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- PDB-6cj3: CRYSTAL STRUCTURE OF PROTEIN CITE FROM MYCOBACTERIUM TUBERCULOSIS... -

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Basic information

Entry
Database: PDB / ID: 6cj3
TitleCRYSTAL STRUCTURE OF PROTEIN CITE FROM MYCOBACTERIUM TUBERCULOSIS IN COMPLEX WITH MAGNESIUM AND PYRUVATE
ComponentsCitrate lyase subunit beta-like protein
KeywordsLYASE / PROTEIN CITE / MYCOBACTERIUM TUBERCULOSIS / PYRUVATE / 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 / PYRUVIC ACID / 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: 1.73 Å
AuthorsFedorov, E.V. / Fedorov, A.A. / 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 26, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 1, 2018Provider: repository / Type: Initial release
Revision 1.1Aug 8, 2018Group: Data collection / Structure summary / Category: audit_author / Item: _audit_author.name
Revision 1.2Feb 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 1.3Jul 31, 2019Group: Data collection / Database references / Category: citation / citation_author
Revision 1.4Aug 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 1.5Jul 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 1.6Mar 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 1.7Oct 25, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 2.0Nov 15, 2023Group: Atomic model / Data collection / Derived calculations
Category: atom_site / chem_comp_atom ...atom_site / chem_comp_atom / chem_comp_bond / pdbx_struct_conn_angle / struct_conn
Item: _atom_site.auth_atom_id / _atom_site.label_atom_id ..._atom_site.auth_atom_id / _atom_site.label_atom_id / _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_1 / _chem_comp_bond.atom_id_2 / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _struct_conn.ptnr2_label_atom_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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,3307
Polymers29,9521
Non-polymers3786
Water2,522140
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)90,98921
Polymers89,8563
Non-polymers1,13318
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 area11600 Å2
ΔGint-56 kcal/mol
Surface area26780 Å2
MethodPISA
Unit cell
Length a, b, c (Å)91.992, 91.992, 221.137
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number155
Space group name H-MH32

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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)
Strain: \ / 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.: 3 / Source method: obtained synthetically / Formula: C2H3O2
#4: Chemical ChemComp-PYR / PYRUVIC ACID


Mass: 88.062 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H4O3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 140 / 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: 3.01 Å3/Da / Density % sol: 59.08 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 7 / Details: magnesium chloride, pyruvate, 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: Dec 6, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 1.73→25 Å / Num. obs: 72884 / % possible obs: 99.98 % / Redundancy: 5.4 % / Rmerge(I) obs: 0.064 / Net I/σ(I): 17.3
Reflection shellResolution: 1.73→1.7584 Å

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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: 6CHU

6chu


Resolution: 1.73→25 Å / SU ML: 0.23 / Cross valid method: THROUGHOUT / σ(F): 0.76 / Phase error: 23.25
RfactorNum. reflection% reflection
Rfree0.2181 2942 4.04 %
Rwork0.1934 --
obs0.1944 72884 99.98 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.73→25 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1764 0 25 140 1929
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0061818
X-RAY DIFFRACTIONf_angle_d0.7822475
X-RAY DIFFRACTIONf_dihedral_angle_d14.4341107
X-RAY DIFFRACTIONf_chiral_restr0.05292
X-RAY DIFFRACTIONf_plane_restr0.005336
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.73-1.75840.35931350.34283339X-RAY DIFFRACTION100
1.7584-1.78870.33981570.33183327X-RAY DIFFRACTION100
1.7887-1.82120.33341060.32073354X-RAY DIFFRACTION100
1.8212-1.85620.34231330.3093351X-RAY DIFFRACTION100
1.8562-1.89410.31861470.29193283X-RAY DIFFRACTION100
1.8941-1.93530.2571570.26333355X-RAY DIFFRACTION100
1.9353-1.98030.31191210.2443340X-RAY DIFFRACTION100
1.9803-2.02980.25991510.21883294X-RAY DIFFRACTION100
2.0298-2.08470.26411170.20893376X-RAY DIFFRACTION100
2.0847-2.1460.23991240.2083339X-RAY DIFFRACTION100
2.146-2.21520.2071480.18553311X-RAY DIFFRACTION100
2.2152-2.29440.231600.17883322X-RAY DIFFRACTION100
2.2944-2.38620.19011320.16843324X-RAY DIFFRACTION100
2.3862-2.49480.18861610.17923317X-RAY DIFFRACTION100
2.4948-2.62620.2231580.18353309X-RAY DIFFRACTION100
2.6262-2.79060.26531250.19893356X-RAY DIFFRACTION100
2.7906-3.00590.19481540.19433316X-RAY DIFFRACTION100
3.0059-3.30810.2221420.18543317X-RAY DIFFRACTION100
3.3081-3.78590.17851220.16143353X-RAY DIFFRACTION100
3.7859-4.76660.181450.14973328X-RAY DIFFRACTION100
4.7666-29.60280.19011470.18613331X-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)
11.35410.3044-0.08262.0206-0.28551.84530.0862-0.03830.19040.19630.0249-0.1435-0.27020.1231-0.08450.177-0.02270.02490.1407-0.03320.17139.8609-33.972917.7583
26.0673-6.47913.40836.9463-4.05798.39750.1185-0.1941-0.03030.4015-0.199-0.9444-0.06860.52430.03890.5636-0.0049-0.14870.9961-0.03830.636223.8479-58.775925.6962
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain A and resseq 2:224
2X-RAY DIFFRACTION2chain A and resseq 250:265

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