOH A 395 O 52.3 120.6 REMARK 620 4 HOH A 411 O 89.7 81.4 91.9 REMARK 620 5 HOH A 422 O 101.0 87.7 93.1 169.1 REMARK 620 N 1 2 3 4 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MN A 206 MN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 NAP A 202 O2X REMARK 620 2 HOH A 351 O 85.2 REMARK 620 N 1 DBREF 8G4Z A 1 159 UNP P0ABQ4 DYR_ECOLI 1 159 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 LEU 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 CSD PHE GLU ILE LEU SEQRES 13 A 159 GLU ARG ARG MODRES 8G4Z CSD A 152 CYS MODIFIED RESIDUE HET CSD A 152 24 HET FOL A 201 49 HET NAP A 202 73 HET MN A 203 1 HET MN A 204 1 HET MN A 205 1 HET MN A 206 1 HET MN A 207 1 HETNAM CSD 3-SULFINOALANINE HETNAM FOL FOLIC ACID HETNAM NAP NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE HETNAM MN MANGANESE (II) ION HETSYN CSD S-CYSTEINESULFINIC ACID; S-SULFINOCYSTEINE HETSYN NAP 2'-MONOPHOSPHOADENOSINE 5'-DIPHOSPHORIBOSE FORMUL 1 CSD C3 H7 N O4 S FORMUL 2 FOL C19 H19 N7 O6 FORMUL 3 NAP C21 H28 N7 O17 P3 FORMUL 4 MN 5(MN 2+) FORMUL 9 HOH *131(H2 O) HELIX 1 AA1 ALA A 9 ASP A 11 5 3 HELIX 2 AA2 LEU A 24 LEU A 36 1 13 HELIX 3 AA3 ARG A 44 GLY A 51 1 8 HELIX 4 AA4 SER A 77 CYS A 85 1 9 HELIX 5 AA5 GLY A 96 LEU A 104 1 9 HELIX 6 AA6 PRO A 105 ALA A 107 5 3 HELIX 7 AA7 GLU A 129 ASP A 131 5 3 SHEET 1 AA1 8 THR A 73 VAL A 75 0 SHEET 2 AA1 8 LYS A 58 LEU A 62 1 N ILE A 61 O THR A 73 SHEET 3 AA1 8 PRO A 39 GLY A 43 1 N VAL A 40 O LYS A 58 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 ILE A 91 SHEET 6 AA1 8 LYS A 109 ILE A 115 1 O THR A 113 N LEU A 8 SHEET 7 AA1 8 TYR A 151 ARG A 158 -1 O GLU A 154 N LEU A 112 SHEET 8 AA1 8 TRP A 133 HIS A 141 -1 N GLU A 134 O GLU A 157 SHEET 1 AA2 2 VAL A 13 GLY A 15 0 SHEET 2 AA2 2 THR A 123 HIS A 124 -1 O THR A 123 N ILE A 14 LINK C TYR A 151 N ACSD A 152 1555 1555 1.33 LINK C TYR A 151 N BCSD A 152 1555 1555 1.32 LINK C ACSD A 152 N PHE A 153 1555 1555 1.33 LINK C BCSD A 152 N PHE A 153 1555 1555 1.33 LINK OD2 ASP A 70 MN MN A 205 1555 4466 2.20 LINK OD1 ASP A 87 MN MN A 205 1555 1555 2.13 LINK O AASP A 116 MN MN A 203 1555 1555 2.15 LINK O BASP A 116 MN MN A 203 1555 1555 2.17 LINK OD1BASP A 127 MN MN A 207 1555 1555 2.32 LINK ND1 HIS A 149 MN MN A 203 1555 1555 2.35 LINK O AARG A 159 MN MN A 203 1555 1655 2.43 LINK O BARG A 159 MN MN A 203 1555 1655 2.12 LINK O2X NAP A 202 MN MN A 206 1555 3655 2.33 LINK MN MN A 203 O HOH A 353 1555 3645 2.11 LINK MN MN A 203 O HOH A 392 1555 1555 2.31 LINK MN MN A 203 O HOH A 417 1555 1555 2.19 LINK MN MN A 206 O HOH A 351 1555 3645 2.35 LINK MN MN A 207 O HOH A 326 1555 1555 2.47 LINK MN MN A 207 O AHOH A 395 1555 1555 2.13 LINK MN MN A 207 O HOH A 411 1555 1555 2.09 LINK MN MN A 207 O HOH A 422 1555 1555 2.30 CISPEP 1 GLY A 95 GLY A 96 0 7.60 CRYST1 34.286 45.530 98.995 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 0.029166 0.000000 0.000000 0.00000 SCALE2 0.000000 0.021964 0.000000 0.00000 SCALE3 0.000000 0.000000 0.010102 0.00000