[English] 日本語
Yorodumi
- PDB-3feg: Crystal structure of human choline kinase beta in complex with ph... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 3feg
TitleCrystal structure of human choline kinase beta in complex with phosphorylated hemicholinium-3 and adenosine nucleotide
ComponentsCholine/ethanolamine kinase
KeywordsTRANSFERASE / non-protein kinase / choline kinase / Structural Genomics Consortium / SGC / hemicholinium-3 / phosphorylation / Kinase / Phosphoprotein
Function / homology
Function and homology information


ethanolamine kinase / choline kinase / ethanolamine kinase activity / CDP-choline pathway / choline kinase activity / Synthesis of PE / phosphatidylethanolamine biosynthetic process / muscle organ development / Synthesis of PC / phosphorylation ...ethanolamine kinase / choline kinase / ethanolamine kinase activity / CDP-choline pathway / choline kinase activity / Synthesis of PE / phosphatidylethanolamine biosynthetic process / muscle organ development / Synthesis of PC / phosphorylation / ATP binding / cytoplasm / cytosol
Similarity search - Function
Choline/ethanolamine kinase / Aminoglycoside 3'-phosphotransferase; Chain: A, domain 2 / Aminoglycoside phosphotransferase (APH), C-terminal lobe / Phosphorylase Kinase; domain 1 / Phosphorylase Kinase; domain 1 / Protein kinase-like domain superfamily / Alpha-Beta Complex / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
ADENOSINE-5'-DIPHOSPHATE / ADENOSINE MONOPHOSPHATE / Chem-HC7 / Choline/ethanolamine kinase
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.302 Å
AuthorsHong, B.S. / Tempel, W. / Rabeh, W.M. / MacKenzie, F. / Arrowsmith, C.H. / Edwards, A.M. / Bountra, C. / Weigelt, J. / Bochkarev, A. / Park, H.W. / Structural Genomics Consortium (SGC)
CitationJournal: J.Biol.Chem. / Year: 2010
Title: Crystal structures of human choline kinase isoforms in complex with hemicholinium-3: single amino acid near the active site influences inhibitor sensitivity.
Authors: Hong, B.S. / Allali-Hassani, A. / Tempel, W. / Finerty, P.J. / Mackenzie, F. / Dimov, S. / Vedadi, M. / Park, H.W.
History
DepositionNov 29, 2008Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 23, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 1, 2017Group: Refinement description / Category: software
Revision 1.3Oct 14, 2020Group: Data collection / Database references / Derived calculations
Category: pdbx_struct_conn_angle / phasing ...pdbx_struct_conn_angle / phasing / struct_conn / struct_ref_seq_dif / struct_site
Item: _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id ..._pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr2_auth_seq_id / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Sep 6, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Choline/ethanolamine kinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,3928
Polymers44,0031
Non-polymers1,3897
Water5,368298
1
A: Choline/ethanolamine kinase
hetero molecules

A: Choline/ethanolamine kinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)90,78416
Polymers88,0052
Non-polymers2,77914
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_656-x+1,y,-z+11
Buried area5690 Å2
ΔGint-70 kcal/mol
Surface area30390 Å2
MethodPISA
Unit cell
Length a, b, c (Å)97.994, 72.987, 62.397
Angle α, β, γ (deg.)90.000, 117.760, 90.000
Int Tables number5
Space group name H-MC121

-
Components

-
Protein , 1 types, 1 molecules A

#1: Protein Choline/ethanolamine kinase / Choline kinase beta / CK / Ethanolamine kinase / EK


Mass: 44002.613 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CHKB, CHETK, CHKL / Plasmid: pET28a-LIC / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)
References: UniProt: Q9Y259, choline kinase, ethanolamine kinase

-
Non-polymers , 7 types, 305 molecules

#2: Chemical ChemComp-HC7 / (2S)-2-[4'-({dimethyl[2-(phosphonooxy)ethyl]ammonio}acetyl)biphenyl-4-yl]-2-hydroxy-4,4-dimethylmorpholin-4-ium / 2-{4-[4-(2-{dimethyl[2-(phosphonatooxy)ethyl]azaniumyl}acetyl)phenyl]phenyl}-2-hydroxy-4,4-dimethylmorpholin-4-ium


Mass: 494.518 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C24H35N2O7P
#3: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#4: Chemical ChemComp-ADP / ADENOSINE-5'-DIPHOSPHATE


Mass: 427.201 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H15N5O10P2 / Comment: ADP, energy-carrying molecule*YM
#5: Chemical ChemComp-AMP / ADENOSINE MONOPHOSPHATE


Mass: 347.221 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H14N5O7P / Comment: AMP*YM
#6: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#7: Chemical ChemComp-UNX / UNKNOWN ATOM OR ION


Num. of mol.: 2 / Source method: obtained synthetically
#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 298 / Source method: isolated from a natural source / Formula: H2O

-
Details

Nonpolymer detailsFOR THE LIGAND HC7 THE STEREO-CENTER AT THE "2" POSITION IS SPECIFIED AS (2S), HOWEVER CAN BE (2R) ...FOR THE LIGAND HC7 THE STEREO-CENTER AT THE "2" POSITION IS SPECIFIED AS (2S), HOWEVER CAN BE (2R) OR (2S) AS THE MORPHOLINIUM RING CAN OPEN LOSING THE SPECIFIED CONFIGURATION.

