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- PDB-5vxo: Crystal Structure Analysis of human CLYBL in complex with propion... -

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Basic information

Entry
Database: PDB / ID: 5vxo
TitleCrystal Structure Analysis of human CLYBL in complex with propionyl-CoA
ComponentsCitrate lyase subunit beta-like protein, mitochondrial
KeywordsLYASE / CLYBL / trimer / propionyl-CoA / citrate form / PEG form
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 family / Pyruvate kinase-like domain superfamily / Pyruvate/Phosphoenolpyruvate kinase-like domain superfamily
Similarity search - Domain/homology
propionyl Coenzyme A / DI(HYDROXYETHYL)ETHER / TRIETHYLENE GLYCOL / PHOSPHATE ION / Citramalyl-CoA lyase, mitochondrial
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.266 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 23, 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

Downloads & links

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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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)114,30648
Polymers108,2273
Non-polymers6,08045
Water6,539363
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area18320 Å2
ΔGint66 kcal/mol
Surface area33600 Å2
MethodPISA
Unit cell
Length a, b, c (Å)49.589, 131.841, 82.440
Angle α, β, γ (deg.)90.000, 93.050, 90.000
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11(chain A and (resseq 40:54 or (resid 55 and (name...
21(chain B and (resseq 40:54 or (resid 55 and (name...
31(chain C and (resseq 40:54 or (resid 55 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
11HISHISASNASN(chain A and (resseq 40:54 or (resid 55 and (name...AA40 - 5417 - 31
12ASPASPASPASP(chain A and (resseq 40:54 or (resid 55 and (name...AA5532
13HISHISILEILE(chain A and (resseq 40:54 or (resid 55 and (name...AA40 - 33717 - 314
14HISHISILEILE(chain A and (resseq 40:54 or (resid 55 and (name...AA40 - 33717 - 314
15HISHISILEILE(chain A and (resseq 40:54 or (resid 55 and (name...AA40 - 33717 - 314
16HISHISILEILE(chain A and (resseq 40:54 or (resid 55 and (name...AA40 - 33717 - 314
17HISHISILEILE(chain A and (resseq 40:54 or (resid 55 and (name...AA40 - 33717 - 314
18HISHISILEILE(chain A and (resseq 40:54 or (resid 55 and (name...AA40 - 33717 - 314
21HISHISASNASN(chain B and (resseq 40:54 or (resid 55 and (name...BB40 - 5417 - 31
22ASPASPASPASP(chain B and (resseq 40:54 or (resid 55 and (name...BB5532
23HISHIS1VU1VU(chain B and (resseq 40:54 or (resid 55 and (name...BB - W40 - 50117
24HISHIS1VU1VU(chain B and (resseq 40:54 or (resid 55 and (name...BB - W40 - 50117
25HISHIS1VU1VU(chain B and (resseq 40:54 or (resid 55 and (name...BB - W40 - 50117
26HISHIS1VU1VU(chain B and (resseq 40:54 or (resid 55 and (name...BB - W40 - 50117
27HISHIS1VU1VU(chain B and (resseq 40:54 or (resid 55 and (name...BB - W40 - 50117
28HISHIS1VU1VU(chain B and (resseq 40:54 or (resid 55 and (name...BB - W40 - 50117
31HISHISASNASN(chain C and (resseq 40:54 or (resid 55 and (name...CC40 - 5417 - 31
32ASPASPASPASP(chain C and (resseq 40:54 or (resid 55 and (name...CC5532
33HISHIS1VU1VU(chain C and (resseq 40:54 or (resid 55 and (name...CC - KA40 - 50117
34HISHIS1VU1VU(chain C and (resseq 40:54 or (resid 55 and (name...CC - KA40 - 50117
35HISHIS1VU1VU(chain C and (resseq 40:54 or (resid 55 and (name...CC - KA40 - 50117
36HISHIS1VU1VU(chain C and (resseq 40:54 or (resid 55 and (name...CC - KA40 - 50117
37HISHIS1VU1VU(chain C and (resseq 40:54 or (resid 55 and (name...CC - KA40 - 50117
38HISHIS1VU1VU(chain C and (resseq 40:54 or (resid 55 and (name...CC - KA40 - 50117

