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- PDB-6chu: CRYSTAL STRUCTURE OF PROTEIN CITE FROM MYCOBACTERIUM TUBERCULOSIS... -

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Basic information

Entry
Database: PDB / ID: 6chu
TitleCRYSTAL STRUCTURE OF PROTEIN CITE FROM MYCOBACTERIUM TUBERCULOSIS IN COMPLEX WITH MAGNESIUM AND ACETATE
ComponentsCitrate lyase subunit beta-like protein
KeywordsLYASE / PROTEIN CITE / MYCOBACTERIUM TUBERCULOSIS / ACETATE / TIM-BARREL
Function / homology
Function and homology information


Lyases; Carbon-carbon lyases / oxaloacetate metabolic process / lyase activity / magnesium ion binding
Similarity search - Function
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
ACETATE ION / Citrate lyase subunit beta-like protein / Citrate lyase subunit beta-like protein
Similarity search - Component
Biological speciesMycobacterium tuberculosis H37Rv (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.61 Å
AuthorsFedorov, A.A. / Fedorov, E.V. / Wang, H. / Bonanno, J.B. / Carvalho, L. / Almo, S.C.
Citation
Journal: Proc.Natl.Acad.Sci.USA / Year: 2019
Title: An essential bifunctional enzyme inMycobacterium tuberculosisfor itaconate dissimilation and leucine catabolism.
Authors: Wang, H. / Fedorov, A.A. / Fedorov, E.V. / Hunt, D.M. / Rodgers, A. / Douglas, H.L. / Garza-Garcia, A. / Bonanno, J.B. / Almo, S.C. / de Carvalho, L.P.S.
#1: Journal: Biorxiv / Year: 2018
Title: Discovery of a novel stereospecific beta-hydroxyacyl-CoA lyase/thioesterase shared by three metabolic pathways in Mycobacterium tuberculosis
Authors: Wang, H. / Fedorov, A.A. / Fedorov, E.V. / Hunt, D.M. / Rodgers, A. / Garza-Garcia, A. / Bonanno, J.B. / Almo, S.C.
History
DepositionFeb 23, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 1, 2018Provider: repository / Type: Initial release
Revision 1.1Feb 13, 2019Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.pdbx_database_id_DOI / _citation.title / _citation.year
Revision 1.2Jul 31, 2019Group: Data collection / Database references / Category: citation / citation_author
Revision 1.3Aug 21, 2019Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID
Revision 1.4Jul 29, 2020Group: Derived calculations / Structure summary
Category: audit_author / pdbx_struct_conn_angle / struct_conn
Item: _audit_author.name / _pdbx_struct_conn_angle.ptnr1_auth_comp_id ..._audit_author.name / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id
Revision 1.5Mar 1, 2023Group: Database references / Source and taxonomy
Category: citation / database_2 ...citation / database_2 / entity_src_gen / struct_ref / struct_ref_seq / struct_ref_seq_dif
Item: _citation.journal_id_ISSN / _database_2.pdbx_DOI ..._citation.journal_id_ISSN / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _entity_src_gen.gene_src_strain / _entity_src_gen.pdbx_gene_src_gene / _entity_src_gen.pdbx_gene_src_ncbi_taxonomy_id / _entity_src_gen.pdbx_gene_src_scientific_name / _struct_ref.db_code / _struct_ref.pdbx_db_accession / _struct_ref_seq.pdbx_db_accession / _struct_ref_seq_dif.pdbx_seq_db_accession_code
Revision 1.6Oct 25, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,2747
Polymers29,9521
Non-polymers3236
Water2,954164
1
A: Citrate lyase subunit beta-like protein
hetero molecules

A: Citrate lyase subunit beta-like protein
hetero molecules

A: Citrate lyase subunit beta-like protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)90,82321
Polymers89,8563
Non-polymers96818
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_445-y-1,x-y-1,z1
crystal symmetry operation3_545-x+y,-x-1,z1
Buried area10640 Å2
ΔGint-82 kcal/mol
Surface area26050 Å2
MethodPISA
Unit cell
Length a, b, c (Å)91.135, 91.135, 220.291
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number155
Space group name H-MH32
Components on special symmetry positions
IDModelComponents
11A-512-

