HEADER TRANSFERASE 07-AUG-09 3ILL TITLE CRYSTAL STRUCTURE OF E. COLI HPPK(D97A) COMPND MOL_ID: 1; COMPND 2 MOLECULE: 2-AMINO-4-HYDROXY-6-HYDROXYMETHYLDIHYDROPTERIDINE COMPND 3 PYROPHOSPHOKINASE; COMPND 4 CHAIN: A; COMPND 5 SYNONYM: 7,8-DIHYDRO-6-HYDROXYMETHYLPTERIN-PYROPHOSPHOKINASE, HPPK, COMPND 6 6-HYDROXYMETHYL-7,8-DIHYDROPTERIN PYROPHOSPHOKINASE, PPPK; COMPND 7 EC: 2.7.6.3; COMPND 8 ENGINEERED: YES; COMPND 9 MUTATION: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: ESCHERICHIA COLI; SOURCE 3 ORGANISM_TAXID: 83333; SOURCE 4 STRAIN: K-12; SOURCE 5 GENE: B0142, FOIK, FOLK, JW0138; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 8 EXPRESSION_SYSTEM_STRAIN: BL21(DE3); SOURCE 9 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 10 EXPRESSION_SYSTEM_PLASMID: PET17B KEYWDS ALPHA BETA, ATP-BINDING, FOLATE BIOSYNTHESIS, KINASE, NUCLEOTIDE- KEYWDS 2 BINDING, TRANSFERASE EXPDTA X-RAY DIFFRACTION AUTHOR J.BLASZCZYK,Y.LI,H.YAN,X.JI REVDAT 5 06-SEP-23 3ILL 1 REMARK REVDAT 4 30-AUG-23 3ILL 1 AUTHOR JRNL REVDAT 3 13-OCT-21 3ILL 1 REMARK SEQADV REVDAT 2 01-NOV-17 3ILL 1 REMARK REVDAT 1 11-AUG-10 3ILL 0 JRNL AUTH Y.LI,J.BLASZCZYK,X.JI,H.YAN JRNL TITL STRUCTURAL AND FUNCTIONAL ROLES OF RESIDUES D95 AND D97 IN JRNL TITL 2 E. COLI HPPK JRNL REF TO BE PUBLISHED JRNL REFN REMARK 1 REMARK 1 REFERENCE 1 REMARK 1 AUTH B.XIAO,G.SHI,X.CHEN,H.YAN,X.JI REMARK 1 TITL CRYSTAL STRUCTURE OF 6-HYDROXYMETHYL-7,8-DIHYDROPTERIN REMARK 1 TITL 2 PYROPHOSPHOKINASE, A POTENTIAL TARGET FOR THE DEVELOPMENT OF REMARK 1 TITL 3 NOVEL ANTIMICROBIAL AGENTS REMARK 1 REF STRUCTURE V. 7 489 1999 REMARK 1 REFN ISSN 0969-2126 REMARK 1 PMID 10378268 REMARK 2 REMARK 2 RESOLUTION. 1.73 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 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) : 1.73 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 25.79 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.360 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.2 REMARK 3 NUMBER OF REFLECTIONS : 16213 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.165 REMARK 3 R VALUE (WORKING SET) : 0.162 REMARK 3 FREE R VALUE : 0.213 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 6.180 REMARK 3 FREE R VALUE TEST SET COUNT : 1002 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 25.7970 - 3.3050 0.99 2199 146 0.1480 0.1710 REMARK 3 2 3.3050 - 2.6240 1.00 2210 152 0.1560 0.2040 REMARK 3 3 2.6240 - 2.2930 1.00 2174 139 0.1600 0.2430 REMARK 3 4 2.2930 - 2.0830 0.99 2190 138 0.1570 0.2020 REMARK 3 5 2.0830 - 1.9340 0.99 2169 142 0.1650 0.2390 REMARK 3 6 1.9340 - 1.8200 0.99 2145 140 0.1830 0.2450 REMARK 3 7 1.8200 - 1.7300 0.98 2124 145 0.2080 0.2630 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 : 0.42 REMARK 3 B_SOL : 61.05 REMARK 3 REMARK 3 ERROR ESTIMATES. REMARK 3 COORDINATE ERROR (MAXIMUM-LIKELIHOOD BASED) : 0.200 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : NULL REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 18.70 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 21.10 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -0.14100 REMARK 3 B22 (A**2) : -1.24400 REMARK 3 B33 (A**2) : 1.38500 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : -2.77600 REMARK 3 B23 (A**2) : 0.00000 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 : 0.006 1361 REMARK 3 ANGLE : 0.995 1867 REMARK 3 CHIRALITY : 0.072 207 REMARK 3 PLANARITY : 0.004 249 REMARK 3 DIHEDRAL : 15.913 510 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: THE STRUCTURE WAS REFINED FOR A TOTAL REMARK 3 OF 14 CYCLES WITH PHENIX. REMARK 4 REMARK 4 3ILL COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 13-AUG-09. REMARK 100 THE DEPOSITION ID IS D_1000054563. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 23-MAR-00 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 8.4 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : NSLS REMARK 200 BEAMLINE : X9B REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.072 REMARK 200 MONOCHROMATOR : SILICON 111 REMARK 200 OPTICS : MIRRORS REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 4 REMARK 200 INTENSITY-INTEGRATION SOFTWARE : DENZO REMARK 200 DATA SCALING SOFTWARE : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 16217 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.730 REMARK 200 RESOLUTION RANGE LOW (A) : 40.