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Components

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Protein , 1 types, 3 molecules ABC

#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.: 3 / Fragment: UNP residues 30-340
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CLYBL, CLB / Plasmid: pET30a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q8N0X4

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Non-polymers , 7 types, 408 molecules

#2: Chemical ChemComp-1VU / propionyl Coenzyme A


Mass: 823.597 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C24H40N7O17P3S
#3: Chemical...
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 28 / Source method: obtained synthetically / Formula: C2H6O2
#4: Chemical
ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: C4H10O3
#5: Chemical ChemComp-PGE / TRIETHYLENE GLYCOL


Mass: 150.173 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C6H14O4
#6: Chemical ChemComp-PG4 / TETRAETHYLENE GLYCOL


Mass: 194.226 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C8H18O5 / Comment: precipitant*YM
#7: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: PO4
#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 363 / Source method: isolated from a natural source / Formula: H2O

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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: 2.72 Å3/Da / Density % sol: 54.81 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 4.2
Details: 1 uL protein at 4 mg/ml and well solution (0.1 M Na2HPO4:citric acid pH 4.2, 40% (v/v) PEG 300)

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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: 2.266→82.323 Å / Num. obs: 47726 / % possible obs: 97.3 % / Redundancy: 3.7 % / Biso Wilson estimate: 32.82 Å2 / CC1/2: 0.995 / Rmerge(I) obs: 0.096 / Rpim(I) all: 0.059 / Rrim(I) all: 0.113 / Net I/σ(I): 11.1 / Num. measured all: 174831
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. measured allNum. unique allCC1/2Rpim(I) allRrim(I) allNet I/σ(I) obs% possible all
2.266-2.2743.80.73219595200.6390.4370.854299.6
10.512-82.3233.60.03418155090.9890.0220.04130.498.6

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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: 2.266→82.323 Å / SU ML: 0.27 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 23.56 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2313 2405 5.04 %
Rwork0.1742 45287 -
obs0.1771 47692 97.21 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 98.94 Å2 / Biso mean: 37.9659 Å2 / Biso min: 14.01 Å2
Refinement stepCycle: final / Resolution: 2.266→82.323 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6942 0 391 363 7696
Biso mean--47.79 40.88 -
Num. residues----894
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0097446
X-RAY DIFFRACTIONf_angle_d1.2219973
X-RAY DIFFRACTIONf_chiral_restr0.0561118
X-RAY DIFFRACTIONf_plane_restr0.0061297
X-RAY DIFFRACTIONf_dihedral_angle_d17.7054599
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A2639X-RAY DIFFRACTION6.675TORSIONAL
12B2639X-RAY DIFFRACTION6.675TORSIONAL
13C2639X-RAY DIFFRACTION6.675TORSIONAL
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 17

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.2664-2.31270.31471240.240427332857100
2.3127-2.3630.29851280.224827892917100
2.363-2.41790.29511390.217226882827100
2.4179-2.47840.25151560.209827192875100
2.4784-2.54540.2611660.204626922858100
2.5454-2.62030.28571420.202527302872100
2.6203-2.70490.28611620.20042682284499
2.7049-2.80160.25751430.19372718286199
2.8016-2.91380.27481470.19842704285199
2.9138-3.04640.26981300.19732705283598
3.0464-3.2070.26921200.17922665278597
3.207-3.40790.2211350.17372626276196
3.4079-3.6710.21551530.15742554270794
3.671-4.04050.1971380.14762549268793
4.0405-4.62510.19161430.13712560270393
4.6251-5.82690.19031430.14782556269993
5.8269-82.37780.20441360.17022617275394

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