HEADER TRANSFERASE/TRANSFERASE INHIBITOR 16-MAY-12 4F7V TITLE CRYSTAL STRUCTURE OF E. COLI HPPK IN COMPLEX WITH BISUBSTRATE ANALOGUE TITLE 2 INHIBITOR J1D (HP26) 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: 469008; SOURCE 8 EXPRESSION_SYSTEM_STRAIN: BL21(DE3); SOURCE 9 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 10 EXPRESSION_SYSTEM_PLASMID: PET17B KEYWDS ALPHA BETA, PYROPHOSPHOKINASE, PYROPHOSPHORYL TRANSFER, TRANSFERASE- KEYWDS 2 TRANSFERASE INHIBITOR COMPLEX EXPDTA X-RAY DIFFRACTION AUTHOR G.SHAW,G.SHI,X.JI REVDAT 4 13-SEP-23 4F7V 1 REMARK REVDAT 3 30-AUG-23 4F7V 1 AUTHOR JRNL REMARK REVDAT 2 25-JUL-12 4F7V 1 JRNL REVDAT 1 11-JUL-12 4F7V 0 JRNL AUTH G.SHI,G.SHAW,Y.LI,Y.WU,H.YAN,X.JI JRNL TITL BISUBSTRATE ANALOG INHIBITORS OF JRNL TITL 2 6-HYDROXYMETHYL-7,8-DIHYDROPTERIN PYROPHOSPHOKINASE: NEW JRNL TITL 3 LEAD EXHIBITS A DISTINCT BINDING MODE. JRNL REF BIOORG.MED.CHEM. V. 20 4303 2012 JRNL REFN ISSN 0968-0896 JRNL PMID 22727779 JRNL DOI 10.1016/J.BMC.2012.05.060 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 1 REFERENCE 2 REMARK 1 AUTH G.SHI,G.SHAW,Y.H.LIANG,P.SUBBURAMAN,Y.LI,Y.WU,H.YAN,X.JI REMARK 1 TITL BISUBSTRATE ANALOGUE INHIBITORS OF REMARK 1 TITL 2 6-HYDROXYMETHYL-7,8-DIHYDROPTERIN PYROPHOSPHOKINASE: NEW REMARK 1 TITL 3 DESIGN WITH IMPROVED PROPERTIES. REMARK 1 REF BIOORG.MED.CHEM. V. 20 47 2012 REMARK 1 REFN ISSN 0968-0896 REMARK 1 PMID 22169600 REMARK 1 DOI 10.1016/J.BMC.2011.11.032 REMARK 2 REMARK 2 RESOLUTION. 1.73 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) : 1.73 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 27.57 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.340 REMARK 3 COMPLETENESS FOR RANGE (%) : 93.6 REMARK 3 NUMBER OF REFLECTIONS : 13829 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.176 REMARK 3 R VALUE (WORKING SET) : 0.172 REMARK 3 FREE R VALUE : 0.222 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 6.800 REMARK 3 FREE R VALUE TEST SET COUNT : 940 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 27.5726 - 3.3079 1.00 2078 151 0.1438 0.1686 REMARK 3 2 3.3079 - 2.6263 1.00 2005 147 0.1589 0.2355 REMARK 3 3 2.6263 - 2.2945 1.00 1945 142 0.1734 0.2261 REMARK 3 4 2.2945 - 2.0848 0.99 1947 141 0.1829 0.2496 REMARK 3 5 2.0848 - 1.9354 0.98 1899 139 0.2006 0.2512 REMARK 3 6 1.9354 - 1.8213 0.88 1693 123 0.2366 0.2959 REMARK 3 7 1.8213 - 1.7300 0.70 1322 97 0.2770 0.3490 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 : 0.37 REMARK 3 B_SOL : 46.99 REMARK 3 REMARK 3 ERROR ESTIMATES. REMARK 3 COORDINATE ERROR (MAXIMUM-LIKELIHOOD BASED) : 0.510 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 22.700 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 16.58 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 20.49 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 0.00000 REMARK 3 B22 (A**2) : 0.00000 REMARK 3 B33 (A**2) : 0.00000 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : 0.00000 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 1372 REMARK 3 ANGLE : 1.379 1881 REMARK 3 CHIRALITY : 0.076 206 REMARK 3 PLANARITY : 0.008 242 REMARK 3 DIHEDRAL : 15.384 533 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 4F7V COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 24-MAY-12. REMARK 100 THE DEPOSITION ID IS D_1000072565. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 17-JUL-10 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 7.