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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 / URIDINE-5'-MONOPHOSPHATE / URIDINE-5'-DIPHOSPHATE / Uridylate kinase
Similarity search - Component
Biological speciesThermus thermophilus HB8 (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: Plos One / Year: 2025
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
Revision 2.0Jul 16, 2025Group: Advisory / Atomic model ...Advisory / Atomic model / Author supporting evidence / Data collection / Derived calculations / Non-polymer description / Refinement description / Source and taxonomy / Structure summary
Category: atom_site / atom_site_anisotrop ...atom_site / atom_site_anisotrop / chem_comp / chem_comp_atom / chem_comp_bond / entity / entity_src_gen / pdbx_contact_author / pdbx_entity_instance_feature / pdbx_entity_nonpoly / pdbx_nonpoly_scheme / pdbx_refine_tls / pdbx_refine_tls_group / pdbx_struct_assembly_gen / pdbx_struct_assembly_prop / pdbx_struct_conn_angle / pdbx_struct_sheet_hbond / pdbx_struct_special_symmetry / pdbx_unobs_or_zero_occ_atoms / pdbx_validate_torsion / refine / refine_hist / refine_ls_restr / refine_ls_shell / struct_asym / struct_conf / struct_conn / struct_sheet / struct_sheet_order / struct_sheet_range
Item: _chem_comp.formula / _chem_comp.formula_weight ..._chem_comp.formula / _chem_comp.formula_weight / _chem_comp.id / _chem_comp.mon_nstd_flag / _chem_comp.name / _chem_comp.type / _entity_src_gen.pdbx_gene_src_scientific_name / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_struct_assembly_prop.value / _pdbx_struct_special_symmetry.auth_seq_id / _pdbx_struct_special_symmetry.label_asym_id / _refine.B_iso_mean / _refine.ls_R_factor_R_free / _refine.ls_R_factor_R_work / _refine.ls_R_factor_obs / _refine.overall_SU_ML / _refine.pdbx_overall_phase_error / _refine_hist.number_atoms_solvent / _refine_hist.number_atoms_total / _refine_hist.pdbx_number_atoms_ligand / _refine_hist.pdbx_number_atoms_protein / _refine_ls_restr.dev_ideal / _refine_ls_restr.number / _refine_ls_shell.R_factor_R_free / _refine_ls_shell.R_factor_R_work
Description: Real space R-factor
Details: During the peer review process of the associated manuscript, concerns were raised regarding the certainty of the binding of one of the ligands to the protein. As a result, the model was ...Details: During the peer review process of the associated manuscript, concerns were raised regarding the certainty of the binding of one of the ligands to the protein. As a result, the model was revised to remove this ligand, and the PDB coordinate file was updated accordingly.
Provider: author / Type: Coordinate replacement
Revision 2.1Sep 17, 2025Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.year / _citation_author.identifier_ORCID

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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)236,71554
Polymers227,7219
Non-polymers8,99445
Water8,071448
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)159,39748
Polymers151,8146
Non-polymers7,58342
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_545-x,-y-1,z1
Buried area29390 Å2
ΔGint-475 kcal/mol
Surface area45890 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)157,01730
Polymers151,8146
Non-polymers5,20324
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation8_444x-1/2,-y-1/2,-z-1/21
Buried area25760 Å2
ΔGint-297 kcal/mol
Surface area44770 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-471-

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 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 , 6 types, 493 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 / Feature type: SUBJECT OF INVESTIGATION / Comment: UDP*YM
#4: Chemical...
ChemComp-SO4 / SULFATE ION


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


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


Mass: 324.181 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C9H13N2O9P / Feature type: SUBJECT OF INVESTIGATION
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 448 / 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: 0.224 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 21.2311
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2032 1999 1.31 %
Rwork0.1805 150040 -
obs0.1808 152039 99.85 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 48.24 Å2
Refinement stepCycle: LAST / Resolution: 2.6→26.32 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms15744 0 541 448 16733
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.007616502
X-RAY DIFFRACTIONf_angle_d1.066822480
X-RAY DIFFRACTIONf_chiral_restr0.05812666
X-RAY DIFFRACTIONf_plane_restr0.00792819
X-RAY DIFFRACTIONf_dihedral_angle_d17.83655918
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.6-2.660.2791400.227410578X-RAY DIFFRACTION99.31
2.66-2.740.22971420.211910630X-RAY DIFFRACTION100
2.74-2.820.23251420.208110643X-RAY DIFFRACTION100
2.82-2.910.23411430.20510689X-RAY DIFFRACTION99.99
2.91-3.010.23781420.22410686X-RAY DIFFRACTION100
3.01-3.130.25791420.20510618X-RAY DIFFRACTION99.95
3.13-3.270.23911420.20210709X-RAY DIFFRACTION99.99
3.27-3.450.19651420.196610631X-RAY DIFFRACTION99.96
3.45-3.660.20341420.192710740X-RAY DIFFRACTION99.92
3.66-3.940.21281440.1710704X-RAY DIFFRACTION99.74
3.94-4.340.19441420.152210711X-RAY DIFFRACTION99.64
4.34-4.960.16651440.14710782X-RAY DIFFRACTION99.84
4.96-6.240.18721440.190810845X-RAY DIFFRACTION99.97
6.24-26.320.1711480.157211074X-RAY DIFFRACTION99.52
Refinement TLS params.Method: refined / Origin x: -21.8528772406 Å / Origin y: -83.9714717399 Å / Origin z: -55.7370037486 Å
111213212223313233
T0.32596751888 Å20.0247674354212 Å20.00321419381853 Å2-0.31900889041 Å20.0504002685755 Å2--0.301489188777 Å2
L0.318202939043 °2-0.129444409903 °20.0557513736038 °2-0.213040599908 °2-0.0580634112756 °2--0.141543638946 °2
S0.0390337535287 Å °0.0837879429735 Å °0.0532745275252 Å °-0.0127700064785 Å °-0.0146576912244 Å °0.100714532101 Å °-0.0294836458761 Å °0.0392570028759 Å °-0.0253578913911 Å °
Refinement TLS groupSelection details: all

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