HEADER OXIDOREDUCTASE 23-JAN-18 5Z6M TITLE HIGH-PRESSURE CRYSTAL STRUCTURE ANALYSIS OF M20 LOOP CLOSED DHFR AT TITLE 2 800 MPA 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 (STRAIN K12); 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 M20 LOOP CLOSED FORM, OXIDOREDUCTASE EXPDTA X-RAY DIFFRACTION AUTHOR N.WATANABE,T.NAGAE,H.YAMADA REVDAT 1 19-SEP-18 5Z6M 0 JRNL AUTH T.NAGAE,H.YAMADA,N.WATANABE JRNL TITL HIGH-PRESSURE PROTEIN CRYSTAL STRUCTURE ANALYSIS OF JRNL TITL 2 ESCHERICHIA COLI DIHYDROFOLATE REDUCTASE COMPLEXED WITH JRNL TITL 3 FOLATE AND NADP. JRNL REF ACTA CRYSTALLOGR D STRUCT V. 74 895 2018 JRNL REF 2 BIOL JRNL REFN ISSN 2059-7983 JRNL PMID 30198899 JRNL DOI 10.1107/S2059798318009397 REMARK 2 REMARK 2 RESOLUTION. 2.20 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX (1.13_2998) 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 : NULL REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.20 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 48.76 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.360 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.6 REMARK 3 NUMBER OF REFLECTIONS : 7454 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.236 REMARK 3 R VALUE (WORKING SET) : 0.232 REMARK 3 FREE R VALUE : 0.306 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.060 REMARK 3 FREE R VALUE TEST SET COUNT : 377 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 48.7745 - 3.1750 1.00 2454 134 0.2242 0.2843 REMARK 3 2 3.1750 - 2.5201 1.00 2345 124 0.2406 0.3498 REMARK 3 3 2.5201 - 2.2016 0.99 2278 119 0.2423 0.3172 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : NULL 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) : 0.310 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 31.850 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 : 0.009 1403 REMARK 3 ANGLE : 1.156 1918 REMARK 3 CHIRALITY : 0.063 199 REMARK 3 PLANARITY : 0.006 245 REMARK 3 DIHEDRAL : 9.798 800 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 5Z6M COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 03-APR-18. REMARK 100 THE DEPOSITION ID IS D_1300006573. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 08-FEB-16 REMARK 200 TEMPERATURE (KELVIN) : 297 REMARK 200 PH : NULL REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : AICHISR REMARK 200 BEAMLINE : BL2S1 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.75 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 315R REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : AIMLESS REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 7493 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.200 REMARK 200 RESOLUTION RANGE LOW (A) : 48.760 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.6 REMARK 200 DATA REDUNDANCY : 3.200 REMARK 200 R MERGE (I) : 0.10900 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 15.9000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.20 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.27 REMARK 200 COMPLETENESS FOR SHELL (%) : NULL REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : 0.66100 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: NULL REMARK 200 SOFTWARE USED: MOLREP REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 35.19 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 1.90 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: PEG 400, CACL, IMIDAZOLE BUFFER, VAPOR REMARK 280 DIFFUSION, HANGING 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 16.95750 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 48.76250 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 