[English] 日本語
Yorodumi
- PDB-7tun: Crystal structure analysis of human CKB complex with a covalent c... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 7tun
TitleCrystal structure analysis of human CKB complex with a covalent compound
ComponentsCreatine kinase B-type
KeywordsTRANSFERASE/TRANSFERASE INHIBITOR / creatine kinase / ATP-binding / covalent inhibitor / cycteine modification / TRANSFERASE-TRANSFERASE INHIBITOR complex
Function / homology
Function and homology information


futile creatine cycle / creatine kinase / Creatine metabolism / phosphocreatine biosynthetic process / creatine kinase activity / RND3 GTPase cycle / substantia nigra development / phosphorylation / ubiquitin protein ligase binding / mitochondrion ...futile creatine cycle / creatine kinase / Creatine metabolism / phosphocreatine biosynthetic process / creatine kinase activity / RND3 GTPase cycle / substantia nigra development / phosphorylation / ubiquitin protein ligase binding / mitochondrion / extracellular space / extracellular exosome / ATP binding / plasma membrane / cytosol
Similarity search - Function
ATP:guanido phosphotransferase, N-terminal / ATP:guanido phosphotransferase, N-terminal domain superfamily / ATP:guanido phosphotransferase, N-terminal domain / Phosphagen kinase N-terminal domain profile. / ATP:guanido phosphotransferase active site / Phosphagen kinase active site signature. / ATP:guanido phosphotransferase / ATP:guanido phosphotransferase, catalytic domain / ATP:guanido phosphotransferase, C-terminal catalytic domain / Phosphagen kinase C-terminal domain profile. / Glutamine synthetase/guanido kinase, catalytic domain
Similarity search - Domain/homology
Chem-KLU / Creatine kinase B-type
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.93 Å
AuthorsSeo, H.-S. / Dhe-Paganon, S.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Cancer Institute (NIH/NCI) United States
CitationJournal: To Be Published
Title: Crystal Structure Analysis of human CKB complex with a covalent compound
Authors: Seo, H.-S. / Dhe-Paganon, S.
History
DepositionFeb 3, 2022Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 15, 2023Provider: repository / Type: Initial release
Revision 1.1Oct 25, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Creatine kinase B-type
B: Creatine kinase B-type
hetero molecules


Theoretical massNumber of molelcules
Total (without water)90,4574
Polymers89,9472
Non-polymers5092
Water1267
1
A: Creatine kinase B-type
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,2282
Polymers44,9741
Non-polymers2551
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Creatine kinase B-type
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,2282
Polymers44,9741
Non-polymers2551
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)101.240, 101.240, 160.870
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number96
Space group name H-MP43212

-
Components

#1: Protein Creatine kinase B-type / Brain creatine kinase / B-CK / Creatine kinase B chain / Creatine phosphokinase B-type / CPK-B


Mass: 44973.598 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CKB, CKBB / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P12277, creatine kinase
#2: Chemical ChemComp-KLU / (2S)-4-(chloroacetyl)-3,4-dihydro-2H-1,4-benzoxazine-2-carboxamide


Mass: 254.670 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C11H11ClN2O3 / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 7 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.29 Å3/Da / Density % sol: 46.32 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / Details: 1.7M Ammonium citrate, pH 7.4

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 0.9792 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jun 10, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 2.93→85.68 Å / Num. obs: 18694 / % possible obs: 100 % / Redundancy: 13 % / Biso Wilson estimate: 75.03 Å2 / Rpim(I) all: 0.083 / Rrim(I) all: 0.299 / Net I/σ(I): 9 / Num. measured all: 242855
Reflection shell

Diffraction-ID: 1 / % possible all: 100

Resolution (Å)Redundancy (%)Mean I/σ(I) obsNum. measured allNum. unique obsRpim(I) allRrim(I) all
2.93-2.9813.71.1127399320.7042.618
7.95-85.7211.128.21181010670.020.07

-
Phasing

PhasingMethod: molecular replacement

-
Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
XDSdata reduction
xia23.5.0data scaling
PHASERphasing
PDB_EXTRACT3.27data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3DRE

3dre


Resolution: 2.93→71.59 Å / SU ML: 0.42 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 29.94 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2638 876 4.71 %
Rwork0.2047 17729 -
obs0.2074 18605 99.8 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 161.9 Å2 / Biso mean: 80.7713 Å2 / Biso min: 47.67 Å2
Refinement stepCycle: final / Resolution: 2.93→71.59 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5671 0 54 7 5732
Biso mean--81.64 59.43 -
Num. residues----740
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 6 / % reflection obs: 100 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all
2.93-3.110.40091450.318928853030
3.11-3.350.36141420.252328853027
3.35-3.690.25011450.222629023047
3.69-4.230.2741440.188829543098
4.23-5.320.25151530.17229563109
5.32-71.590.221470.196931473294
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.5642-0.1113-0.40161.2092-0.50440.6224-0.01850.59320.0319-0.35770.1070.083-0.61410.0096-00.7107-0.03880.01560.7559-0.09340.763418.064135.55194.6533
21.5187-0.2058-0.40240.9387-0.00711.83-0.0968-0.0376-0.2522-0.11680.0745-0.09640.261-0.0764-0.00030.5857-0.01390.04220.6615-0.00010.6355.805419.320718.5655
32.4521-0.44790.23540.4849-0.27781.7186-0.0596-0.0556-0.00470.03150.0443-0.035-0.1774-0.16380.00040.67420.00860.03810.5921-0.00810.608-2.827817.424222.9563
41.2925-0.128-0.91340.71650.48231.396-0.1285-0.60670.16440.17780.0444-0.0776-0.11350.1744-0.00060.62020.07030.0220.88150.01340.671913.182621.341541.159
53.21930.78740.78273.0962-1.12971.96950.04870.02050.0533-0.23040.0773-0.14270.07340.03130.00050.7598-0.1402-0.00420.92510.00850.6332-11.275934.2262-1.4617
62.2625-0.64740.50971.4177-0.0740.7562-0.2503-0.25750.4895-0.08510.21210.0173-0.4519-0.1731-00.94820.0160.01280.86930.0020.81181.263359.2031.7114
70.49770.59180.04741.6865-0.21970.3385-0.4099-0.15510.1882-0.26110.2030.3808-0.501-0.1613-0.00140.93860.1198-0.0881.177-0.08170.747-10.35857.7060.0413
80.39010.5457-0.3050.8807-0.3450.2748-0.6166-0.20530.19260.1462-0.07950.39-0.3868-0.28110.00011.10830.2426-0.2231.05650.04570.937-21.94566.51965.7072
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 5 through 42 )A5 - 42
2X-RAY DIFFRACTION2chain 'A' and (resid 43 through 180 )A43 - 180
3X-RAY DIFFRACTION3chain 'A' and (resid 181 through 286 )A181 - 286
4X-RAY DIFFRACTION4chain 'A' and (resid 287 through 381 )A287 - 381
5X-RAY DIFFRACTION5chain 'B' and (resid 5 through 96 )B5 - 96
6X-RAY DIFFRACTION6chain 'B' and (resid 97 through 267 )B97 - 267
7X-RAY DIFFRACTION7chain 'B' and (resid 268 through 307 )B268 - 307
8X-RAY DIFFRACTION8chain 'B' and (resid 308 through 381 )B308 - 381

+
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