HEADER OXIDOREDUCTASE 12-SEP-22 7FQ4 TITLE DHFR:NADP+:FOL COMPLEX AT 310 K (CRYSTAL 2) 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 K-12; SOURCE 3 ORGANISM_TAXID: 83333; SOURCE 4 STRAIN: K12; 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,D.R.HEKSTRA REVDAT 1 20-SEP-23 7FQ4 0 JRNL AUTH J.B.GREISMAN,K.M.DALTON,D.E.BROOKNER,D.R.HEKSTRA JRNL TITL DHFR:NADP+:FOL COMPLEX AT 310 K JRNL REF TO BE PUBLISHED JRNL REFN REMARK 2 REMARK 2 RESOLUTION. 1.33 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 : GEOSTD + MONOMER LIBRARY + CDL V1.2 REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.33 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 26.70 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.340 REMARK 3 COMPLETENESS FOR RANGE (%) : 98.2 REMARK 3 NUMBER OF REFLECTIONS : 67692 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.148 REMARK 3 R VALUE (WORKING SET) : 0.146 REMARK 3 FREE R VALUE : 0.186 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.900 REMARK 3 FREE R VALUE TEST SET COUNT : 3317 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 26.7000 - 3.8200 1.00 2725 137 0.1583 0.1578 REMARK 3 2 3.8200 - 3.0300 0.98 2702 112 0.1312 0.2017 REMARK 3 3 3.0300 - 2.6500 1.00 2730 141 0.1288 0.1986 REMARK 3 4 2.6500 - 2.4100 1.00 2760 127 0.1251 0.1522 REMARK 3 5 2.4100 - 2.2400 1.00 2715 151 0.1015 0.1451 REMARK 3 6 2.2400 - 2.1000 1.00 2692 158 0.0993 0.1193 REMARK 3 7 2.1000 - 2.0000 1.00 2755 136 0.0925 0.1278 REMARK 3 8 2.0000 - 1.9100 1.00 2740 129 0.0931 0.1405 REMARK 3 9 1.9100 - 1.8400 0.99 2728 124 0.0991 0.1417 REMARK 3 10 1.8400 - 1.7700 0.99 2697 136 0.1138 0.1777 REMARK 3 11 1.7700 - 1.7200 0.96 2660 110 0.1408 0.1755 REMARK 3 12 1.7200 - 1.6700 0.99 2698 128 0.1444 0.2055 REMARK 3 13 1.6700 - 1.6300 1.00 2717 165 0.1494 0.1697 REMARK 3 14 1.6300 - 1.5900 0.99 2731 143 0.1573 0.2409 REMARK 3 15 1.5900 - 1.5500 1.00 2687 133 0.1903 0.2278 REMARK 3 16 1.5500 - 1.5200 0.98 2714 150 0.2048 0.2725 REMARK 3 17 1.5200 - 1.4900 1.00 2669 156 0.2262 0.2896 REMARK 3 18 1.4900 - 1.4600 0.97 2651 143 0.2599 0.3399 REMARK 3 19 1.4600 - 1.4300 1.00 2733 148 0.2843 0.2858 REMARK 3 20 1.4300 - 1.4100 0.97 2658 144 0.2836 0.3340 REMARK 3 21 1.4100 - 1.3900 0.99 2665 142 0.3185 0.3689 REMARK 3 22 1.3900 - 1.3600 0.99 2730 131 0.3169 0.3206 REMARK 3 23 1.3600 - 1.3400 0.96 2613 149 0.3276 0.3676 REMARK 3 24 1.3400 - 1.3300 0.81 2205 124 0.3420 0.3315 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) : 0.189 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 19.789 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 15.77 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 24.37 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 : 0.008 1700 REMARK 3 ANGLE : 1.037 2351 REMARK 3 CHIRALITY : 0.082 233 REMARK 3 PLANARITY : 0.008 313 REMARK 3 DIHEDRAL : 13.170 628 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 7FQ4 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 12-SEP-22. REMARK 100 THE DEPOSITION ID IS D_1001405205. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 20-NOV-21 REMARK 200 TEMPERATURE (KELVIN) : 310 REMARK 200 PH : 5.4 - 5.8 REMARK 200 NUMBER OF CRYSTALS USED : NULL REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : SSRL REMARK 200 BEAMLINE : BL12-1 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : NULL REMARK 200 WAVELENGTH OR RANGE (A) : 0.826533 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS EIGER2 S 16M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : DIALS 3.5.2 REMARK 200 DATA SCALING SOFTWARE : DIALS 3.5.2 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 67810 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.330 REMARK 200 RESOLUTION RANGE LOW (A) : 33.420 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.1 REMARK 200 DATA REDUNDANCY : 27.30 REMARK 200 R MERGE (I) : 