HEADER TRANSFERASE/TRANSFERASE INHIBITOR 28-OCT-11 3UDE TITLE CRYSTAL STRUCTURE OF E. COLI HPPK IN COMPLEX WITH BISUBSTRATE ANALOGUE TITLE 2 INHIBITOR J1B 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 3UDE 1 REMARK REVDAT 3 30-AUG-23 3UDE 1 AUTHOR JRNL REMARK REVDAT 2 18-JAN-12 3UDE 1 JRNL REVDAT 1 04-JAN-12 3UDE 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. 1.88 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) : 1.88 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 29.47 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.340 REMARK 3 COMPLETENESS FOR RANGE (%) : 93.5 REMARK 3 NUMBER OF REFLECTIONS : 10902 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.184 REMARK 3 R VALUE (WORKING SET) : 0.178 REMARK 3 FREE R VALUE : 0.237 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 8.700 REMARK 3 FREE R VALUE TEST SET COUNT : 949 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 29.4768 - 3.5954 1.00 1614 154 0.1878 0.2333 REMARK 3 2 3.5954 - 2.8546 0.99 1531 145 0.1613 0.2204 REMARK 3 3 2.8546 - 2.4939 0.99 1504 144 0.1567 0.2387 REMARK 3 4 2.4939 - 2.2660 0.98 1473 141 0.1724 0.2182 REMARK 3 5 2.2660 - 2.1036 0.96 1426 135 0.1795 0.2538 REMARK 3 6 2.1036 - 1.9796 0.89 1329 126 0.1918 0.2638 REMARK 3 7 1.9796 - 1.8810 0.73 1076 104 0.2426 0.3092 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 : 0.38 REMARK 3 B_SOL : 47.70 REMARK 3 REMARK 3 ERROR ESTIMATES. REMARK 3 COORDINATE ERROR (MAXIMUM-LIKELIHOOD BASED) : 0.500 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 23.610 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 20.00 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 28.73 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -6.78820 REMARK 3 B22 (A**2) : 3.36260 REMARK 3 B33 (A**2) : -4.71530 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 1355 REMARK 3 ANGLE : 1.382 1857 REMARK 3 CHIRALITY : 0.076 203 REMARK 3 PLANARITY : 0.008 239 REMARK 3 DIHEDRAL : 14.552 519 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 3UDE 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_1000068613. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 18-AUG-09 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 8.5 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) : 1.00000 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 : 11525 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.820 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 (%) : 89.7 REMARK 200 DATA REDUNDANCY : 6.100 REMARK 200 R MERGE (I) : 0.08400 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 8.2000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.82 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.89 REMARK 200 COMPLETENESS FOR SHELL (%) : 51.9 REMARK 200 DATA REDUNDANCY IN SHELL : 2.50 REMARK 200 R MERGE FOR SHELL (I) : 0.56100 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 3ILJ REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 35.30 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 1.90 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: PEG 3350, AMMONIUM ACETATE, BIS-TRIS, REMARK 280 PH 8.5, VAPOR 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 26.45500 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 35.49000 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 26.45500 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 35.49000 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 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 VAL A 83 REMARK 465 ARG A 84 REMARK 465 LYS A 85 REMARK 465 ALA A 86 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 GLN A 48 4.29 -68.16 REMARK 500 ASP A 49 51.37 -111.06 REMARK 500 LEU A 94 117.93 -162.94 REMARK 500 ALA A 132 58.25 -151.04 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 J1B A 171 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ACT A 191 REMARK 900 REMARK 900 RELATED ENTRIES 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 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 3UDE 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 J1B A 171 43 HET ACT A 191 4 HETNAM J1B 5'-S-[1-(2-{[(2-AMINO-7,7-DIMETHYL-4-OXO-3,4,7,8- HETNAM 2 J1B TETRAHYDROPTERIDIN-6-YL)METHYL]AMINO}ETHYL)PIPERIDIN- HETNAM 3 J1B 4-YL]-5'-THIOADENOSINE HETNAM ACT ACETATE ION FORMUL 2 J1B C26 H38 N12 O4 S FORMUL 3 ACT C2 H3 O2 1- FORMUL 4 HOH *88(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 GLU A 61 N HIS A 32 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 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 GLU A 61 N HIS A 32 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 GLY A 90 PRO A 91 0 0.66 CISPEP 2 VAL A 113 PRO A 114 0 -0.15 SITE 1 AC1 22 LYS A 23 THR A 42 PRO A 43 LEU A 45 SITE 2 AC1 22 TYR A 53 ASN A 55 LEU A 70 GLN A 74 SITE 3 AC1 22 TRP A 89 GLY A 90 ASP A 95 ASP A 97 SITE 4 AC1 22 ILE A 98 ARG A 110 LEU A 111 THR A 112 SITE 5 AC1 22 TYR A 116 PHE A 123 HIS A 148 ACT A 191 SITE 6 AC1 22 HOH A 221 HOH A 236 SITE 1 AC2 7 GLY A 8 ASN A 55 ASP A 95 ASP A 97 SITE 2 AC2 7 PHE A 123 J1B A 171 HOH A 284 CRYST1 52.910 70.980 36.380 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 0.018900 0.000000 0.000000 0.00000 SCALE2 0.000000 0.014089 0.000000 0.00000 SCALE3 0.000000 0.000000 0.027491 0.00000