HOH

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Components

#1: Protein Citrate lyase subunit beta-like protein


Mass: 29951.939 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium tuberculosis H37Rv (bacteria)
Gene: citE, Rv2498c / Production host: Escherichia coli (E. coli)
References: UniProt: P9WPE1, UniProt: P9WPE0*PLUS, Lyases; Carbon-carbon lyases
#2: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#3: Chemical
ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C2H3O2
#4: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 164 / 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: 2.94 Å3/Da / Density % sol: 58.15 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 7 / Details: magnesium chloride, sodium acetate

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 31-ID / Wavelength: 0.979 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Oct 18, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 1.61→25 Å / Num. obs: 88184 / % possible obs: 99.8 % / Redundancy: 4.7 % / Rmerge(I) obs: 0.073 / Net I/σ(I): 12.2
Reflection shellResolution: 1.61→1.6321 Å / Num. unique obs: 3368 / % possible all: 99

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Processing

Software
NameVersionClassification
PHENIX(1.12_2829: ???)refinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1U5H

1u5h


Resolution: 1.61→24.767 Å / SU ML: 0.22 / Cross valid method: THROUGHOUT / σ(F): 0.87 / Phase error: 23.86
RfactorNum. reflection% reflection
Rfree0.2059 3546 4.02 %
Rwork0.2023 --
obs0.2024 88184 99.77 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.61→24.767 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1758 0 21 164 1943
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0061823
X-RAY DIFFRACTIONf_angle_d0.7842483
X-RAY DIFFRACTIONf_dihedral_angle_d12.6881109
X-RAY DIFFRACTIONf_chiral_restr0.051294
X-RAY DIFFRACTIONf_plane_restr0.005335
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.61-1.63210.36491110.37063368X-RAY DIFFRACTION99
1.6321-1.65540.32941230.35733423X-RAY DIFFRACTION99
1.6554-1.68010.31181340.34633336X-RAY DIFFRACTION99
1.6801-1.70630.36571330.33693378X-RAY DIFFRACTION100
1.7063-1.73430.30361320.33093429X-RAY DIFFRACTION100
1.7343-1.76420.42151410.33283357X-RAY DIFFRACTION100
1.7642-1.79630.30071440.31943369X-RAY DIFFRACTION100
1.7963-1.83080.29821360.28933410X-RAY DIFFRACTION100
1.8308-1.86820.28721660.27073356X-RAY DIFFRACTION100
1.8682-1.90880.25711270.25533392X-RAY DIFFRACTION100
1.9088-1.95310.26181680.243368X-RAY DIFFRACTION100
1.9531-2.0020.20921410.21493389X-RAY DIFFRACTION100
2.002-2.05610.18391550.19673383X-RAY DIFFRACTION100
2.0561-2.11650.21551350.2043371X-RAY DIFFRACTION100
2.1165-2.18480.19721390.19443403X-RAY DIFFRACTION100
2.1848-2.26290.20221240.17823408X-RAY DIFFRACTION100
2.2629-2.35340.1851510.17583372X-RAY DIFFRACTION100
2.3534-2.46040.18691290.18283444X-RAY DIFFRACTION100
2.4604-2.590.19081650.18833363X-RAY DIFFRACTION100
2.59-2.75210.27631340.19613396X-RAY DIFFRACTION100
2.7521-2.96420.16541460.20533372X-RAY DIFFRACTION100
2.9642-3.26190.21281720.18563373X-RAY DIFFRACTION100
3.2619-3.73260.16491800.17873353X-RAY DIFFRACTION100
3.7326-4.69740.16221150.15483430X-RAY DIFFRACTION100
4.6974-24.76980.17861450.1813395X-RAY DIFFRACTION100
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)
11.05190.19170.06551.37240.02761.5781-0.00470.11930.1768-0.06630.0866-0.0868-0.21650.0812-0.08120.1838-0.01540.03410.15370.00150.179711.9906-34.605319.4858
26.17225.1192.5576.20871.47957.2611-0.25880.17990.3068-0.3599-0.00740.1241-0.26660.21020.19630.75260.24620.05240.79430.16150.6111-16.6429-34.541810.981
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain A and resseq 0:221
2X-RAY DIFFRACTION2chain A and resseq 250:265

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