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- PDB-1tev: Crystal structure of the human UMP/CMP kinase in open conformation -

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Basic information

Entry
Database: PDB / ID: 1tev
TitleCrystal structure of the human UMP/CMP kinase in open conformation
ComponentsUMP-CMP kinase
KeywordsTRANSFERASE / Kinase / Ploop / NMP binding region / LID region / Conformational Changes
Function / homology
Function and homology information


UMP/CMP kinase / CDP biosynthetic process / nucleoside monophosphate kinase activity / (d)CMP kinase activity / CMP kinase activity / dCMP kinase activity / uridine kinase activity / UMP kinase activity / pyrimidine ribonucleotide biosynthetic process / nucleobase-containing small molecule interconversion ...UMP/CMP kinase / CDP biosynthetic process / nucleoside monophosphate kinase activity / (d)CMP kinase activity / CMP kinase activity / dCMP kinase activity / uridine kinase activity / UMP kinase activity / pyrimidine ribonucleotide biosynthetic process / nucleobase-containing small molecule interconversion / nucleoside-diphosphate kinase / UDP biosynthetic process / Interconversion of nucleotide di- and triphosphates / nucleoside diphosphate kinase activity / 'de novo' pyrimidine nucleobase biosynthetic process / nucleolus / extracellular exosome / nucleoplasm / ATP binding / nucleus / cytosol / cytoplasm
Similarity search - Function
UMP-CMP kinase / Adenylate kinase, conserved site / Adenylate kinase signature. / Adenylate kinase/UMP-CMP kinase / Adenylate kinase / P-loop containing nucleotide triphosphate hydrolases / Rossmann fold / P-loop containing nucleoside triphosphate hydrolase / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å
AuthorsSegura-Pena, D. / Sekulic, N. / Ort, S. / Konrad, M. / Lavie, A.
CitationJournal: J.Biol.Chem. / Year: 2004
Title: Substrate-induced Conformational Changes in Human UMP/CMP Kinase.
Authors: Sekulic, N. / Ort, S. / Konrad, M. / Lavie, A.
History
DepositionMay 25, 2004Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 22, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 11, 2017Group: Refinement description / Category: software / Item: _software.classification / _software.name
Revision 1.4Aug 23, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / 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 / _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

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Assembly

Deposited unit
A: UMP-CMP kinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,3492
Polymers22,2531
Non-polymers961
Water2,000111
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)62.750, 62.750, 226.310
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number179
Space group name H-MP6522

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Components

#1: Protein UMP-CMP kinase / Cytidylate kinase / Deoxycytidylate kinase / Cytidine monophosphate kinase / hUMPK


Mass: 22253.359 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: UCK / Plasmid: pGEX-RB / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P30085, UMP/CMP kinase
#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 111 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 2

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Sample preparation

CrystalDensity Matthews: 2.9 Å3/Da / Density % sol: 57.5 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 4.6
Details: PEG 4000, Magnesium Sulfate, Sodium Acetate, pH 4.6, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1 Å
DetectorType: MARRESEARCH / Detector: CCD / Date: Nov 27, 2002
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.1→30 Å / Num. all: 15467 / Num. obs: 15467 / % possible obs: 94.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 13 % / Biso Wilson estimate: 27.73075 Å2 / Rsym value: 0.116 / Net I/σ(I): 15.27
Reflection shellResolution: 2.1→2.2 Å / Redundancy: 10.8 % / Num. unique all: 1737 / Rsym value: 0.393 / % possible all: 90.3

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Processing

Software
NameVersionClassification
REFMAC5.1.24refinement
MAR345data collection
XDSdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1UKE

1uke


Resolution: 2.1→15 Å / Cor.coef. Fo:Fc: 0.944 / Cor.coef. Fo:Fc free: 0.918 / SU B: 6.547 / SU ML: 0.165 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.25 / ESU R Free: 0.223 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.27473 1442 10 %RANDOM
Rwork0.21574 ---
all0.22168 14381 --
obs0.22168 14381 88.49 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 39.674 Å2
Baniso -1Baniso -2Baniso -3
1-0.14 Å20.07 Å20 Å2
2--0.14 Å20 Å2
3----0.21 Å2
Refine analyzeLuzzati coordinate error obs: 0.3 Å
Refinement stepCycle: LAST / Resolution: 2.1→15 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1540 0 5 111 1656
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.0221566
X-RAY DIFFRACTIONr_bond_other_d0.0020.021418
X-RAY DIFFRACTIONr_angle_refined_deg1.4441.9752100
X-RAY DIFFRACTIONr_angle_other_deg0.86733329
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.5855193
X-RAY DIFFRACTIONr_chiral_restr0.0910.2227
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.021730
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02299
X-RAY DIFFRACTIONr_nbd_refined0.210.2332
X-RAY DIFFRACTIONr_nbd_other0.2310.21634
X-RAY DIFFRACTIONr_nbtor_other0.0880.2996
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2130.269
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2070.212
X-RAY DIFFRACTIONr_symmetry_vdw_other0.1920.249
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2220.26
X-RAY DIFFRACTIONr_mcbond_it0.9051.5959
X-RAY DIFFRACTIONr_mcangle_it1.75121544
X-RAY DIFFRACTIONr_scbond_it2.5033607
X-RAY DIFFRACTIONr_scangle_it4.2964.5556
LS refinement shellResolution: 2.1→2.153 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.36 82
Rwork0.297 749

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