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- PDB-5vxs: Crystal Structure Analysis of human CLYBL in apo form -

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Basic information

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


(3S)-malyl-CoA thioesterase / positive regulation of cobalamin metabolic process / 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 / positive regulation of cobalamin metabolic process / 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 / Phosphoenolpyruvate-binding domains / Pyruvate kinase-like domain superfamily / Pyruvate/Phosphoenolpyruvate kinase-like domain superfamily / TIM Barrel / Alpha-Beta Barrel / Alpha Beta
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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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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
Water00
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

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Components

#1: Protein
Citrate lyase subunit beta-like protein, mitochondrial / 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


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

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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: 2.7 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

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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

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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

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