[English] 日本語
Yorodumi
- PDB-5vxs: Crystal Structure Analysis of human CLYBL in apo form -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 5vxs
TitleCrystal Structure Analysis of human CLYBL in apo form
ComponentsCitrate lyase subunit beta-like protein, mitochondrialATP citrate synthase
KeywordsLYASE / CLYBL / trimer / apo
Function / homology
Function and homology information


(3S)-malyl-CoA thioesterase / regulation of cobalamin metabolic process / positive regulation of cobalamin metabolic process / Transferases; Acyltransferases; Acyl groups converted into alkyl groups on transfer / (S)-citramalyl-CoA lyase / (S)-citramalyl-CoA lyase activity / malate synthase / malate synthase activity / protein homotrimerization / hydrolase activity ...(3S)-malyl-CoA thioesterase / regulation of cobalamin metabolic process / positive regulation of cobalamin metabolic process / Transferases; Acyltransferases; Acyl groups converted into alkyl groups on transfer / (S)-citramalyl-CoA lyase / (S)-citramalyl-CoA lyase activity / malate synthase / malate synthase activity / protein homotrimerization / hydrolase activity / magnesium ion binding / mitochondrion
Similarity search - Function
Citramalyl-CoA lyase / Citrate lyase beta subunit-like / HpcH/HpaI aldolase/citrate lyase domain / HpcH/HpaI aldolase/citrate lyase family / Pyruvate kinase-like domain superfamily / Pyruvate/Phosphoenolpyruvate kinase-like domain superfamily
Similarity search - Domain/homology
CITRIC ACID / Citramalyl-CoA lyase, mitochondrial
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.954 Å
AuthorsShen, H.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of Diabetes and Digestive and Kidney Disease (NIH/NIDDK)R24DK080261 United States
CitationJournal: Cell / Year: 2017
Title: The Human Knockout Gene CLYBL Connects Itaconate to Vitamin B12.
Authors: Shen, H. / Campanello, G.C. / Flicker, D. / Grabarek, Z. / Hu, J. / Luo, C. / Banerjee, R. / Mootha, V.K.
History
DepositionMay 24, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 1, 2017Provider: repository / Type: Initial release
Revision 1.1Nov 8, 2017Group: Database references / Category: citation
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2Nov 15, 2017Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.3Dec 25, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.4Oct 4, 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 / software / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _software.name / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Citrate lyase subunit beta-like protein, mitochondrial
B: Citrate lyase subunit beta-like protein, mitochondrial
C: Citrate lyase subunit beta-like protein, mitochondrial
D: Citrate lyase subunit beta-like protein, mitochondrial
E: Citrate lyase subunit beta-like protein, mitochondrial
F: Citrate lyase subunit beta-like protein, mitochondrial
hetero molecules


Theoretical massNumber of molelcules
Total (without water)216,8378
Polymers216,4536
Non-polymers3842
Water0
1
A: Citrate lyase subunit beta-like protein, mitochondrial
B: Citrate lyase subunit beta-like protein, mitochondrial
C: Citrate lyase subunit beta-like protein, mitochondrial
hetero molecules


Theoretical massNumber of molelcules
Total (without water)108,4194
Polymers108,2273
Non-polymers1921
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5180 Å2
ΔGint-31 kcal/mol
Surface area36670 Å2
MethodPISA
2
D: Citrate lyase subunit beta-like protein, mitochondrial
E: Citrate lyase subunit beta-like protein, mitochondrial
F: Citrate lyase subunit beta-like protein, mitochondrial
hetero molecules


Theoretical massNumber of molelcules
Total (without water)108,4194
Polymers108,2273
Non-polymers1921
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5470 Å2
ΔGint-32 kcal/mol
Surface area37350 Å2
MethodPISA
Unit cell
Length a, b, c (Å)154.629, 154.629, 156.506
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number152
Space group name H-MP3121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11(chain A and (resseq 40 or (resid 42 and (name...
21(chain B and (resseq 40 or (resid 42 and (name...
31(chain C and (resseq 40 or (resid 42 and (name...
41(chain D and (resseq 40 or (resid 42 and (name...
51(chain E and (resseq 40 or (resid 42 and (name...
61(chain F and (resseq 40 or (resid 42 and (name...

