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- PDB-5vxc: Crystal Structure Analysis of human CLYBL in complex with free CoASH -

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Basic information

Entry
Database: PDB / ID: 5vxc
TitleCrystal Structure Analysis of human CLYBL in complex with free CoASH
ComponentsCitrate lyase subunit beta-like protein, mitochondrialATP citrate synthase
KeywordsLYASE / trimer / CoASH / formate form
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
COENZYME A / Citramalyl-CoA lyase, mitochondrial
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.872 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 ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / software / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.value / _software.name / _struct_conn.pdbx_dist_value / _struct_conn.ptnr2_auth_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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,8673
Polymers36,0761
Non-polymers7922
Water3,693205
1
A: Citrate lyase subunit beta-like protein, mitochondrial
hetero molecules

A: Citrate lyase subunit beta-like protein, mitochondrial
hetero molecules

A: Citrate lyase subunit beta-like protein, mitochondrial
hetero molecules


Theoretical massNumber of molelcules
Total (without water)110,6029
Polymers108,2273
Non-polymers2,3766
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-y,x-y,z1
crystal symmetry operation3_555-x+y,-x,z1
Buried area12520 Å2
ΔGint-72 kcal/mol
Surface area34220 Å2
MethodPISA
Unit cell
Length a, b, c (Å)76.515, 76.515, 139.428
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number146
Space group name H-MH3
Components on special symmetry positions
IDModelComponents
11A-536-

HOH

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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.: 1 / Fragment: UNP residues 40-340
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
#2: Chemical ChemComp-COA / COENZYME A / Coenzyme A


Mass: 767.534 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C21H36N7O16P3S
#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 205 / 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: 2.36 Å3/Da / Density % sol: 47.79 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 4.6
Details: 1 uL protein at 4 mg/ml and well solution (0.1 M sodium acetate:HCl pH4.6, 3.5 M sodium formate)

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.2.2 / Wavelength: 0.99997 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: 0.99997 Å / Relative weight: 1
ReflectionResolution: 1.872→59.849 Å / Num. obs: 24985 / % possible obs: 99.5 % / Redundancy: 5.5 % / Biso Wilson estimate: 20.54 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.087 / Rpim(I) all: 0.042 / Rrim(I) all: 0.097 / Net I/σ(I): 15.7 / Num. measured all: 137154
Reflection shellResolution: 1.872→1.878 Å / Redundancy: 5.3 % / Rmerge(I) obs: 0.802 / Num. unique all: 263 / CC1/2: 0.81 / Rpim(I) all: 0.394 / Rrim(I) all: 0.896 / % possible all: 100

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Processing

Software
NameVersionClassification
Aimlessdata scaling
PDB_EXTRACT3.22data extraction
autoPROCdata reduction
PHASERphasing
PHENIX1.10.1_2155refinement
BUSTER2.10.1refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1z6k

1z6k


Resolution: 1.872→59.849 Å / SU ML: 0.27 / Cross valid method: FREE R-VALUE / σ(F): 1.96 / Phase error: 23.74
RfactorNum. reflection% reflection
Rfree0.2196 1265 5.07 %
Rwork0.1813 --
obs0.1832 24969 99.48 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 71.12 Å2 / Biso mean: 21.4507 Å2 / Biso min: 8.02 Å2
Refinement stepCycle: final / Resolution: 1.872→59.849 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2341 0 49 205 2595
Biso mean--23.91 28.38 -
Num. residues----301
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.012442
X-RAY DIFFRACTIONf_angle_d0.8623297
X-RAY DIFFRACTIONf_chiral_restr0.049375
X-RAY DIFFRACTIONf_plane_restr0.005434
X-RAY DIFFRACTIONf_dihedral_angle_d16.1161510
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 9

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.8719-1.94690.38851300.32732631276199
1.9469-2.03550.29161520.231526282780100
2.0355-2.14280.28971450.2152628277399
2.1428-2.27710.25541340.18872632276699
2.2771-2.45290.2561450.177526512796100
2.4529-2.69970.20051410.178826142755100
2.6997-3.09040.2261380.175126572795100
3.0904-3.89350.16781420.15622612275499
3.8935-59.87940.18451380.159726512789100

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