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

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Basic information

Entry
Database: PDB / ID: 6arb
TitleCRYSTAL STRUCTURE OF PROTEIN CitE FROM MYCOBACTERIUM TUBERCULOSIS IN COMPLEX WITH MAGNESIUM, PYRUVATE AND COENZYME A
ComponentsCitrate lyase subunit beta-like proteinATP citrate synthase
KeywordsLYASE / PROTEIN CitE / MYCOBACTERIUM TUBERCULOSIS / 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
COENZYME A / PHOSPHATE 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: 1.717 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 22, 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
Revision 2.0Nov 15, 2023Group: Atomic model / Data collection / Derived calculations
Category: atom_site / atom_site_anisotrop ...atom_site / atom_site_anisotrop / 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 / _atom_site_anisotrop.pdbx_auth_atom_id / _atom_site_anisotrop.pdbx_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
B: Citrate lyase subunit beta-like protein
C: Citrate lyase subunit beta-like protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)93,24120
Polymers89,8563
Non-polymers3,38517
Water8,017445
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area15490 Å2
ΔGint-60 kcal/mol
Surface area28950 Å2
MethodPISA
Unit cell
Length a, b, c (Å)127.533, 73.491, 86.459
Angle α, β, γ (deg.)90.00, 99.14, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-508-

HOH

21C-430-

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, 462 molecules

#2: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Mg
#3: Chemical ChemComp-PYR / PYRUVIC ACID / Pyruvic acid


Mass: 88.062 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3H4O3
#4: Chemical ChemComp-COA / COENZYME A / Coenzyme A


Mass: 767.534 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C21H36N7O16P3S
#5: Chemical ChemComp-PO4 / PHOSPHATE ION / Phosphate


Mass: 94.971 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: PO4
#6: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C3H8O3
#7: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 445 / 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: 2.23 Å3/Da / Density % sol: 44.74 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.5 / Details: 0.4 M Ammonium phosphate, 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: Jun 15, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97931 Å / Relative weight: 1
ReflectionResolution: 1.717→28.454 Å / Num. obs: 163623 / % possible obs: 98.93 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4.6 % / Rmerge(I) obs: 0.109 / Net I/σ(I): 15.6

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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: 1U5H

1u5h


Resolution: 1.717→28.454 Å / SU ML: 0.54 / Cross valid method: THROUGHOUT / σ(F): 1.26 / Phase error: 26.18 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2616 6498 3.97 %
Rwork0.219 --
obs0.2207 163623 98.93 %
Solvent computationShrinkage radii: 0.83 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 48.315 Å2 / ksol: 0.41 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-1.6012 Å2-0 Å2-0.8368 Å2
2--0.2971 Å2-0 Å2
3----1.8984 Å2
Refinement stepCycle: LAST / Resolution: 1.717→28.454 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5976 0 210 445 6631
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0076274
X-RAY DIFFRACTIONf_angle_d1.0568545
X-RAY DIFFRACTIONf_dihedral_angle_d14.8052302
X-RAY DIFFRACTIONf_chiral_restr0.069975
X-RAY DIFFRACTIONf_plane_restr0.0051119
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.7173-1.73680.38521720.36184580X-RAY DIFFRACTION87
1.7368-1.75730.37462030.35335145X-RAY DIFFRACTION96
1.7573-1.77870.37612260.325132X-RAY DIFFRACTION98
1.7787-1.80120.33161930.30175340X-RAY DIFFRACTION99
1.8012-1.82490.34371830.32015231X-RAY DIFFRACTION99
1.8249-1.84990.3252050.28835249X-RAY DIFFRACTION99
1.8499-1.87630.37572390.32595282X-RAY DIFFRACTION99
1.8763-1.90430.3322500.27485154X-RAY DIFFRACTION99
1.9043-1.93410.3112250.25545304X-RAY DIFFRACTION99
1.9341-1.96580.27712260.2345243X-RAY DIFFRACTION100
1.9658-1.99970.30972660.23785241X-RAY DIFFRACTION100
1.9997-2.0360.28472230.23365207X-RAY DIFFRACTION100
2.036-2.07520.28631850.23025312X-RAY DIFFRACTION99
2.0752-2.11750.25851930.22155352X-RAY DIFFRACTION100
2.1175-2.16350.25071910.21465385X-RAY DIFFRACTION100
2.1635-2.21390.28472070.21795223X-RAY DIFFRACTION100
2.2139-2.26920.26512040.22515263X-RAY DIFFRACTION100
2.2692-2.33050.28012570.22115242X-RAY DIFFRACTION100
2.3305-2.39910.27662230.20685287X-RAY DIFFRACTION100
2.3991-2.47650.27152190.2015267X-RAY DIFFRACTION100
2.4765-2.56490.25312270.20215253X-RAY DIFFRACTION100
2.5649-2.66750.28212480.20685273X-RAY DIFFRACTION100
2.6675-2.78880.26452480.21255291X-RAY DIFFRACTION100
2.7888-2.93570.27022050.2045307X-RAY DIFFRACTION100
2.9357-3.11950.21162340.20475221X-RAY DIFFRACTION100
3.1195-3.360.25822240.19595318X-RAY DIFFRACTION100
3.36-3.69740.22382180.19085256X-RAY DIFFRACTION100
3.6974-4.2310.21572090.19245260X-RAY DIFFRACTION99
4.231-5.32490.1992100.18995297X-RAY DIFFRACTION100
5.3249-28.45760.26331850.22975210X-RAY DIFFRACTION98
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)
10.6184-0.1783-0.15150.47410.19591.0445-0.02560.0623-0.0875-0.0137-0.02990.07570.1845-0.19230.03520.0744-0.0482-0.00150.09630.00530.0884-13.9019-3.5818-23.0409
20.4198-0.0013-0.09040.919-0.16340.9559-0.01190.0158-0.029-0.1101-0.0267-0.1430.07550.23480.02640.06440.0230.01170.1414-0.00860.099618.98364.7959-22.9733
30.62460.2090.14170.57660.07090.9258-0.08250.04340.1085-0.07960.0410.0807-0.3474-0.12560.02950.11130.0043-0.00790.00620.00690.0528-4.831628.9474-23.1521
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain A
2X-RAY DIFFRACTION2chain B
3X-RAY DIFFRACTION3chain C

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