NCS domain segments:

Ens-ID: 1

Dom-IDComponent-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11HISHISHISHIS(chain A and (resseq 40 or (resid 42 and (name...AA4017
12TYRTYRTYRTYR(chain A and (resseq 40 or (resid 42 and (name...AA4219
13HISHISILEILE(chain A and (resseq 40 or (resid 42 and (name...AA40 - 33717 - 314
14HISHISILEILE(chain A and (resseq 40 or (resid 42 and (name...AA40 - 33717 - 314
15HISHISILEILE(chain A and (resseq 40 or (resid 42 and (name...AA40 - 33717 - 314
16HISHISILEILE(chain A and (resseq 40 or (resid 42 and (name...AA40 - 33717 - 314
17HISHISILEILE(chain A and (resseq 40 or (resid 42 and (name...AA40 - 33717 - 314
18HISHISILEILE(chain A and (resseq 40 or (resid 42 and (name...AA40 - 33717 - 314
19HISHISILEILE(chain A and (resseq 40 or (resid 42 and (name...AA40 - 33717 - 314
110HISHISILEILE(chain A and (resseq 40 or (resid 42 and (name...AA40 - 33717 - 314
111HISHISILEILE(chain A and (resseq 40 or (resid 42 and (name...AA40 - 33717 - 314
21HISHISHISHIS(chain B and (resseq 40 or (resid 42 and (name...BB4017
22TYRTYRTYRTYR(chain B and (resseq 40 or (resid 42 and (name...BB4219
23HISHISLYSLYS(chain B and (resseq 40 or (resid 42 and (name...BB40 - 33817 - 315
24HISHISLYSLYS(chain B and (resseq 40 or (resid 42 and (name...BB40 - 33817 - 315
25HISHISLYSLYS(chain B and (resseq 40 or (resid 42 and (name...BB40 - 33817 - 315
26HISHISLYSLYS(chain B and (resseq 40 or (resid 42 and (name...BB40 - 33817 - 315
27HISHISLYSLYS(chain B and (resseq 40 or (resid 42 and (name...BB40 - 33817 - 315
28HISHISLYSLYS(chain B and (resseq 40 or (resid 42 and (name...BB40 - 33817 - 315
29HISHISLYSLYS(chain B and (resseq 40 or (resid 42 and (name...BB40 - 33817 - 315
210HISHISLYSLYS(chain B and (resseq 40 or (resid 42 and (name...BB40 - 33817 - 315
211HISHISLYSLYS(chain B and (resseq 40 or (resid 42 and (name...BB40 - 33817 - 315
31HISHISHISHIS(chain C and (resseq 40 or (resid 42 and (name...CC4017
32TYRTYRTYRTYR(chain C and (resseq 40 or (resid 42 and (name...CC4219
33HISHISLYSLYS(chain C and (resseq 40 or (resid 42 and (name...CC40 - 34017 - 317
34HISHISLYSLYS(chain C and (resseq 40 or (resid 42 and (name...CC40 - 34017 - 317
35HISHISLYSLYS(chain C and (resseq 40 or (resid 42 and (name...CC40 - 34017 - 317
36HISHISLYSLYS(chain C and (resseq 40 or (resid 42 and (name...CC40 - 34017 - 317
37HISHISLYSLYS(chain C and (resseq 40 or (resid 42 and (name...CC40 - 34017 - 317
38HISHISLYSLYS(chain C and (resseq 40 or (resid 42 and (name...CC40 - 34017 - 317
39HISHISLYSLYS(chain C and (resseq 40 or (resid 42 and (name...CC40 - 34017 - 317
310HISHISLYSLYS(chain C and (resseq 40 or (resid 42 and (name...CC40 - 34017 - 317
