HEADER TRANSFERASE/TRANSFERASE INHIBITOR 27-OCT-11 3UD5 TITLE CRYSTAL STRUCTURE OF E. COLI HPPK IN COMPLEX WITH BISUBSTRATE ANALOGUE TITLE 2 INHIBITOR J1A COMPND MOL_ID: 1; COMPND 2 MOLECULE: 2-AMINO-4-HYDROXY-6-HYDROXYMETHYLDIHYDROPTERIDINE COMPND 3 PYROPHOSPHOKINASE; COMPND 4 CHAIN: A; COMPND 5 SYNONYM: 6-HYDROXYMETHYL-7,8-DIHYDROPTERIN PYROPHOSPHOKINASE, PPPK, COMPND 6 7,8-DIHYDRO-6-HYDROXYMETHYLPTERIN-PYROPHOSPHOKINASE, HPPK; COMPND 7 EC: 2.7.6.3; COMPND 8 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: ESCHERICHIA COLI; SOURCE 3 ORGANISM_TAXID: 83333; SOURCE 4 STRAIN: K12; 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, KINASE, ATP BINDING, PYROPHOSPHORYL TRANSFER, KEYWDS 2 TRANSFERASE-TRANSFERASE INHIBITOR COMPLEX EXPDTA X-RAY DIFFRACTION AUTHOR G.SHAW,G.SHI,X.JI REVDAT 4 13-SEP-23 3UD5 1 REMARK REVDAT 3 30-AUG-23 3UD5 1 AUTHOR JRNL REMARK REVDAT 2 18-JAN-12 3UD5 1 JRNL REVDAT 1 04-JAN-12 3UD5 0 JRNL AUTH G.SHI,G.SHAW,Y.H.LIANG,P.SUBBURAMAN,Y.LI,Y.WU,H.YAN,X.JI JRNL TITL BISUBSTRATE ANALOGUE INHIBITORS OF JRNL TITL 2 6-HYDROXYMETHYL-7,8-DIHYDROPTERIN PYROPHOSPHOKINASE: NEW JRNL TITL 3 DESIGN WITH IMPROVED PROPERTIES. JRNL REF BIOORG.MED.CHEM. V. 20 47 2012 JRNL REFN ISSN 0968-0896 JRNL PMID 22169600 JRNL DOI 10.1016/J.BMC.2011.11.032 REMARK 1 REMARK 1 REFERENCE 1 REMARK 1 AUTH G.SHI,J.BLASZCZYK,X.JI,H.YAN REMARK 1 TITL BISUBSTRATE ANALOGUE INHIBITORS OF REMARK 1 TITL 2 6-HYDROXYMETHYL-7,8-DIHYDROPTERIN PYROPHOSPHOKINASE: REMARK 1 TITL 3 SYNTHESIS AND BIOCHEMICAL AND CRYSTALLOGRAPHIC STUDIES. REMARK 1 REF J.MED.CHEM. V. 44 1364 2001 REMARK 1 REFN ISSN 0022-2623 REMARK 1 PMID 11311059 REMARK 2 REMARK 2 RESOLUTION. 2.00 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.7.2_869 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) : 2.00 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 29.84 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.380 REMARK 3 COMPLETENESS FOR RANGE (%) : 90.7 REMARK 3 NUMBER OF REFLECTIONS : 9252 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.164 REMARK 3 R VALUE (WORKING SET) : 0.160 REMARK 3 FREE R VALUE : 0.205 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 8.910 REMARK 3 FREE R VALUE TEST SET COUNT : 824 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 29.8441 - 3.6326 0.97 1534 150 0.1694 0.1791 REMARK 3 2 3.6326 - 2.8841 0.99 1536 150 0.1472 0.1912 REMARK 3 3 2.8841 - 2.5197 1.00 1539 151 0.1488 0.2255 REMARK 3 4 2.5197 - 2.2894 0.94 1435 140 0.1606 0.2422 REMARK 3 5 2.2894 - 2.1254 0.82 1288 126 0.1659 0.2265 REMARK 3 6 2.1254 - 2.0000 0.72 1096 107 0.1643 0.2617 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 : 0.34 REMARK 3 B_SOL : 44.43 REMARK 3 REMARK 3 ERROR ESTIMATES. REMARK 3 COORDINATE ERROR (MAXIMUM-LIKELIHOOD BASED) : 0.540 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 23.670 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 22.90 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 31.03 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 26.06040 REMARK 3 B22 (A**2) : -7.77680 REMARK 3 B33 (A**2) : -3.26670 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : 9.19490 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 : 0.012 1415 REMARK 3 ANGLE : 1.302 1936 REMARK 3 CHIRALITY : 0.076 211 REMARK 3 PLANARITY : 0.008 251 REMARK 3 DIHEDRAL : 15.858 537 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 3UD5 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 11-NOV-11. REMARK 100 THE DEPOSITION ID IS D_1000068604. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 05-NOV-09 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 6.