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : -3.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.2 REMARK 200 DATA REDUNDANCY : 3.400 REMARK 200 R MERGE (I) : 0.08100 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 7.0000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.73 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.79 REMARK 200 COMPLETENESS FOR SHELL (%) : 98.2 REMARK 200 DATA REDUNDANCY IN SHELL : 3.40 REMARK 200 R MERGE FOR SHELL (I) : 0.58500 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 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: PHENIX REMARK 200 STARTING MODEL: PDB ENTRY 1HKA REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 44.26 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.21 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: PEG 4000, SODIUM ACETATE, MAGNESIUM REMARK 280 CHLORIDE, TRIS-HCL., PH 8.4, VAPOR DIFFUSION, HANGING DROP, REMARK 280 TEMPERATURE 292K 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 16.74000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 32.16500 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 4 -1.000000 0.000000 0.000000 16.74000 REMARK 290 SMTRY2 4 0.000000 1.000000 0.000000 32.16500 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 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 CL CL A 193 LIES ON A SPECIAL POSITION. REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CL A 191 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CL A 192 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CL A 193 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 1HKA RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF E. COLI HPPK REMARK 900 RELATED ID: 3ILI RELATED DB: PDB REMARK 900 RELATED ID: 3ILL RELATED DB: PDB REMARK 900 RELATED ID: 3ILO RELATED DB: PDB DBREF 3ILL A 1 158 UNP P26281 HPPK_ECOLI 2 159 SEQADV 3ILL ALA A 97 UNP P26281 ASP 98 ENGINEERED MUTATION SEQRES 1 A 158 THR VAL ALA TYR ILE ALA ILE GLY SER ASN LEU ALA SER SEQRES 2 A 158 PRO LEU GLU GLN VAL ASN ALA ALA LEU LYS ALA LEU GLY SEQRES 3 A 158 ASP ILE PRO GLU SER HIS ILE LEU THR VAL SER SER PHE SEQRES 4 A 158 TYR ARG THR PRO PRO LEU GLY PRO GLN ASP GLN PRO ASP SEQRES 5 A 158 TYR LEU ASN ALA ALA VAL ALA LEU GLU THR SER LEU ALA SEQRES 6 A 158 PRO GLU GLU LEU LEU ASN HIS THR GLN ARG ILE GLU LEU SEQRES 7 A 158 GLN GLN GLY ARG VAL ARG LYS ALA GLU ARG TRP GLY PRO SEQRES 8 A 158 ARG THR LEU ASP LEU ALA ILE MET LEU PHE GLY ASN GLU SEQRES 9 A 158 VAL ILE ASN THR GLU ARG LEU THR VAL PRO HIS TYR ASP SEQRES 10 A 158 MET LYS ASN ARG GLY PHE MET LEU TRP PRO LEU PHE GLU SEQRES 11 A 158 ILE ALA PRO GLU LEU VAL PHE PRO ASP GLY GLU MET LEU SEQRES 12 A 158 ARG GLN ILE LEU HIS THR ARG ALA PHE ASP LYS LEU ASN SEQRES 13 A 158 LYS TRP HET CL A 191 1 HET CL A 192 1 HET CL A 193 1 HETNAM CL CHLORIDE ION FORMUL 2 CL 3(CL 1-) FORMUL 5 HOH *186(H2 O) HELIX 1 1 PRO A 14 ASP A 27 1 14 HELIX 2 2 ALA A 65 GLY A 81 1 17 HELIX 3 3 ASP A 117 ASN A 120 5 4 HELIX 4 4 ARG A 121 ALA A 132 1 12 HELIX 5 5 MET A 142 ALA A 151 1 10 SHEET 1 A 4 SER A 31 VAL A 36 0 SHEET 2 A 4 TYR A 53 THR A 62 -1 O ALA A 59 N LEU A 34 SHEET 3 A 4 VAL A 2 SER A 9 -1 N ALA A 3 O LEU A 60 SHEET 4 A 4 LEU A 94 PHE A 101 -1 O ASP A 95 N GLY A 8 SHEET 1 B 4 SER A 31 VAL A 36 0 SHEET 2 B 4 TYR A 53 THR A 62 -1 O ALA A 59 N LEU A 34 SHEET 3 B 4 TYR A 40 THR A 42 -1 N THR A 42 O TYR A 53 SHEET 4 B 4 ASN A 156 LYS A 157 -1 O ASN A 156 N ARG A 41 SHEET 1 C 2 ILE A 106 ASN A 107 0 SHEET 2 C 2 THR A 112 VAL A 113 -1 O VAL A 113 N ILE A 106 CISPEP 1 VAL A 113 PRO A 114 0 -2.18 SITE 1 AC1 5 PRO A 114 LYS A 119 PRO A 138 ASP A 139 SITE 2 AC1 5 HOH A 372 SITE 1 AC2 3 ARG A 82 VAL A 83 LYS A 154 SITE 1 AC3 4 ARG A 41 TRP A 158 HOH A 211 HOH A 258 CRYST1 33.480 64.330 74.730 90.00 100.62 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 0.029869 0.000000 0.005601 0.00000 SCALE2 0.000000 0.015545 0.000000 0.00000 SCALE3 0.000000 0.000000 0.013615 0.00000