311HISHISLYSLYS(chain C and (resseq 40 or (resid 42 and (name...CC40 - 34017 - 317
41HISHISHISHIS(chain D and (resseq 40 or (resid 42 and (name...DD4017
42TYRTYRTYRTYR(chain D and (resseq 40 or (resid 42 and (name...DD4219
43HISHISILEILE(chain D and (resseq 40 or (resid 42 and (name...DD40 - 33717 - 314
44HISHISILEILE(chain D and (resseq 40 or (resid 42 and (name...DD40 - 33717 - 314
45HISHISILEILE(chain D and (resseq 40 or (resid 42 and (name...DD40 - 33717 - 314
46HISHISILEILE(chain D and (resseq 40 or (resid 42 and (name...DD40 - 33717 - 314
47HISHISILEILE(chain D and (resseq 40 or (resid 42 and (name...DD40 - 33717 - 314
48HISHISILEILE(chain D and (resseq 40 or (resid 42 and (name...DD40 - 33717 - 314
49HISHISILEILE(chain D and (resseq 40 or (resid 42 and (name...DD40 - 33717 - 314
410HISHISILEILE(chain D and (resseq 40 or (resid 42 and (name...DD40 - 33717 - 314
411HISHISILEILE(chain D and (resseq 40 or (resid 42 and (name...DD40 - 33717 - 314
51HISHISHISHIS(chain E and (resseq 40 or (resid 42 and (name...EE4017
52TYRTYRTYRTYR(chain E and (resseq 40 or (resid 42 and (name...EE4219
53HISHISLYSLYS(chain E and (resseq 40 or (resid 42 and (name...EE40 - 34017 - 317
54HISHISLYSLYS(chain E and (resseq 40 or (resid 42 and (name...EE40 - 34017 - 317
55HISHISLYSLYS(chain E and (resseq 40 or (resid 42 and (name...EE40 - 34017 - 317
56HISHISLYSLYS(chain E and (resseq 40 or (resid 42 and (name...EE40 - 34017 - 317
57HISHISLYSLYS(chain E and (resseq 40 or (resid 42 and (name...EE40 - 34017 - 317
58HISHISLYSLYS(chain E and (resseq 40 or (resid 42 and (name...EE40 - 34017 - 317
59HISHISLYSLYS(chain E and (resseq 40 or (resid 42 and (name...EE40 - 34017 - 317
510HISHISLYSLYS(chain E and (resseq 40 or (resid 42 and (name...EE40 - 34017 - 317
511HISHISLYSLYS(chain E and (resseq 40 or (resid 42 and (name...EE40 - 34017 - 317
61HISHISHISHIS(chain F and (resseq 40 or (resid 42 and (name...FF4017
62TYRTYRTYRTYR(chain F and (resseq 40 or (resid 42 and (name...FF4219
63HISHISLYSLYS(chain F and (resseq 40 or (resid 42 and (name...FF40 - 34017 - 317
64HISHISLYSLYS(chain F and (resseq 40 or (resid 42 and (name...FF40 - 34017 - 317
65HISHISLYSLYS(chain F and (resseq 40 or (resid 42 and (name...FF40 - 34017 - 317
66HISHISLYSLYS(chain F and (resseq 40 or (resid 42 and (name...FF40 - 34017 - 317
67HISHISLYSLYS(chain F and (resseq 40 or (resid 42 and (name...FF40 - 34017 - 317
68HISHISLYSLYS(chain F and (resseq 40 or (resid 42 and (name...FF40 - 34017 - 317
69HISHISLYSLYS(chain F and (resseq 40 or (resid 42 and (name...FF40 - 34017 - 317
610HISHISLYSLYS(chain F and (resseq 40 or (resid 42 and (name...FF40 - 34017 - 317
611HISHISLYSLYS(chain F and (resseq 40 or (resid 42 and (name...FF40 - 34017 - 317

