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- PDB-9uvp: Crystal structure of UMPK from S. aureus in complex with ATP and U5P -

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Basic information

Entry
Database: PDB / ID: 9uvp
TitleCrystal structure of UMPK from S. aureus in complex with ATP and U5P
ComponentsUridylate kinase
KeywordsTRANSFERASE / Allosteric effect / hexamers
Function / homology
Function and homology information


UMP kinase / UMP kinase activity / 'de novo' CTP biosynthetic process / UDP biosynthetic process / ATP binding / cytosol
Similarity search - Function
Uridylate kinase, bacteria / Uridylate kinase / Aspartate/glutamate/uridylate kinase / Acetylglutamate kinase-like superfamily / Amino acid kinase family
Similarity search - Domain/homology
ADENOSINE-5'-TRIPHOSPHATE / PHOSPHATE ION / URIDINE-5'-MONOPHOSPHATE / Uridylate kinase
Similarity search - Component
Biological speciesStaphylococcus aureus subsp. aureus NCTC 8325 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.56775592138 Å
AuthorsGao, Y. / Niu, L.W.
Funding support China, 1items
OrganizationGrant numberCountry
Chinese Academy of Sciences China
CitationJournal: To Be Published
Title: Crystal structure of UMPK from S. aureus in complex with ATP and U5P
Authors: Gao, Y. / Niu, L.W.
History
DepositionMay 10, 2025Deposition site: PDBJ / Processing site: PDBC
Revision 1.0May 13, 2026Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Uridylate kinase
B: Uridylate kinase
C: Uridylate kinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)83,4309
Polymers81,5803
Non-polymers1,8506
Water21612
1
A: Uridylate kinase
B: Uridylate kinase
C: Uridylate kinase
hetero molecules

A: Uridylate kinase
B: Uridylate kinase
C: Uridylate kinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)166,86018
Polymers163,1616
Non-polymers3,70012
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_555y,x,-z1
Buried area20300 Å2
ΔGint-92 kcal/mol
Surface area54000 Å2
MethodPISA
Unit cell
Length a, b, c (Å)72.551, 72.551, 298.059
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number92
Space group name H-MP41212
Space group name HallP4abw2nw
Symmetry operation#1: x,y,z
#2: -y+1/2,x+1/2,z+1/4
#3: y+1/2,-x+1/2,z+3/4
#4: x+1/2,-y+1/2,-z+3/4
#5: -x+1/2,y+1/2,-z+1/4
#6: -x,-y,z+1/2
#7: y,x,-z
#8: -y,-x,-z+1/2

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Components

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Protein , 1 types, 3 molecules ABC

#1: Protein Uridylate kinase / UK / Uridine monophosphate kinase / UMP kinase / UMPK


Mass: 27193.484 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Staphylococcus aureus subsp. aureus NCTC 8325 (bacteria)
Gene: pyrH, SAOUHSC_01235 / Production host: Escherichia coli (E. coli) / References: UniProt: Q2FZ22, UMP kinase

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Non-polymers , 5 types, 18 molecules

#2: Chemical ChemComp-U5P / URIDINE-5'-MONOPHOSPHATE


Mass: 324.181 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C9H13N2O9P / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-ATP / ADENOSINE-5'-TRIPHOSPHATE


Mass: 507.181 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H16N5O13P3 / Feature type: SUBJECT OF INVESTIGATION / Comment: ATP, energy-carrying molecule*YM
#4: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: PO4 / Feature type: SUBJECT OF INVESTIGATION
#5: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 12 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY
Has protein modificationN

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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: 2.5 Å3/Da / Density % sol: 50.75 %
Crystal growTemperature: 289.15 K / Method: vapor diffusion, sitting drop
Details: 0.2 M Ammonium citrate tribasic pH7.0, 20% w/v Polyethylene glycol 3350, 2 mmol/L Magnesium chloride

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL10U2 / Wavelength: 0.979021 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Aug 27, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979021 Å / Relative weight: 1
ReflectionResolution: 2.56775592138→50 Å / Num. obs: 25820 / % possible obs: 97 % / Redundancy: 5.18 % / Biso Wilson estimate: 63.0777455116 Å2 / CC1/2: 0.8849 / Rmerge(I) obs: 0.0918 / Net I/σ(I): 15.43
Reflection shellResolution: 2.57→2.66 Å / Rmerge(I) obs: 0.2997 / Num. unique obs: 1828 / CC1/2: 0.719

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Processing

Software
NameVersionClassification
MOLREPphasing
PHENIX1.11.1_2575refinement
autoPXdata processing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.56775592138→48.5077052743 Å / SU ML: 0.393180947553 / Cross valid method: FREE R-VALUE / σ(F): 1.64763722511 / Phase error: 24.9969495431
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.244957560861 1283 4.97171200496 %
Rwork0.213683576868 24523 -
obs0.21527205531 25806 97.1611445783 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 75.5384239367 Å2
Refinement stepCycle: LAST / Resolution: 2.56775592138→48.5077052743 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5413 0 115 12 5540
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.002620752480035592
X-RAY DIFFRACTIONf_angle_d0.5926702484767550
X-RAY DIFFRACTIONf_chiral_restr0.044287575385883
X-RAY DIFFRACTIONf_plane_restr0.00240341948607949
X-RAY DIFFRACTIONf_dihedral_angle_d17.43272324593400
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.5678-2.67060.3657830767461320.3283146411932638X-RAY DIFFRACTION96.2139631817
2.6706-2.79210.329797103311450.2854058324162691X-RAY DIFFRACTION98.2674982675
2.7921-2.93930.3155692708961360.2661825072292684X-RAY DIFFRACTION97.8826796251
2.9393-3.12340.2936437306431410.2632854633722697X-RAY DIFFRACTION98.2346832814
3.1234-3.36450.3086511844361510.2420577122652691X-RAY DIFFRACTION98.0338047603
3.3645-3.7030.2813280867471360.2230975065952736X-RAY DIFFRACTION97.7535738598
3.703-4.23850.2517635590251580.1962285984762727X-RAY DIFFRACTION97.2035040431
4.2385-5.3390.1898309045021450.1825814582322760X-RAY DIFFRACTION96.5757978723
5.339-48.50770527430.1966253409411390.1885570791392899X-RAY DIFFRACTION94.5828144458

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