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : APS REMARK 200 BEAMLINE : 22-ID 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 : GRAPHITE REMARK 200 OPTICS : MIRRORS REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : MARMOSAIC 300 MM CCD REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : HKL-2000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 10236 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.900 REMARK 200 RESOLUTION RANGE LOW (A) : 30.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : -3.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 87.0 REMARK 200 DATA REDUNDANCY : 6.500 REMARK 200 R MERGE (I) : 0.08900 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 16.2000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.90 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.02 REMARK 200 COMPLETENESS FOR SHELL (%) : 63.3 REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : 0.28900 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: FOURIER SYNTHESIS REMARK 200 SOFTWARE USED: PHENIX REMARK 200 STARTING MODEL: PDB ENTRY 1EQM REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 41.66 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.11 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: PEG 3350, BIS-TRIS, PH 6.5, VAPOR REMARK 280 DIFFUSION, SITTING DROP, 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 39.96000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 26.42000 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 4 -1.000000 0.000000 0.000000 39.96000 REMARK 290 SMTRY2 4 0.000000 1.000000 0.000000 26.42000 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 LYS A 85 55.47 -112.11 REMARK 500 ALA A 86 -74.25 70.40 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 J1A A 171 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE EDO A 191 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE EDO A 192 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 1EX8 RELATED DB: PDB REMARK 900 STRUCTURE OF E. COLI HPPK IN COMPLEX WITH BISUBSTRATE ANALOGUE REMARK 900 INHIBITOR A4P REMARK 900 RELATED ID: 3UDE RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF E. COLI HPPK IN COMPLEX WITH BISUBSTRATE REMARK 900 ANALOGUE INHIBITOR J1B REMARK 900 RELATED ID: 3UDV RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF E. COLI HPPK IN COMPLEX WITH BISUBSTRATE REMARK 900 ANALOGUE INHIBITOR J1C DBREF 3UD5 A 1 158 UNP P26281 HPPK_ECOLI 2 159 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 ASP 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 J1A A 171 41 HET EDO A 191 4 HET EDO A 192 4 HETNAM J1A 5'-S-[1-(2-{[(2-AMINO-4-OXO-3,4-DIHYDROPTERIDIN-6-YL) HETNAM 2 J1A METHYL]AMINO}ETHYL)PIPERIDIN-4-YL]-5'-THIOADENOSINE HETNAM EDO 1,2-ETHANEDIOL HETSYN EDO ETHYLENE GLYCOL FORMUL 2 J1A C24 H32 N12 O4 S FORMUL 3 EDO 2(C2 H6 O2) FORMUL 5 HOH *106(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 97 N ALA A 6 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 ARG A 82 LYS A 85 0 SHEET 2 C 2 ARG A 88 ARG A 92 -1 O ARG A 88 N LYS A 85 SHEET 1 D 2 ILE A 106 ASN A 107 0 SHEET 2 D 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 -3.59 SITE 1 AC1 18 THR A 42 PRO A 43 LEU A 45 TYR A 53 SITE 2 AC1 18 ASN A 55 GLN A 74 ASP A 95 ASP A 97 SITE 3 AC1 18 ILE A 98 ARG A 110 LEU A 111 THR A 112 SITE 4 AC1 18 PHE A 123 HIS A 148 EDO A 192 HOH A 221 SITE 5 AC1 18 HOH A 242 HOH A 279 SITE 1 AC2 3 TYR A 53 ARG A 92 ASP A 95 SITE 1 AC3 8 ALA A 6 GLY A 8 ASN A 55 ASP A 95 SITE 2 AC3 8 ASP A 97 PHE A 123 MET A 124 J1A A 171 CRYST1 79.920 52.840 36.760 90.00 102.57 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 0.012513 0.000000 0.002790 0.00000 SCALE2 0.000000 0.018926 0.000000 0.00000 SCALE3 0.000000 0.000000 0.027869 0.00000