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- PDB-4a7w: Crystal structure of uridylate kinase from Helicobacter pylori -

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Basic information

Entry
Database: PDB / ID: 4a7w
TitleCrystal structure of uridylate kinase from Helicobacter pylori
ComponentsURIDYLATE KINASE
KeywordsTRANSFERASE
Function / homology
Function and homology information


UMP kinase / UMP kinase activity / 'de novo' CTP biosynthetic process / UDP biosynthetic process / phosphorylation / ATP binding / cytosol
Similarity search - Function
Uridylate kinase, bacteria / Uridylate kinase / Carbamate kinase / Acetylglutamate kinase-like / Aspartate/glutamate/uridylate kinase / Amino acid kinase family / Acetylglutamate kinase-like superfamily / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
GUANOSINE-5'-TRIPHOSPHATE / Uridylate kinase
Similarity search - Component
Biological speciesHELICOBACTER PYLORI (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsChu, C.H. / Chen, P.C. / Liu, M.H. / Sun, Y.J.
CitationJournal: Acta Crystallogr.,Sect.D / Year: 2012
Title: Structures of Helicobacter Pylori Uridylate Kinase: Insight Into Release of the Product Udp
Authors: Chu, C.H. / Chen, P.C. / Liu, M.H. / Li, Y.C. / Hsiao, C.D. / Sun, Y.J.
History
DepositionNov 15, 2011Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 27, 2012Provider: repository / Type: Initial release
Revision 1.1Jul 11, 2012Group: Other
Revision 1.2Dec 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: URIDYLATE KINASE
B: URIDYLATE KINASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)53,6476
Polymers52,4172
Non-polymers1,2314
Water5,693316
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4150 Å2
ΔGint-29.6 kcal/mol
Surface area19770 Å2
MethodPISA
Unit cell
Length a, b, c (Å)137.420, 137.420, 152.891
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number155
Space group name H-MH32
Components on special symmetry positions
IDModelComponents
11B-2125-

HOH

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Components

#1: Protein URIDYLATE KINASE / UK / URIDINE MONOPHOSPHATE KINASE / UMP KINASE / UMPK


Mass: 26208.449 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HELICOBACTER PYLORI (bacteria) / Strain: 26695 / Plasmid: PQE30 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): K-12 / Variant (production host): SG13009 / References: UniProt: P56106, UMP kinase
#2: Chemical ChemComp-GTP / GUANOSINE-5'-TRIPHOSPHATE / Guanosine triphosphate


Mass: 523.180 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H16N5O14P3 / Comment: GTP, energy-carrying molecule*YM
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 316 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.65 Å3/Da / Density % sol: 54 % / Description: NONE

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSRRC / Beamline: BL13B1 / Wavelength: 1
DetectorType: ADSC CCD / Detector: CCD / Date: Dec 21, 2009
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.8→30 Å / Num. obs: 51462 / % possible obs: 99.9 % / Observed criterion σ(I): 2 / Redundancy: 11.1 % / Biso Wilson estimate: 19.16 Å2 / Rmerge(I) obs: 0.07 / Net I/σ(I): 37.3
Reflection shellResolution: 1.8→1.86 Å / Redundancy: 11.1 % / Rmerge(I) obs: 0.5 / Mean I/σ(I) obs: 4.3 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX(PHENIX.REFINE)refinement
HKL-2000data reduction
SCALEPACKdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2BND

2bnd


Resolution: 1.8→25.288 Å / SU ML: 0.19 / σ(F): 1.34 / Phase error: 28.29 / Stereochemistry target values: LS_WUNIT_K1 / Details: RESIDUES 1-5 AND 60-68 ARE DISORDERED.
RfactorNum. reflection% reflection
Rfree0.2268 2612 5.1 %
Rwork0.1882 --
obs0.1903 51379 99.83 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 42.262 Å2 / ksol: 0.362 e/Å3
Displacement parametersBiso mean: 25.4 Å2
Baniso -1Baniso -2Baniso -3
1--1.1814 Å20 Å20 Å2
2---1.1814 Å20 Å2
3---2.3629 Å2
Refinement stepCycle: LAST / Resolution: 1.8→25.288 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3428 0 76 316 3820
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0063539
X-RAY DIFFRACTIONf_angle_d1.0384781
X-RAY DIFFRACTIONf_dihedral_angle_d16.1981306
X-RAY DIFFRACTIONf_chiral_restr0.07568
X-RAY DIFFRACTIONf_plane_restr0.003597
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.7988-1.8630.2692570.26484816X-RAY DIFFRACTION99
1.863-1.93760.24052510.25114847X-RAY DIFFRACTION100
1.9376-2.02570.2432550.22634832X-RAY DIFFRACTION100
2.0257-2.13250.25122680.2234828X-RAY DIFFRACTION100
2.1325-2.2660.24442440.21574895X-RAY DIFFRACTION100
2.266-2.44080.23632690.20524846X-RAY DIFFRACTION100
2.4408-2.68620.22942520.19934900X-RAY DIFFRACTION100
2.6862-3.07430.25152620.18564886X-RAY DIFFRACTION100
3.0743-3.87110.21752780.16074899X-RAY DIFFRACTION100
3.8711-25.29080.19032760.14655018X-RAY DIFFRACTION100

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