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- PDB-6aq4: CRYSTAL STRUCTURE OF PROTEIN CiTE FROM MYCOBACTERIUM TUBERCULOSIS... -

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Basic information

Entry
Database: PDB / ID: 6aq4
TitleCRYSTAL STRUCTURE OF PROTEIN CiTE FROM MYCOBACTERIUM TUBERCULOSIS IN COMPLEX WITH MAGNESIUM, PYRUVATE AND CITRAMALYL-COA
ComponentsCitrate lyase subunit beta-like protein
KeywordsLYASE / Mycobacterium tuberculosis / CitE / Citramalyl-CoA / TIM-barrel fold / trimer
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
Citramalyl-CoA / PHOSPHATE ION / PYRUVIC ACID / Citrate lyase subunit beta-like protein
Similarity search - Component
Biological speciesMycobacterium tuberculosis H37Rv (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.825 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 18, 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 ...Database references / Derived calculations / Source and taxonomy / Structure summary
Category: citation / database_2 ...citation / database_2 / entity / entity_src_gen / pdbx_struct_conn_angle / pdbx_struct_mod_residue / struct_conn / struct_conn_type / 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.pdbx_description / _entity.pdbx_ec / _entity_src_gen.pdbx_beg_seq_num / _entity_src_gen.pdbx_end_seq_num / _entity_src_gen.pdbx_gene_src_gene / _entity_src_gen.pdbx_gene_src_ncbi_taxonomy_id / _entity_src_gen.pdbx_gene_src_scientific_name / _entity_src_gen.pdbx_seq_type / _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.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _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_conn.ptnr2_label_seq_id / _struct_conn_type.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
Revision 2.1Oct 9, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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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)92,50619
Polymers89,9043
Non-polymers2,60316
Water8,521473
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area11140 Å2
ΔGint-121 kcal/mol
Surface area29250 Å2
MethodPISA
Unit cell
Length a, b, c (Å)138.541, 88.365, 81.252
Angle α, β, γ (deg.)90.00, 108.54, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11C-531-

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


Mass: 29967.939 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, Lyases; Carbon-carbon lyases

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Non-polymers , 7 types, 489 molecules

#2: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Mg
#3: Chemical ChemComp-CQM / Citramalyl-CoA


Mass: 897.633 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C26H42N7O20P3S
#4: Chemical ChemComp-PO4 / PHOSPHATE ION


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


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#6: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: Cl
#7: Chemical ChemComp-PYR / PYRUVIC ACID


Mass: 88.062 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H4O3
#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 473 / Source method: isolated from a natural source / Formula: H2O

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Details

Has protein modificationY

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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: 2.62 Å3/Da / Density % sol: 53.1 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.8 / Details: 0.4M 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: Jul 11, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97931 Å / Relative weight: 1
ReflectionResolution: 1.825→29.276 Å / Num. obs: 154090 / % possible obs: 94.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4.2 % / Rmerge(I) obs: 0.052 / Net I/σ(I): 17.9

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Processing

Software
NameVersionClassification
PHENIX1.7.1_743refinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1U5H

1u5h


Resolution: 1.825→29.276 Å / SU ML: 0.58 / Cross valid method: FREE R-VALUE / σ(F): 0.31 / Phase error: 25.88 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2331 6140 3.98 %
Rwork0.1907 --
obs0.1924 154090 94.8 %
Solvent computationShrinkage radii: 1.06 Å / VDW probe radii: 1.3 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 43.627 Å2 / ksol: 0.34 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--3.2314 Å20 Å22.3154 Å2
2--8.9499 Å2-0 Å2
3----5.7185 Å2
Refinement stepCycle: LAST / Resolution: 1.825→29.276 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5964 0 155 473 6592
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0076256
X-RAY DIFFRACTIONf_angle_d1.0328525
X-RAY DIFFRACTIONf_dihedral_angle_d14.9552308
X-RAY DIFFRACTIONf_chiral_restr0.068973
X-RAY DIFFRACTIONf_plane_restr0.0041126
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.8246-1.84540.47351910.43014170X-RAY DIFFRACTION81
1.8454-1.86710.42631850.40924649X-RAY DIFFRACTION88
1.8671-1.88980.44911770.37384822X-RAY DIFFRACTION93
1.8898-1.91380.34772220.34224868X-RAY DIFFRACTION94
1.9138-1.93890.35812110.32184946X-RAY DIFFRACTION95
1.9389-1.96550.35471940.30544967X-RAY DIFFRACTION95
1.9655-1.99360.31222170.27864905X-RAY DIFFRACTION96
1.9936-2.02330.29152100.26544955X-RAY DIFFRACTION96
2.0233-2.05490.32681590.26645111X-RAY DIFFRACTION96
2.0549-2.08860.29011870.25474843X-RAY DIFFRACTION94
2.0886-2.12460.30381950.23294998X-RAY DIFFRACTION96
2.1246-2.16320.2551940.22515074X-RAY DIFFRACTION96
2.1632-2.20480.2532310.21834968X-RAY DIFFRACTION96
2.2048-2.24980.28431970.22374907X-RAY DIFFRACTION95
2.2498-2.29870.2381830.19924987X-RAY DIFFRACTION96
2.2987-2.35220.23212210.19915063X-RAY DIFFRACTION96
2.3522-2.4110.19792110.19545032X-RAY DIFFRACTION96
2.411-2.47610.27152150.18864924X-RAY DIFFRACTION96
2.4761-2.54890.23432010.18415016X-RAY DIFFRACTION96
2.5489-2.63120.22862260.19184977X-RAY DIFFRACTION96
2.6312-2.72510.27062170.19434982X-RAY DIFFRACTION95
2.7251-2.83420.2652270.21255016X-RAY DIFFRACTION96
2.8342-2.9630.24612300.21254956X-RAY DIFFRACTION97
2.963-3.11910.28471960.20995014X-RAY DIFFRACTION96
3.1191-3.31430.26172460.19634924X-RAY DIFFRACTION95
3.3143-3.56970.22371720.18244966X-RAY DIFFRACTION95
3.5697-3.92820.17821930.15584896X-RAY DIFFRACTION94
3.9282-4.49490.18272050.13024927X-RAY DIFFRACTION95
4.4949-5.65640.18032060.13295025X-RAY DIFFRACTION97
5.6564-29.27950.15082210.14395062X-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)
11.28430.002-0.24950.94260.05792.0838-0.0004-0.29030.10090.0608-0.0299-0.158-0.20210.53920.05350.119-0.0712-0.03220.2897-0.01910.1039-26.21899.6604-18.8594
21.609-0.9187-0.52440.59740.37221.7475-0.2392-0.1891-0.67680.1846-0.06830.3220.6660.00430.12680.34980.07390.09850.11120.04670.3752-44.3518-19.2509-21.8032
31.58920.3916-0.61181.46860.26272.09570.0213-0.29970.03430.0802-0.03370.3259-0.5658-0.6170.0760.11990.1574-0.03570.2635-0.05850.1024-59.880910.4052-17.2011
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain A
2X-RAY DIFFRACTION2chain B
3X-RAY DIFFRACTION3chain C

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