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- PDB-6as5: CRYSTAL STRUCTURE OF PROTEIN CitE FROM MYCOBACTERIUM TUBERCULOSIS... -

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Basic information

Entry
Database: PDB / ID: 6as5
TitleCRYSTAL STRUCTURE OF PROTEIN CitE FROM MYCOBACTERIUM TUBERCULOSIS IN COMPLEX WITH MAGNESIUM, ACETOACETATE AND COENZYME A
ComponentsCitrate lyase subunit beta-like proteinATP citrate synthase
KeywordsLYASE / PROTEIN CitE / MYCOBACTERIUM TUBERCULOSIS / ACETOACETATE / COENZYME A / TIM-BARREL
Function / homology
Function and homology information


Lyases; Carbon-carbon lyases / oxaloacetate metabolic process / lyase activity / magnesium ion binding / metal ion binding
Similarity search - Function
Citrate lyase beta subunit-like / HpcH/HpaI aldolase/citrate lyase domain / HpcH/HpaI aldolase/citrate lyase family / 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
ACETOACETIC ACID / COENZYME A / 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: 2.035 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
DepositionAug 23, 2017Deposition 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 1.4Mar 1, 2023Group: Database references / Derived calculations / Source and taxonomy
Category: citation / database_2 ...citation / database_2 / entity_src_gen / pdbx_struct_conn_angle / struct_conn / 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 / _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.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _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 / _struct_ref.db_code / _struct_ref.pdbx_db_accession / _struct_ref_seq.pdbx_db_accession / _struct_ref_seq_dif.details / _struct_ref_seq_dif.pdbx_seq_db_accession_code
Revision 1.5Oct 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
B: Citrate lyase subunit beta-like protein
C: Citrate lyase subunit beta-like protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)93,01017
Polymers89,8563
Non-polymers3,15414
Water4,234235
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area11180 Å2
ΔGint-119 kcal/mol
Surface area32060 Å2
MethodPISA
Unit cell
Length a, b, c (Å)126.579, 72.998, 85.788
Angle α, β, γ (deg.)90.00, 98.83, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-462-

HOH

Detailstrimer by gel filtration

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Components

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Protein , 1 types, 3 molecules ABC

#1: Protein Citrate lyase subunit beta-like protein / ATP citrate synthase


Mass: 29951.939 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium tuberculosis H37Rv (bacteria)
Gene: citE, Rv2498c / Production host: Escherichia coli K-12 (bacteria)
References: UniProt: P9WPE1, UniProt: P9WPE0*PLUS, Lyases; Carbon-carbon lyases

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Non-polymers , 6 types, 249 molecules

#2: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Mg
#3: Chemical ChemComp-COA / COENZYME A / Coenzyme A


Mass: 767.534 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C21H36N7O16P3S
#4: Chemical ChemComp-AAE / ACETOACETIC ACID / Acetoacetic acid


Mass: 102.089 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C4H6O3
#5: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: SO4
#6: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#7: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 235 / 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: 2.18 Å3/Da / Density % sol: 43.56 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6 / Details: 2.0 M Ammonium sulfate, no buffer

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 31-ID / Wavelength: 0.97931 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Apr 13, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97931 Å / Relative weight: 1
ReflectionResolution: 2.035→31.27 Å / Num. obs: 48935 / % possible obs: 98.59 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4.4 % / Rmerge(I) obs: 0.126 / Net I/σ(I): 19.2

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Processing

Software
NameVersionClassification
PHENIX1.7.1_743refinement
MOSFLMdata reduction
HKL-2000data scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1U5V

1u5v


Resolution: 2.035→31.27 Å / SU ML: 0.72 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 29.63 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2773 1987 4.06 %
Rwork0.2169 --
obs0.2194 48935 98.59 %
Solvent computationShrinkage radii: 0.95 Å / VDW probe radii: 1.2 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 36.758 Å2 / ksol: 0.399 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-0.4451 Å2-0 Å2-1.0344 Å2
2--0.9971 Å2-0 Å2
3----1.4422 Å2
Refinement stepCycle: LAST / Resolution: 2.035→31.27 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5952 0 195 235 6382
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0076248
X-RAY DIFFRACTIONf_angle_d1.138515
X-RAY DIFFRACTIONf_dihedral_angle_d15.9062301
X-RAY DIFFRACTIONf_chiral_restr0.068973
X-RAY DIFFRACTIONf_plane_restr0.0041116
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.0353-2.08620.37011540.28513333X-RAY DIFFRACTION99
2.0862-2.14260.33721460.25513399X-RAY DIFFRACTION100
2.1426-2.20560.31811360.23423346X-RAY DIFFRACTION100
2.2056-2.27680.29711420.24533332X-RAY DIFFRACTION99
2.2768-2.35810.32391530.21943390X-RAY DIFFRACTION100
2.3581-2.45250.34531360.23343373X-RAY DIFFRACTION100
2.4525-2.56410.31431470.24833352X-RAY DIFFRACTION100
2.5641-2.69920.32061330.24253409X-RAY DIFFRACTION100
2.6992-2.86820.32851440.23783361X-RAY DIFFRACTION100
2.8682-3.08950.25211550.21633367X-RAY DIFFRACTION99
3.0895-3.40.2561400.20123401X-RAY DIFFRACTION99
3.4-3.89130.26181280.18633257X-RAY DIFFRACTION95
3.8913-4.89950.2021380.18433222X-RAY DIFFRACTION94
4.8995-31.27320.23631350.21223406X-RAY DIFFRACTION97
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)
10.76220.1094-0.26730.456-0.14931.1205-0.0316-0.1029-0.06370.0235-0.0031-0.11030.22190.22770.02780.08790.043-0.03020.1071-0.00380.084113.7279-3.975623.0616
20.5365-0.0856-0.21410.83820.15261.11-0.0211-0.0164-0.0640.121-0.02610.130.1343-0.31680.02370.0591-0.0515-0.0170.12980.02360.0711-18.96374.659722.958
30.8139-0.03010.29440.86520.16041.117-0.0799-0.04860.1086-0.01670.0464-0.0468-0.34250.06970.02920.1393-0.01220.0021-0.0115-0.01030.04354.994228.807723.001
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain A
2X-RAY DIFFRACTION2chain B
3X-RAY DIFFRACTION3chain C

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