HEADER HYDROLASE 12-DEC-16 5U7E TITLE APO DIHYDRONEOPTERIN TRIPHOSPHATE PYROPHOSPHOHYDROLASE FROM E. COLI COMPND MOL_ID: 1; COMPND 2 MOLECULE: DIHYDRONEOPTERIN TRIPHOSPHATE DIPHOSPHATASE; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: DIHYDRONEOPTERIN TRIPHOSPHATE PYROPHOSPHATASE,DATP COMPND 5 PYROPHOSPHOHYDROLASE; COMPND 6 EC: 3.6.1.67; COMPND 7 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: ESCHERICHIA COLI O157:H7; SOURCE 3 ORGANISM_TAXID: 83334; SOURCE 4 GENE: NUDB, Z2917, ECS2575; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS NUDIX HYDROLASE, DIHYDRONEOPTERIN TRIPHOSPHATE PYROPHOSPHOHYDROLASE, KEYWDS 2 HYDROLASE EXPDTA X-RAY DIFFRACTION AUTHOR E.NGUYEN,S.E.HILL,R.L.LIEBERMAN REVDAT 5 04-OCT-23 5U7E 1 REMARK REVDAT 4 16-MAR-22 5U7E 1 REMARK REVDAT 3 22-NOV-17 5U7E 1 REMARK REVDAT 2 09-AUG-17 5U7E 1 JRNL REVDAT 1 21-JUN-17 5U7E 0 JRNL AUTH S.E.HILL,E.NGUYEN,C.U.UKACHUKWU,D.M.FREEMAN,S.QUIRK, JRNL AUTH 2 R.L.LIEBERMAN JRNL TITL METAL ION COORDINATION IN THE E. COLI NUDIX HYDROLASE JRNL TITL 2 DIHYDRONEOPTERIN TRIPHOSPHATE PYROPHOSPHATASE: NEW CLUES JRNL TITL 3 INTO CATALYTIC MECHANISM. JRNL REF PLOS ONE V. 12 80241 2017 JRNL REFN ESSN 1932-6203 JRNL PMID 28742822 JRNL DOI 10.1371/JOURNAL.PONE.0180241 REMARK 2 REMARK 2 RESOLUTION. 1.94 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX (1.10.1_2155: ???) 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) : 1.94 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 29.07 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.370 REMARK 3 COMPLETENESS FOR RANGE (%) : 92.5 REMARK 3 NUMBER OF REFLECTIONS : 8908 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.200 REMARK 3 R VALUE (WORKING SET) : 0.195 REMARK 3 FREE R VALUE : 0.238 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 10.150 REMARK 3 FREE R VALUE TEST SET COUNT : 904 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 29.0745 - 3.5271 0.90 1347 151 0.1652 0.1940 REMARK 3 2 3.5271 - 2.8003 0.90 1298 148 0.1949 0.2434 REMARK 3 3 2.8003 - 2.4465 0.92 1308 144 0.2214 0.2629 REMARK 3 4 2.4465 - 2.2229 0.95 1375 160 0.2214 0.2817 REMARK 3 5 2.2229 - 2.0636 0.95 1359 145 0.2198 0.2762 REMARK 3 6 2.0636 - 1.9420 0.93 1317 156 0.2374 0.2946 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) : 0.260 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 27.160 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 : 0.002 1236 REMARK 3 ANGLE : 0.423 1684 REMARK 3 CHIRALITY : 0.043 188 REMARK 3 PLANARITY : 0.003 218 REMARK 3 DIHEDRAL : 10.959 747 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 5U7E COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 16-DEC-16. REMARK 100 THE DEPOSITION ID IS D_1000225437. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 25-NOV-15 REMARK 200 TEMPERATURE (KELVIN) : 80 REMARK 200 PH : NULL REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : APS REMARK 200 BEAMLINE : 22-BM REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.0 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : IMAGE PLATE REMARK 200 DETECTOR MANUFACTURER : MAR SCANNER 300 MM PLATE REMARK 200 INTENSITY-INTEGRATION SOFTWARE : NULL REMARK 200 DATA SCALING SOFTWARE : HKL-3000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 8908 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.942 REMARK 200 RESOLUTION RANGE LOW (A) : 29.071 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 92.6 REMARK 200 DATA REDUNDANCY : 6.300 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 12.8100 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : NULL REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : NULL REMARK 200 COMPLETENESS FOR SHELL (%) : NULL REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : NULL 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: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: HKL-3000, PHASER REMARK 200 STARTING MODEL: 2O1C REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 34.54 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 1.88 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 36% PEG 8000, 0.05M AMMONIUM SULFATE, REMARK 280 VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 298K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: C 1 2 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,Y,-Z REMARK 290 3555 X+1/2,Y+1/2,Z 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 0.00000 REMARK 290 SMTRY2 2 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 3 1.000000 0.000000 0.000000 26.66100 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 21.45250 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 4 -1.000000 0.000000 0.000000 26.66100 REMARK 290 SMTRY2 4 0.000000 1.000000 0.000000 21.45250 REMARK 290 SMTRY3 4 0.000000 0.000000 -1.000000 0.00000 REMARK 290 REMARK 290 REMARK: NULL REMARK 300 REMARK 300 BIOMOLECULE: 1, 2 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 350 REMARK 350 BIOMOLECULE: 2 REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 1090 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 14080 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -38.0 KCAL/MOL 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 350 BIOMT1 2 -1.000000 0.000000 0.000000 -53.32200 REMARK 350 BIOMT2 2 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT3 2 0.000000 0.000000 -1.000000 0.00000 REMARK 375 REMARK 375 SPECIAL POSITION REMARK 375 THE FOLLOWING ATOMS ARE FOUND TO BE WITHIN 0.15 ANGSTROMS REMARK 375 OF A SYMMETRY RELATED ATOM AND ARE ASSUMED TO BE ON SPECIAL REMARK 375 POSITIONS. REMARK 375 REMARK 375 ATOM RES CSSEQI REMARK 375 S SO4 A 201 LIES ON A SPECIAL POSITION. REMARK 375 HOH A 310 LIES ON A SPECIAL POSITION. REMARK 375 HOH A 416 LIES ON A SPECIAL POSITION. 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 MET A 1 REMARK 465 LYS A 2 REMARK 465 ASP A 3 REMARK 465 LYS A 4 REMARK 465 ALA A 149 REMARK 465 ALA A 150 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 361 O HOH A 405 1.83 REMARK 500 O HOH A 420 O HOH A 427 1.96 REMARK 500 OE1 GLN A 76 O HOH A 301 1.97 REMARK 500 O HOH A 326 O HOH A 340 2.01 REMARK 500 O HOH A 411 O HOH A 427 2.03 REMARK 500 O HOH A 395 O HOH A 418 2.03 REMARK 500 O HOH A 344 O HOH A 415 2.03 REMARK 500 NE2 GLN A 140 O HOH A 302 2.03 REMARK 500 NH1 ARG A 30 O HOH A 303 2.12 REMARK 