-
Components

#1: Protein
Citrate lyase subunit beta-like protein, mitochondrial / ATP citrate synthase / Citrate lyase beta-like / Beta-methylmalate synthase / Malate synthase


Mass: 36075.527 Da / Num. of mol.: 6 / Fragment: UNP residues 30-340
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CLYBL, CLB / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q8N0X4
#2: Chemical ChemComp-CIT / CITRIC ACID / Citric acid


Mass: 192.124 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H8O7

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.7 Å3/Da / Density % sol: 54.44 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: 1 uL protein at 4 mg/ml and 1 uL of the well solution, which is 85% dilution 0.2 M Ammonium Citrate Dibasic, 20% (w/v) PEG 3350
PH range: 4.5 - 5.5

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.2.2 / Wavelength: 0.999973 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Sep 12, 2014
RadiationMonochromator: Double-crystal Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.999973 Å / Relative weight: 1
ReflectionResolution: 2.954→156.506 Å / Num. obs: 45801 / % possible obs: 100 % / Redundancy: 21.8 % / Biso Wilson estimate: 86.56 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.106 / Rpim(I) all: 0.023 / Rrim(I) all: 0.109 / Net I/σ(I): 25.6 / Num. measured all: 999784
Reflection shell

Diffraction-ID: 1 / % possible all: 100

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. measured allNum. unique allCC1/2Rpim(I) allRrim(I) allNet I/σ(I) obs
2.954-2.96422.51.792107584780.7560.3851.8332.4
13.709-156.506170.04488585220.9960.0110.04566.7

-
Processing

Software
NameVersionClassification
PHENIX1.10.1_2155refinement
Aimlessdata scaling
autoPROCdata reduction
PHASERphasing
PDB_EXTRACT3.22data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5VXC

5vxc


Resolution: 2.954→133.913 Å / SU ML: 0.48 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 30.32 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2724 2309 5.05 %
Rwork0.2047 43435 -
obs0.2081 45744 99.93 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 158.59 Å2 / Biso mean: 81.1219 Å2 / Biso min: 39.08 Å2
Refinement stepCycle: final / Resolution: 2.954→133.913 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms13436 0 26 0 13462
Biso mean--86.14 --
Num. residues----1728
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00913682
X-RAY DIFFRACTIONf_angle_d1.1218470
X-RAY DIFFRACTIONf_chiral_restr0.0622134
X-RAY DIFFRACTIONf_plane_restr0.0072380
X-RAY DIFFRACTIONf_dihedral_angle_d16.5968443
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A6651X-RAY DIFFRACTION14.702TORSIONAL
12B6651X-RAY DIFFRACTION14.702TORSIONAL
13C6651X-RAY DIFFRACTION14.702TORSIONAL
14D6651X-RAY DIFFRACTION14.702TORSIONAL
15E6651X-RAY DIFFRACTION14.702TORSIONAL
16F6651X-RAY DIFFRACTION14.702TORSIONAL
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 16

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.9541-3.01830.40281420.347926902832100
3.0183-3.08860.39011440.293326792823100
3.0886-3.16580.40721380.276726942832100
3.1658-3.25140.31661350.26726592794100
3.2514-3.34710.37681370.256727212858100
3.3471-3.45510.33161390.264126912830100
3.4551-3.57860.34711630.251826722835100
3.5786-3.72190.2811440.23127082852100
3.7219-3.89130.2921500.219426892839100
3.8913-4.09650.27471410.209726972838100
4.0965-4.35320.25091510.199126952846100
4.3532-4.68930.27481500.177727302880100
4.6893-5.16120.21991360.164127312867100
5.1612-5.90810.26411740.182727112885100
5.9081-7.44350.23811350.207227832918100
7.4435-134.05040.22451300.16962885301599

+
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