0.41200 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 24.5000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.33 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.36 REMARK 200 COMPLETENESS FOR SHELL (%) : NULL REMARK 200 DATA REDUNDANCY IN SHELL : 28.60 REMARK 200 R MERGE FOR SHELL (I) : 4.52200 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 0.600 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: FOURIER SYNTHESIS REMARK 200 SOFTWARE USED: PHENIX 1.20.1_4487 REMARK 200 STARTING MODEL: 7LVC REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 42.05 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.12 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 20 MM IMADAZOLE (PH 5.4-5.8), 16-21% REMARK 280 PEG 400, 125 MM MNCL2, PH 5.6, 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 17.07650 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 49.60950 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 22.61450 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 49.60950 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 17.07650 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 22.61450 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 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 69 115.00 -172.45 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 204 MN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ARG A 52 NH1 REMARK 620 2 ASP A 70 OD2 30.3 REMARK 620 3 ASP A 87 OD1 46.8 46.9 REMARK 620 4 HOH A 305 O 50.6 48.6 4.2 REMARK 620 5 HOH A 458 O 48.9 44.5 6.3 4.7 REMARK 620 N 1 2 3 4 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 13.1 REMARK 620 3 HIS A 149 ND1 90.9 103.2 REMARK 620 4 ARG A 159 O 12.9 19.9 93.1 REMARK 620 5 HOH A 313 O 100.3 87.6 167.1 99.3 REMARK 620 6 HOH A 416 O 82.3 84.1 102.8 69.4 85.1 REMARK 620 7 HOH A 432 O 164.7 156.6 99.1 152.9 71.3 84.3 REMARK 620 N 1 2 3 4 5 6 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 HOH A 306 O REMARK 620 2 HOH A 338 O 78.7 REMARK 620 3 HOH A 449 O 97.5 74.9 REMARK 620 4 HOH A 457 O 66.3 144.8 105.1 REMARK 620 N 1 2 3 DBREF 7FQ4 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 7FQ4 CSD A 152 CYS MODIFIED RESIDUE HET CSD A 152 39 HET FOL A 201 98 HET NAP A 202 73 HET MN A 203 1 HET MN A 204 1 HET MN A 205 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 3(MN 2+) FORMUL 7 HOH *164(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 GLY A 86 1 10 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 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 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 VAL A 136 O ILE A 155 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 1.32 LINK C TYR A 151 N BCSD A 152 1555 1555 1.33 LINK C TYR A 151 N CCSD A 152 1555 1555 1.32 LINK C ACSD A 152 N PHE A 153 1555 1555 1.32 LINK C BCSD A 152 N PHE A 153 1555 1555 1.32 LINK C CCSD A 152 N PHE A 153 1555 1555 1.33 LINK NH1AARG A 52 MN MN A 204 1555 1455 2.62 LINK OD2 ASP A 70 MN MN A 204 1555 4466 2.04 LINK OD1AASP A 87 MN MN A 204 1555 1555 2.03 LINK O AASP A 116 MN MN A 203 1555 1555 2.13 LINK O BASP A 116 MN MN A 203 1555 1555 2.20 LINK ND1 HIS A 149 MN MN A 203 1555 1555 2.27 LINK O BARG A 159 MN MN A 203 1555 1655 2.34 LINK MN MN A 203 O HOH A 313 1555 3645 1.99 LINK MN MN A 203 O HOH A 416 1555 1555 2.54 LINK MN MN A 203 O AHOH A 432 1555 1555 2.02 LINK MN MN A 204 O AHOH A 305 1555 1555 2.04 LINK MN MN A 204 O HOH A 458 1555 1555 2.35 LINK MN MN A 205 O HOH A 306 1555 1555 2.20 LINK MN MN A 205 O HOH A 338 1555 1555 2.26 LINK MN MN A 205 O HOH A 449 1555 1555 1.85 LINK MN MN A 205 O HOH A 457 1555 1555 2.12 CISPEP 1 GLY A 95 GLY A 96 0 9.14 CRYST1 34.153 45.229 99.219 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 0.029280 0.000000 0.000000 0.00000 SCALE2 0.000000 0.022110 0.000000 0.00000 SCALE3 0.000000 0.000000 0.010079 0.00000