HEADER TRANSFERASE/TRANSFERASE INHIBITOR 28-OCT-11 3UDV
TITLE CRYSTAL STRUCTURE OF E. COLI HPPK IN COMPLEX WITH BISUBSTRATE ANALOGUE
TITLE 2 INHIBITOR J1C
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 3UDV 1 REMARK
REVDAT 3 30-AUG-23 3UDV 1 AUTHOR JRNL REMARK
REVDAT 2 18-JAN-12 3UDV 1 JRNL
REVDAT 1 04-JAN-12 3UDV 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) : 29.92
REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.340
REMARK 3 COMPLETENESS FOR RANGE (%) : 92.8
REMARK 3 NUMBER OF REFLECTIONS : 10754
REMARK 3
REMARK 3 FIT TO DATA USED IN REFINEMENT.
REMARK 3 R VALUE (WORKING + TEST SET) : 0.216
REMARK 3 R VALUE (WORKING SET) : 0.210
REMARK 3 FREE R VALUE : 0.275
REMARK 3 FREE R VALUE TEST SET SIZE (%) : 8.550
REMARK 3 FREE R VALUE TEST SET COUNT : 920
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 29.9246 - 3.5945 1.00 1611 151 0.1926 0.2331
REMARK 3 2 3.5945 - 2.8538 1.00 1547 145 0.1873 0.2601
REMARK 3 3 2.8538 - 2.4933 1.00 1496 140 0.2063 0.2929
REMARK 3 4 2.4933 - 2.2654 0.97 1450 136 0.2263 0.2976
REMARK 3 5 2.2654 - 2.1031 0.94 1413 131 0.2565 0.3442
REMARK 3 6 2.1031 - 1.9791 0.86 1265 119 0.2630 0.3664
REMARK 3 7 1.9791 - 1.8800 0.72 1052 98 0.2528 0.2881
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 : 41.37
REMARK 3
REMARK 3 ERROR ESTIMATES.
REMARK 3 COORDINATE ERROR (MAXIMUM-LIKELIHOOD BASED) : 0.480
REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 28.540
REMARK 3
REMARK 3 B VALUES.
REMARK 3 FROM WILSON PLOT (A**2) : NULL
REMARK 3 MEAN B VALUE (OVERALL, A**2) : 27.39
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 : 0.013 1365
REMARK 3 ANGLE : 1.376 1876
REMARK 3 CHIRALITY : 0.087 208
REMARK 3 PLANARITY : 0.008 242
REMARK 3 DIHEDRAL : 14.998 531
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 3UDV 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_1000068630.
REMARK 200
REMARK 200 EXPERIMENTAL DETAILS
REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION
REMARK 200 DATE OF DATA COLLECTION : 13-FEB-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-ID
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 300 MM CCD
REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000
REMARK 200 DATA SCALING SOFTWARE : SCALEPACK, HKL-2000
REMARK 200
REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 11716
REMARK 200 RESOLUTION RANGE HIGH (A) : 1.790
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 (%) : 87.6
REMARK 200 DATA REDUNDANCY : 6.000
REMARK 200 R MERGE (I) : 0.07400
REMARK 200 R SYM (I) : NULL
REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 11.8000
REMARK 200
REMARK 200 IN THE HIGHEST RESOLUTION SHELL.
REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.79
REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.85
REMARK 200 COMPLETENESS FOR SHELL (%) : 50.4
REMARK 200 DATA REDUNDANCY IN SHELL : 2.80
REMARK 200 R MERGE FOR SHELL (I) : 0.32200
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 3UDE
REMARK 200
REMARK 200 REMARK: NULL
REMARK 280
REMARK 280 CRYSTAL
REMARK 280 SOLVENT CONTENT, VS (%): 34.87
REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 1.89
REMARK 280
REMARK 280 CRYSTALLIZATION CONDITIONS: PEG 3350, AMMONIUM ACETATE, BIS-TRIS,
REMARK 280 PH 7.5, 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 26.50000
REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 35.32000
REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 0.00000
REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 26.50000
REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 35.32000
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 480
REMARK 480 ZERO OCCUPANCY ATOM
REMARK 480 THE FOLLOWING RESIDUES HAVE ATOMS MODELED WITH ZERO
REMARK 480 OCCUPANCY. THE LOCATION AND PROPERTIES OF THESE ATOMS
REMARK 480 MAY NOT BE RELIABLE. (M=MODEL NUMBER; RES=RESIDUE NAME;
REMARK 480 C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE):
REMARK 480 M RES C SSEQI ATOMS
REMARK 480 VAL A 2 CA CB CG1 CG2
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 LEU A 45 96.34 -69.05
REMARK 500 TRP A 89 31.65 -91.08
REMARK 500 LEU A 94 112.19 -171.73
REMARK 500 PRO A 114 154.29 -48.00
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 J1C 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: 3UDE RELATED DB: PDB
REMARK 900 CRYSTAL STRUCTURE OF E. COLI HPPK IN COMPLEX WITH BISUBSTRATE
REMARK 900 ANALOGUE INHIBITOR J1B
DBREF 3UDV 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 J1C A 171 44
HET ACT A 191 4
HETNAM J1C 5'-S-[1-(2-{[(2-AMINO-7,7-DIMETHYL-4-OXO-3,4,7,8-
HETNAM 2 J1C TETRAHYDROPTERIDIN-6-YL)CARBONYL]AMINO}ETHYL)
HETNAM 3 J1C PIPERIDIN-4-YL]-5'-THIOADENOSINE
HETNAM ACT ACETATE ION
FORMUL 2 J1C C26 H36 N12 O5 S
FORMUL 3 ACT C2 H3 O2 1-
FORMUL 4 HOH *91(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 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 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 0.75
CISPEP 2 VAL A 113 PRO A 114 0 -8.61
SITE 1 AC1 23 LYS A 23 THR A 42 PRO A 43 LEU A 45
SITE 2 AC1 23 TYR A 53 ASN A 55 GLN A 74 GLU A 77
SITE 3 AC1 23 ARG A 88 TRP A 89 GLY A 90 ARG A 92
SITE 4 AC1 23 ASP A 95 ASP A 97 ILE A 98 ARG A 110
SITE 5 AC1 23 THR A 112 PHE A 123 ACT A 191 HOH A 232
SITE 6 AC1 23 HOH A 254 HOH A 255 HOH A 263
SITE 1 AC2 7 ALA A 6 GLY A 8 ASN A 55 ASP A 97
SITE 2 AC2 7 MET A 124 J1C A 171 HOH A 227
CRYST1 53.000 70.640 36.250 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 0.018867 0.000000 0.000000 0.00000
SCALE2 0.000000 0.014156 0.000000 0.00000
SCALE3 0.000000 0.000000 0.027587 0.00000