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.24 Å3/Da / Density % sol: 45.18 %
Crystal growTemperature: 291 K / Method: vapor diffusion / pH: 6.5
Details: protein buffer: 0.01M Tris pH 8, 0.5M sodium chloride, 0.005M magnesium chloride, 0.01M DTT, 0.003M hemicholinium-3, 0.005M ADP; precipitant: 0.1M sodium cacodylate, 30% PEG-4000, 0.2M ...Details: protein buffer: 0.01M Tris pH 8, 0.5M sodium chloride, 0.005M magnesium chloride, 0.01M DTT, 0.003M hemicholinium-3, 0.005M ADP; precipitant: 0.1M sodium cacodylate, 30% PEG-4000, 0.2M ammonium sulfate, VAPOR DIFFUSION, temperature 291K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-B / Wavelength: 0.97243 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Mar 6, 2008
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97243 Å / Relative weight: 1
ReflectionResolution: 1.3→30 Å / Num. obs: 92472 / % possible obs: 97.6 % / Redundancy: 3.6 % / Rmerge(I) obs: 0.04 / Χ2: 1.578 / Net I/σ(I): 14.4
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2% possible all
1.3-1.352.40.55977501.17182.4
1.35-1.43.10.4790421.30295.9
1.4-1.463.60.36293811.32699.4
1.46-1.543.70.23794301.39499.9
1.54-1.643.70.16194721.485100
1.64-1.763.70.11294651.625100
1.76-1.943.80.07294711.8100
1.94-2.223.80.04595261.826100
2.22-2.83.80.03394831.75499.9
2.8-303.70.02794521.75398

-
Phasing

PhasingMethod: molecular replacement

-
Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
PHASERphasing
REFMAC5.4.0069refinement
PDB_EXTRACT3.005data extraction
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: pdb entry 2ig7

2ig7


Resolution: 1.302→28.296 Å / Cor.coef. Fo:Fc: 0.97 / Cor.coef. Fo:Fc free: 0.959 / WRfactor Rfree: 0.201 / WRfactor Rwork: 0.162 / SU B: 1.51 / SU ML: 0.029 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.05 / ESU R Free: 0.05 / Stereochemistry target values: Engh & Huber
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. Hemicholinium restraints were calculated by the PRODRG server.
RfactorNum. reflection% reflectionSelection details
Rfree0.193 4612 4.99 %RANDOM
Rwork0.158 ---
obs0.16 92425 97.405 %-
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: 14.43 Å2
Baniso -1Baniso -2Baniso -3
1-0.077 Å20 Å20.052 Å2
2---0.128 Å20 Å2
3---0.1 Å2
Refinement stepCycle: LAST / Resolution: 1.302→28.296 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2732 0 92 298 3122
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0170.0223105
X-RAY DIFFRACTIONr_bond_other_d0.0020.022122
X-RAY DIFFRACTIONr_angle_refined_deg1.4622.0154267
X-RAY DIFFRACTIONr_angle_other_deg1.8813.0025114
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.3815377
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.73423.947152
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.04715508
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.8741518
X-RAY DIFFRACTIONr_chiral_restr0.0870.2433
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.0213413
X-RAY DIFFRACTIONr_gen_planes_other0.0030.02652
X-RAY DIFFRACTIONr_mcbond_it2.90521754
X-RAY DIFFRACTIONr_mcbond_other1.5822696
X-RAY DIFFRACTIONr_mcangle_it3.7232852
X-RAY DIFFRACTIONr_scbond_it3.66721351
X-RAY DIFFRACTIONr_scangle_it4.87131393
X-RAY DIFFRACTIONr_rigid_bond_restr2.2535227
X-RAY DIFFRACTIONr_sphericity_free11.5473302
X-RAY DIFFRACTIONr_sphericity_bonded5.36635117
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.302-1.3360.2972680.2635137691178.209
1.336-1.3720.2962990.2175961680192.045
1.372-1.4120.2553070.1926212667097.736
1.412-1.4550.2413300.1686070643699.441
1.455-1.5030.2013100.1485902622399.823
1.503-1.5550.1762820.1295736602699.867
1.555-1.6140.1622940.1235542584399.88
1.614-1.680.1743020.125275557899.982
1.68-1.7540.1442650.1235114538199.963
1.754-1.8390.1742880.12548725160100
1.839-1.9380.1682220.12646674889100
1.938-2.0550.1622230.134411463599.978
2.055-2.1960.162320.1374137437099.977
2.196-2.3710.1782040.1393868407599.926
2.371-2.5960.1921780.1553586376799.92
2.596-2.8990.1861720.1753227340099.971
2.899-3.3420.2351650.1862805298699.464
3.342-4.0790.1681060.1682450257999.108
4.079-5.7090.191000.1661850198998.039
5.709-28.2960.311650.251991116890.411

+
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://pdbjlvh1.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