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- PDB-2v4y: THE STRUCTURE OF E. COLI UMP KINASE IN COMPLEX WITH ITS ALLOSTERI... -

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Basic information

Entry
Database: PDB / ID: 2v4y
TitleTHE STRUCTURE OF E. COLI UMP KINASE IN COMPLEX WITH ITS ALLOSTERIC REGULATOR GTP
ComponentsURIDYLATE KINASE
KeywordsTRANSFERASE / NUCLEOTIDE-BINDING / PYRIMIDINE BIOSYNTHESIS / ATP-BINDING / ALLOSTERIC ENZYME / GTP / KINASE / ALLOSTERY / NMP KINASE
Function / homology
Function and homology information


UMP kinase / UMP kinase activity / 'de novo' CTP biosynthetic process / pyrimidine nucleotide biosynthetic process / UDP biosynthetic process / phosphorylation / ATP binding / identical protein 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 speciesESCHERICHIA COLI (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.8 Å
AuthorsMeyer, P. / Evrin, C. / Briozzo, P. / Joly, N. / Barzu, O. / Gilles, A.M.
CitationJournal: J.Biol.Chem. / Year: 2008
Title: Structural and Functional Characterization of Escherichia Coli Ump Kinase in Complex with its Allosteric Regulator GTP.
Authors: Meyer, P. / Evrin, C. / Briozzo, P. / Joly, N. / Barzu, O. / Gilles, A.M.
History
DepositionSep 30, 2008Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 21, 2008Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Dec 13, 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
C: URIDYLATE KINASE
D: URIDYLATE KINASE
E: URIDYLATE KINASE
F: URIDYLATE KINASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)162,27418
Polymers155,9966
Non-polymers6,27812
Water21612
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area22360 Å2
ΔGint-149.9 kcal/mol
Surface area50370 Å2
MethodPISA
Unit cell
Length a, b, c (Å)66.280, 145.780, 146.600
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-ID
11
21
31
41
51
61

NCS domain segments:
Dom-IDComponent-IDEns-IDSelection details
111CHAIN A AND (RESSEQ 5:172 OR RESSEQ 183:241 )
211CHAIN B AND (RESSEQ 5:172 OR RESSEQ 183:241 )
311CHAIN C AND (RESSEQ 5:172 OR RESSEQ 183:241 )
411CHAIN D AND (RESSEQ 5:171 OR RESSEQ 183:241 )
511CHAIN E AND (RESSEQ 5:172 OR RESSEQ 183:241 )
611CHAIN F AND (RESSEQ 5:172 OR RESSEQ 183:241 )

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Components

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


Mass: 25999.277 Da / Num. of mol.: 6 / Mutation: YES
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) ESCHERICHIA COLI (E. coli) / Strain: K-12 / Plasmid: PET28A / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / Variant (production host): PDIA17 / References: UniProt: P0A7E9, UMP kinase
#2: Chemical
ChemComp-GTP / GUANOSINE-5'-TRIPHOSPHATE / Guanosine triphosphate


Mass: 523.180 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: C10H16N5O14P3 / Comment: GTP, energy-carrying molecule*YM
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 12 / Source method: isolated from a natural source / Formula: H2O
Compound detailsENGINEERED RESIDUE IN CHAIN A, ASP 159 TO ASN ENGINEERED RESIDUE IN CHAIN B, ASP 159 TO ASN ...ENGINEERED RESIDUE IN CHAIN A, ASP 159 TO ASN ENGINEERED RESIDUE IN CHAIN B, ASP 159 TO ASN ENGINEERED RESIDUE IN CHAIN C, ASP 159 TO ASN ENGINEERED RESIDUE IN CHAIN D, ASP 159 TO ASN ENGINEERED RESIDUE IN CHAIN E, ASP 159 TO ASN ENGINEERED RESIDUE IN CHAIN F, ASP 159 TO ASN
Nonpolymer detailsGUANOSINE-5'-TRIPHOSPHATE (GTP): IN A1243, B1243, C1243, D1243, E1243, F1243 ONLY THE PHOSPHATE ...GUANOSINE-5'-TRIPHOSPHATE (GTP): IN A1243, B1243, C1243, D1243, E1243, F1243 ONLY THE PHOSPHATE MOIETY IS VISIBLE.

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.18 Å3/Da / Density % sol: 43.5 % / Description: NONE
Crystal growDetails: 43% PEG 400, 100 MM SODIUM ACETATE, PH 4.6, 22.5 MM GTP, 100 MM NACL.

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 1.2826
DetectorType: ADSC CCD / Detector: CCD
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.2826 Å / Relative weight: 1
ReflectionResolution: 2.8→49.15 Å / Num. obs: 34062 / % possible obs: 99.4 % / Observed criterion σ(I): -3 / Redundancy: 7 % / Rmerge(I) obs: 0.14 / Net I/σ(I): 12.2
Reflection shellResolution: 2.8→2.88 Å / Redundancy: 7 % / Rmerge(I) obs: 0.81 / Mean I/σ(I) obs: 2.5 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX(PHENIX.REFINE)refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2BNF

2bnf


Resolution: 2.8→49.038 Å / SU ML: 0.43 / σ(F): 1.36 / Phase error: 24.01 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2387 1794 5 %
Rwork0.2074 --
obs0.209 34062 99.97 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 43.97 Å2 / ksol: 0.348 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-3.8982 Å2-0 Å20 Å2
2---4.5698 Å2-0 Å2
3---0.6717 Å2
Refinement stepCycle: LAST / Resolution: 2.8→49.038 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10625 0 270 12 10907
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d011032
X-RAY DIFFRACTIONf_angle_d0.9614948
X-RAY DIFFRACTIONf_dihedral_angle_d17.684089
X-RAY DIFFRACTIONf_chiral_restr0.051736
X-RAY DIFFRACTIONf_plane_restr01869
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDTypeRms dev position (Å)
11A1720X-RAY DIFFRACTIONPOSITIONAL
12B1720X-RAY DIFFRACTIONPOSITIONAL0.045
13C1720X-RAY DIFFRACTIONPOSITIONAL0.034
14D1713X-RAY DIFFRACTIONPOSITIONAL0.033
15E1720X-RAY DIFFRACTIONPOSITIONAL0.035
16F1720X-RAY DIFFRACTIONPOSITIONAL0.044
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.8-2.87570.33491370.30992595X-RAY DIFFRACTION100
2.8757-2.96040.36541240.3022555X-RAY DIFFRACTION100
2.9604-3.05590.33011370.29132589X-RAY DIFFRACTION100
3.0559-3.16510.33261450.2872568X-RAY DIFFRACTION100
3.1651-3.29180.27861380.25962591X-RAY DIFFRACTION100
3.2918-3.44160.26741400.22332562X-RAY DIFFRACTION100
3.4416-3.6230.25691430.21342589X-RAY DIFFRACTION100
3.623-3.84990.21071400.19022598X-RAY DIFFRACTION100
3.8499-4.1470.25171450.18342613X-RAY DIFFRACTION100
4.147-4.5640.18671150.16992632X-RAY DIFFRACTION100
4.564-5.22380.20111530.1622627X-RAY DIFFRACTION100
5.2238-6.57890.21591280.18732686X-RAY DIFFRACTION100
6.5789-49.04520.19591490.18592786X-RAY DIFFRACTION100

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