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : APS REMARK 200 BEAMLINE : 22-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 : GRAPHITE REMARK 200 OPTICS : MIRRORS REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : MARMOSAIC 225 MM CCD REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 14746 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.670 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 (%) : 89.0 REMARK 200 DATA REDUNDANCY : 4.900 REMARK 200 R MERGE (I) : 0.08600 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 9.1000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.67 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.73 REMARK 200 COMPLETENESS FOR SHELL (%) : 49.1 REMARK 200 DATA REDUNDANCY IN SHELL : 2.50 REMARK 200 R MERGE FOR SHELL (I) : 0.41100 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 1.850 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: PHASER REMARK 200 STARTING MODEL: PDB ENTRY 3UDV REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 34.98 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 1.89 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: PEG 3350, NACL, HEPES, PH 7.5, VAPOR REMARK 280 DIFFUSION, SITTING DROP, TEMPERATURE 292K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 21 21 2 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 26.55900 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 35.29050 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 26.55900 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 35.29050 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 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 HOH A 442 LIES ON A SPECIAL POSITION. REMARK 375 HOH A 470 LIES ON A SPECIAL POSITION. 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 49 42.85 -95.48 REMARK 500 VAL A 83 33.91 -81.40 REMARK 500 LYS A 85 2.89 -54.15 REMARK 500 LEU A 94 117.42 -167.98 REMARK 500 ALA A 132 62.78 -151.44 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 J1D A 201 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 1EX8 RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF E. COLI HPPK IN COMPLEX WITH BISUBSTRATE REMARK 900 ANALOGUE INHIBITOR A4P (HP4A) REMARK 900 RELATED ID: 3UD5 RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF E. COLI HPPK IN COMPLEX WITH BISUBSTRATE REMARK 900 ANALOGUE INHIBITOR J1A (HP19) 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 (HP17) 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 (HP18) DBREF 4F7V 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 J1D A 201 44 HETNAM J1D 5'-{[2-({N-[(2-AMINO-7,7-DIMETHYL-4-OXO-3,4,7,8- HETNAM 2 J1D TETRAHYDROPTERIDIN-6-YL)CARBONYL]GLYCYL}AMINO) HETNAM 3 J1D ETHYL]SULFONYL}-5'-DEOXYADENOSINE FORMUL 2 J1D C23 H30 N12 O8 S FORMUL 3 HOH *171(H2 O) HELIX 1 1 PRO A 14 ILE A 28 1 15 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 ASP A 95 PHE A 101 -1 O MET A 99 N TYR A 4 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 TYR A 40 O ASN A 55 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 GLY A 90 PRO A 91 0 -0.04 CISPEP 2 VAL A 113 PRO A 114 0 -4.44 SITE 1 AC1 30 THR A 42 PRO A 43 LEU A 45 TYR A 53 SITE 2 AC1 30 ASN A 55 LEU A 70 GLN A 74 GLU A 77 SITE 3 AC1 30 LYS A 85 TRP A 89 GLY A 90 ARG A 92 SITE 4 AC1 30 ASP A 95 LEU A 96 ASP A 97 ILE A 98 SITE 5 AC1 30 ARG A 110 LEU A 111 THR A 112 TYR A 116 SITE 6 AC1 30 ARG A 121 PHE A 123 HIS A 148 HOH A 369 SITE 7 AC1 30 HOH A 370 HOH A 378 HOH A 398 HOH A 433 SITE 8 AC1 30 HOH A 450 HOH A 458 CRYST1 53.118 70.581 36.261 90.00 90.00 90.00 P 21 21 2 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 0.018826 0.000000 0.000000 0.00000 SCALE2 0.000000 0.014168 0.000000 0.00000 SCALE3 0.000000 0.000000 0.027578 0.00000