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- PDB-8yh1: Crystal structure of Thermus thermophilus UMP kinase complexed wi... -

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Basic information

Entry
Database: PDB / ID: 8yh1
TitleCrystal structure of Thermus thermophilus UMP kinase complexed with a phosphoryl group acceptor and donor.
ComponentsUridylate kinase
KeywordsTRANSFERASE / Uridine kinase / Allosteric effector / Thermus thermophilus / CYTOSOLIC PROTEIN
Function / homology
Function and homology information


UMP kinase / UMP kinase activity / 'de novo' CTP biosynthetic process / UDP biosynthetic process / ATP binding / cytoplasm
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'-DIPHOSPHATE / GUANOSINE-5'-TRIPHOSPHATE / URIDINE-5'-MONOPHOSPHATE / URIDINE-5'-DIPHOSPHATE / Uridylate kinase
Similarity search - Component
Biological speciesThermus thermophilus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.6 Å
AuthorsFukui, K. / Nishiwaki, A. / Nakagawa, N. / Kuramitsu, S. / Masui, R.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: To Be Published
Title: The crystal structure of Thermus thermophilus UMP kinase complexed with a phosphoryl group acceptor and donor.
Authors: Fukui, K. / Nishiwaki, A. / Nakagawa, N. / Kuramitsu, S. / Masui, R.
History
DepositionFeb 27, 2024Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Mar 5, 2025Provider: repository / Type: Initial release

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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
G: Uridylate kinase
H: Uridylate kinase
I: Uridylate kinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)239,85560
Polymers227,7219
Non-polymers12,13351
Water8,179454
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)162,53654
Polymers151,8146
Non-polymers10,72248
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_545-x,-y-1,z1
Buried area16420 Å2
ΔGint-109 kcal/mol
Surface area47540 Å2
MethodPISA
2
D: Uridylate kinase
F: Uridylate kinase
G: Uridylate kinase
H: Uridylate kinase
hetero molecules

E: Uridylate kinase
I: Uridylate kinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)158,58633
Polymers151,8146
Non-polymers6,77227
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation8_444x-1/2,-y-1/2,-z-1/21
Buried area16420 Å2
ΔGint-109 kcal/mol
Surface area46710 Å2
MethodPISA
Unit cell
Length a, b, c (Å)150.217, 232.197, 284.841
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number23
Space group name H-MI222
Space group name HallI22
Symmetry operation#1: x,y,z
#2: x,-y,-z
#3: -x,y,-z
#4: -x,-y,z
#5: x+1/2,y+1/2,z+1/2
#6: x+1/2,-y+1/2,-z+1/2
#7: -x+1/2,y+1/2,-z+1/2
#8: -x+1/2,-y+1/2,z+1/2
Components on special symmetry positions
IDModelComponents
11B-475-

HOH

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Components

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Protein , 1 types, 9 molecules ABCDEFGHI

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


Mass: 25302.348 Da / Num. of mol.: 9
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermus thermophilus (strain ATCC 27634 / DSM 579 / HB8) (bacteria)
Strain: ATCC 27634 / DSM 579 / HB8 / Gene: pyrH, TTHA0859 / Plasmid: pET-11a / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P43891, UMP kinase

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Non-polymers , 7 types, 505 molecules

#2: Chemical
ChemComp-ADP / ADENOSINE-5'-DIPHOSPHATE


Mass: 427.201 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C10H15N5O10P2 / Feature type: SUBJECT OF INVESTIGATION / Comment: ADP, energy-carrying molecule*YM
#3: Chemical
ChemComp-UDP / URIDINE-5'-DIPHOSPHATE


Type: RNA linking / Mass: 404.161 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C9H14N2O12P2 / Comment: UDP*YM
#4: Chemical
ChemComp-GTP / GUANOSINE-5'-TRIPHOSPHATE


Mass: 523.180 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C10H16N5O14P3 / Feature type: SUBJECT OF INVESTIGATION / Comment: GTP, energy-carrying molecule*YM
#5: Chemical...
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 22 / Source method: obtained synthetically / Formula: SO4
#6: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Mg / Feature type: SUBJECT OF INVESTIGATION
#7: Chemical
ChemComp-U5P / URIDINE-5'-MONOPHOSPHATE


Mass: 324.181 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C9H13N2O9P
#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 454 / 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

Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.8
Details: 0.1 M MES, 2.0 M ammonium sulfate, 10 mM cobalt chloride

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Data collection

DiffractionMean temperature: 90 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL26B2 / Wavelength: 1 Å
DetectorType: RIGAKU RAXIS V / Detector: IMAGE PLATE / Date: May 19, 2008
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.6→26.32 Å / Num. obs: 152039 / % possible obs: 100 % / Redundancy: 13 % / Biso Wilson estimate: 42.67 Å2 / Rmerge(I) obs: 0.047 / Net I/σ(I): 39.9
Reflection shellResolution: 2.6→2.693 Å / Rmerge(I) obs: 0.226 / Mean I/σ(I) obs: 2.66 / Num. unique obs: 15086

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
HKL-2000data reduction
HKL-2000data scaling
PHENIX1.20.1_4487model building
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.6→26.32 Å / SU ML: 0.2369 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 22.7539
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2103 1999 1.31 %
Rwork0.1884 150040 -
obs0.1887 152039 99.85 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 46.98 Å2
Refinement stepCycle: LAST / Resolution: 2.6→26.32 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms15750 0 733 454 16937
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.003216712
X-RAY DIFFRACTIONf_angle_d0.803622811
X-RAY DIFFRACTIONf_chiral_restr0.04762690
X-RAY DIFFRACTIONf_plane_restr0.00322826
X-RAY DIFFRACTIONf_dihedral_angle_d18.72396007
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.6-2.660.29791400.244710578X-RAY DIFFRACTION99.31
2.66-2.740.24321420.226810630X-RAY DIFFRACTION100
2.74-2.820.24631420.224510643X-RAY DIFFRACTION100
2.82-2.910.25791430.224410689X-RAY DIFFRACTION99.99
2.91-3.010.23641420.235810686X-RAY DIFFRACTION100
3.01-3.130.27111420.218210618X-RAY DIFFRACTION99.95
3.13-3.270.23891420.212310709X-RAY DIFFRACTION99.99
3.27-3.450.22061420.206410631X-RAY DIFFRACTION99.96
3.45-3.660.21511420.20210740X-RAY DIFFRACTION99.92
3.66-3.940.20521440.175610704X-RAY DIFFRACTION99.74
3.94-4.340.20561420.15710711X-RAY DIFFRACTION99.64
4.34-4.960.1681440.152110782X-RAY DIFFRACTION99.84
4.96-6.240.18331440.189810845X-RAY DIFFRACTION99.97
6.24-26.320.17941480.163411074X-RAY DIFFRACTION99.52

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