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 <I/SIGMA(I)> 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 <I/SIGMA(I)> 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