20.92450 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 48.76250 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 16.95750 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 20.92450 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 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 GLY A -2 REMARK 465 SER A -1 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 OE1 GLU A 139 O HOH A 301 1.92 REMARK 500 O LEU A 36 O HOH A 302 2.05 REMARK 500 O ARG A 159 O HOH A 303 2.10 REMARK 500 NZ LYS A 38 OE2 GLU A 90 2.11 REMARK 500 NH2 ARG A 98 O HOH A 304 2.18 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 ALA A 19 -148.46 -140.40 REMARK 500 TRP A 22 55.14 -154.68 REMARK 500 ASN A 23 85.29 -45.32 REMARK 500 ARG A 52 129.76 -174.47 REMARK 500 ASP A 69 114.38 -167.30 REMARK 500 SER A 138 119.32 -165.75 REMARK 500 ASP A 144 -145.10 -144.49 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 FOL A 201 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue NAP A 202 DBREF 5Z6M A 1 159 UNP P0ABQ4 DYR_ECOLI 1 159 SEQADV 5Z6M GLY A -2 UNP P0ABQ4 EXPRESSION TAG SEQADV 5Z6M SER A -1 UNP P0ABQ4 EXPRESSION TAG SEQADV 5Z6M HIS A 0 UNP P0ABQ4 EXPRESSION TAG SEQRES 1 A 162 GLY SER HIS MET ILE SER LEU ILE ALA ALA LEU ALA VAL SEQRES 2 A 162 ASP ARG VAL ILE GLY MET GLU ASN ALA MET PRO TRP ASN SEQRES 3 A 162 LEU PRO ALA ASP LEU ALA TRP PHE LYS ARG ASN THR LEU SEQRES 4 A 162 ASN LYS PRO VAL ILE MET GLY ARG HIS THR TRP GLU SER SEQRES 5 A 162 ILE GLY ARG PRO LEU PRO GLY ARG LYS ASN ILE ILE LEU SEQRES 6 A 162 SER SER GLN PRO GLY THR ASP ASP ARG VAL THR TRP VAL SEQRES 7 A 162 LYS SER VAL ASP GLU ALA ILE ALA ALA CYS GLY ASP VAL SEQRES 8 A 162 PRO GLU ILE MET VAL ILE GLY GLY GLY ARG VAL TYR GLU SEQRES 9 A 162 GLN PHE LEU PRO LYS ALA GLN LYS LEU TYR LEU THR HIS SEQRES 10 A 162 ILE ASP ALA GLU VAL GLU GLY ASP THR HIS PHE PRO ASP SEQRES 11 A 162 TYR GLU PRO ASP ASP TRP GLU SER VAL PHE SER GLU PHE SEQRES 12 A 162 HIS ASP ALA ASP ALA GLN ASN SER HIS SER TYR CME PHE SEQRES 13 A 162 GLU ILE LEU GLU ARG ARG MODRES 5Z6M CME A 152 CYS MODIFIED RESIDUE HET CME A 152 10 HET FOL A 201 32 HET NAP A 202 48 HETNAM CME S,S-(2-HYDROXYETHYL)THIOCYSTEINE HETNAM FOL FOLIC ACID HETNAM NAP NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE HETSYN NAP 2'-MONOPHOSPHOADENOSINE 5'-DIPHOSPHORIBOSE FORMUL 1 CME C5 H11 N O3 S2 FORMUL 2 FOL C19 H19 N7 O6 FORMUL 3 NAP C21 H28 N7 O17 P3 FORMUL 4 HOH *41(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 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 THR A 113 N LEU A 8 SHEET 7 AA1 8 TYR A 151 ARG A 158 -1 O LEU A 156 N LEU A 110 SHEET 8 AA1 8 TRP A 133 HIS A 141 -1 N HIS A 141 O TYR A 151 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 CME A 152 1555 1555 1.32 LINK C CME A 152 N PHE A 153 1555 1555 1.33 CISPEP 1 GLY A 95 GLY A 96 0 2.03 SITE 1 AC1 13 ILE A 5 ALA A 6 ALA A 7 MET A 20 SITE 2 AC1 13 ASP A 27 LEU A 28 TRP A 30 PHE A 31 SITE 3 AC1 13 LEU A 54 ILE A 94 TYR A 100 THR A 113 SITE 4 AC1 13 NAP A 202 SITE 1 AC2 29 ALA A 6 ALA A 7 ILE A 14 GLY A 15 SITE 2 AC2 29 ASN A 18 ALA A 19 TRP A 22 GLY A 43 SITE 3 AC2 29 ARG A 44 HIS A 45 THR A 46 LEU A 62 SITE 4 AC2 29 SER A 63 SER A 64 GLN A 65 LYS A 76 SITE 5 AC2 29 ILE A 94 GLY A 96 GLY A 97 ARG A 98 SITE 6 AC2 29 VAL A 99 TYR A 100 GLN A 102 ASP A 131 SITE 7 AC2 29 GLU A 139 FOL A 201 HOH A 305 HOH A 308 SITE 8 AC2 29 HOH A 316 CRYST1 33.915 41.849 97.525 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 0.029485 0.000000 0.000000 0.00000 SCALE2 0.000000 0.023895 0.000000 0.00000 SCALE3 0.000000 0.000000 0.010254 0.00000