500 OE1 GLN A 19 O HOH A 304 2.12 REMARK 500 OD1 ASP A 64 O HOH A 305 2.17 REMARK 500 OG1 THR A 99 O HOH A 306 2.19 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CLOSE CONTACTS REMARK 500 REMARK 500 THE FOLLOWING ATOMS THAT ARE RELATED BY CRYSTALLOGRAPHIC REMARK 500 SYMMETRY ARE IN CLOSE CONTACT. AN ATOM LOCATED WITHIN 0.15 REMARK 500 ANGSTROMS OF A SYMMETRY RELATED ATOM IS ASSUMED TO BE ON A REMARK 500 SPECIAL POSITION AND IS, THEREFORE, LISTED IN REMARK 375 REMARK 500 INSTEAD OF REMARK 500. ATOMS WITH NON-BLANK ALTERNATE REMARK 500 LOCATION INDICATORS ARE NOT INCLUDED IN THE CALCULATIONS. REMARK 500 REMARK 500 DISTANCE CUTOFF: REMARK 500 2.2 ANGSTROMS FOR CONTACTS NOT INVOLVING HYDROGEN ATOMS REMARK 500 1.6 ANGSTROMS FOR CONTACTS INVOLVING HYDROGEN ATOMS REMARK 500 REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI SSYMOP DISTANCE REMARK 500 O HOH A 349 O HOH A 349 2456 1.67 REMARK 500 O HOH A 382 O HOH A 407 4355 1.86 REMARK 500 O HOH A 400 O HOH A 406 3545 2.07 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 9 26.13 -77.71 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 SO4 A 201 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue GOL A 202 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 5U7F RELATED DB: PDB REMARK 900 RELATED ID: 5U7H RELATED DB: PDB DBREF 5U7E A 1 150 UNP P0AFC1 NUDB_ECO57 1 150 SEQRES 1 A 150 MET LYS ASP LYS VAL TYR LYS ARG PRO VAL SER ILE LEU SEQRES 2 A 150 VAL VAL ILE TYR ALA GLN ASP THR LYS ARG VAL LEU MET SEQRES 3 A 150 LEU GLN ARG ARG ASP ASP PRO ASP PHE TRP GLN SER VAL SEQRES 4 A 150 THR GLY SER VAL GLU GLU GLY GLU THR ALA PRO GLN ALA SEQRES 5 A 150 ALA MET ARG GLU VAL LYS GLU GLU VAL THR ILE ASP VAL SEQRES 6 A 150 VAL ALA GLU GLN LEU THR LEU ILE ASP CYS GLN ARG THR SEQRES 7 A 150 VAL GLU PHE GLU ILE PHE SER HIS LEU ARG HIS ARG TYR SEQRES 8 A 150 ALA PRO GLY VAL THR ARG ASN THR GLU SER TRP PHE CYS SEQRES 9 A 150 LEU ALA LEU PRO HIS GLU ARG GLN ILE VAL PHE THR GLU SEQRES 10 A 150 HIS LEU ALA TYR LYS TRP LEU ASP ALA PRO ALA ALA ALA SEQRES 11 A 150 ALA LEU THR LYS SER TRP SER ASN ARG GLN ALA ILE GLU SEQRES 12 A 150 GLN PHE VAL ILE ASN ALA ALA HET SO4 A 201 5 HET GOL A 202 14 HETNAM SO4 SULFATE ION HETNAM GOL GLYCEROL HETSYN GOL GLYCERIN; PROPANE-1,2,3-TRIOL FORMUL 2 SO4 O4 S 2- FORMUL 3 GOL C3 H8 O3 FORMUL 4 HOH *130(H2 O) HELIX 1 AA1 THR A 48 VAL A 61 1 14 HELIX 2 AA2 PHE A 84 TYR A 91 5 8 HELIX 3 AA3 ASP A 125 THR A 133 1 9 HELIX 4 AA4 SER A 135 VAL A 146 1 12 SHEET 1 AA1 4 VAL A 39 SER A 42 0 SHEET 2 AA1 4 VAL A 10 ALA A 18 -1 N VAL A 14 O VAL A 39 SHEET 3 AA1 4 ARG A 97 LEU A 107 1 O LEU A 107 N TYR A 17 SHEET 4 AA1 4 LEU A 72 GLU A 82 -1 N VAL A 79 O GLU A 100 SHEET 1 AA2 3 TRP A 36 GLN A 37 0 SHEET 2 AA2 3 VAL A 24 ARG A 29 -1 N LEU A 27 O GLN A 37 SHEET 3 AA2 3 HIS A 118 LEU A 124 -1 O LEU A 124 N VAL A 24 SITE 1 AC1 5 PHE A 81 GLU A 82 ARG A 97 TRP A 136 SITE 2 AC1 5 HOH A 328 SITE 1 AC2 1 ARG A 90 CRYST1 53.322 42.905 56.953 90.00 91.80 90.00 C 1 2 1 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 0.018754 0.000000 0.000588 0.00000 SCALE2 0.000000 0.023307 0.000000 0.00000 SCALE3 0.000000 0.000000 0.017567 0.00000