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- PDB-7e9v: The Crystal Structure of human UMP-CMP kinase from Biortus. -

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Basic information

Entry
Database: PDB / ID: 7e9v
TitleThe Crystal Structure of human UMP-CMP kinase from Biortus.
ComponentsUMP-CMP kinase
KeywordsTRANSFERASE / catalytic activity / cytidylate kinase activity / kinase activity / transferase activity
Function / homology
Function and homology information


UMP/CMP kinase / CDP biosynthetic process / nucleoside monophosphate kinase activity / cytidylate 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 / cytidylate 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 / phosphorylation / nucleolus / extracellular exosome / nucleoplasm / ATP binding / nucleus / cytosol / cytoplasm
Similarity search - Function
UMP-CMP kinase / Adenylate kinase / Adenylate kinase, conserved site / Adenylate kinase signature. / Adenylate kinase/UMP-CMP kinase / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å
AuthorsWang, F. / Lin, D. / Wang, R. / Wei, X. / Shen, Z. / Wang, M.
Funding support China, 1items
OrganizationGrant numberCountry
The Natural Science Foundation of Jiangsu ProvinceBK20170222 China
CitationJournal: To Be Published
Title: The Crystal Structure of human UMP-CMP kinase from Biortus.
Authors: Wang, F. / Lin, D. / Wang, R. / Wei, X. / Shen, Z. / Wang, M.
History
DepositionMar 5, 2021Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Mar 24, 2021Provider: repository / Type: Initial release
Revision 1.1Nov 29, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: atom_type / chem_comp_atom ...atom_type / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _atom_type.pdbx_N_electrons / _atom_type.pdbx_scat_Z ..._atom_type.pdbx_N_electrons / _atom_type.pdbx_scat_Z / _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: UMP-CMP kinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,4502
Polymers24,3541
Non-polymers961
Water57632
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area210 Å2
ΔGint-17 kcal/mol
Surface area10710 Å2
MethodPISA
Unit cell
Length a, b, c (Å)61.926, 61.926, 225.397
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number179
Space group name H-MP6522
Components on special symmetry positions
IDModelComponents
11A-316-

HOH

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Components

#1: Protein UMP-CMP kinase / Deoxycytidylate kinase / CK / dCMP kinase / Nucleoside-diphosphate kinase / Uridine ...Deoxycytidylate kinase / CK / dCMP kinase / Nucleoside-diphosphate kinase / Uridine monophosphate/cytidine monophosphate kinase / UMP/CMP kinase / UMP/CMPK


Mass: 24353.602 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CMPK1, CMK, CMPK, UCK, UMK, UMPK / Production host: Escherichia coli (E. coli)
References: UniProt: P30085, UMP/CMP kinase, nucleoside-diphosphate kinase
#2: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


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


Mass: 18.015 Da / Num. of mol.: 32 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 2.56 Å3/Da / Density % sol: 56.94 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / Details: 2.5M (NH4)2SO4, 0.1M Tris pH8.5

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: CLSI / Beamline: 08ID-1 / Wavelength: 0.97949 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Aug 27, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97949 Å / Relative weight: 1
ReflectionResolution: 2.1→48.473 Å / Num. obs: 15960 / % possible obs: 100 % / Redundancy: 18.1 % / Rmerge(I) obs: 0.075 / Net I/σ(I): 24
Reflection shellResolution: 2.1→2.16 Å / Rmerge(I) obs: 0.937 / Num. unique obs: 1267

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Processing

Software
NameVersionClassification
REFMAC5.8.0258refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1TEV

1tev


Resolution: 2.1→48.473 Å / Cor.coef. Fo:Fc: 0.959 / Cor.coef. Fo:Fc free: 0.938 / SU B: 5.099 / SU ML: 0.133 / Cross valid method: FREE R-VALUE / ESU R: 0.185 / ESU R Free: 0.172
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.2497 818 5.153 %
Rwork0.205 15056 -
all0.207 --
obs-15874 99.987 %
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT
Displacement parametersBiso mean: 48.109 Å2
Baniso -1Baniso -2Baniso -3
1-1.072 Å20.536 Å20 Å2
2--1.072 Å20 Å2
3----3.478 Å2
Refinement stepCycle: LAST / Resolution: 2.1→48.473 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1528 0 5 32 1565
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0131553
X-RAY DIFFRACTIONr_bond_other_d0.0010.0171477
X-RAY DIFFRACTIONr_angle_refined_deg1.6361.6462081
X-RAY DIFFRACTIONr_angle_other_deg1.4011.5913448
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.0735190
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.57723.8184
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.21815307
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.241159
X-RAY DIFFRACTIONr_chiral_restr0.0780.2198
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.021710
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02301
X-RAY DIFFRACTIONr_nbd_refined0.2210.2309
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1750.21319
X-RAY DIFFRACTIONr_nbtor_refined0.1680.2752
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0820.2750
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1090.239
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.270.210
X-RAY DIFFRACTIONr_nbd_other0.1750.247
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.2160.23
X-RAY DIFFRACTIONr_mcbond_it3.9734.76766
X-RAY DIFFRACTIONr_mcbond_other3.9684.755764
X-RAY DIFFRACTIONr_mcangle_it5.0717.108954
X-RAY DIFFRACTIONr_mcangle_other5.0697.108954
X-RAY DIFFRACTIONr_scbond_it5.3155.392787
X-RAY DIFFRACTIONr_scbond_other5.3145.399784
X-RAY DIFFRACTIONr_scangle_it7.9047.8051127
X-RAY DIFFRACTIONr_scangle_other7.9137.8151122
X-RAY DIFFRACTIONr_lrange_it8.93555.5971700
X-RAY DIFFRACTIONr_lrange_other8.955.4821697
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.1-2.1550.323710.2531065X-RAY DIFFRACTION100
2.155-2.2130.283550.2441068X-RAY DIFFRACTION100
2.213-2.2780.403540.2541006X-RAY DIFFRACTION100
2.278-2.3470.307580.24993X-RAY DIFFRACTION100
2.347-2.4240.262510.21969X-RAY DIFFRACTION100
2.424-2.5090.235420.213942X-RAY DIFFRACTION100
2.509-2.6040.249400.222928X-RAY DIFFRACTION100
2.604-2.710.314410.215874X-RAY DIFFRACTION100
2.71-2.830.258520.208846X-RAY DIFFRACTION100
2.83-2.9680.272440.208810X-RAY DIFFRACTION100
2.968-3.1280.362260.242790X-RAY DIFFRACTION100
3.128-3.3170.285510.241715X-RAY DIFFRACTION100
3.317-3.5450.293390.236697X-RAY DIFFRACTION100
3.545-3.8270.234360.208663X-RAY DIFFRACTION100
3.827-4.190.189350.171604X-RAY DIFFRACTION100
4.19-4.6820.215360.163556X-RAY DIFFRACTION100
4.682-5.3990.238250.186504X-RAY DIFFRACTION100
5.399-6.5960.189190.189446X-RAY DIFFRACTION100
6.596-9.2580.217240.168352X-RAY DIFFRACTION100
9.258-48.4730.199190.175228X-RAY DIFFRACTION99.1968

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