[English] 日本語
Yorodumi
- PDB-7e9v: The Crystal Structure of human UMP-CMP kinase from Biortus. -

+
Open data


ID or keywords:

Loading...

-
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 / (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 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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
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

-
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


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.: 32 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
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

-
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

-
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

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more