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- PDB-6con: Crystal structure of Mycobacterium tuberculosis IpdAB -

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Basic information

Entry
Database: PDB / ID: 6con
TitleCrystal structure of Mycobacterium tuberculosis IpdAB
Components
  • CoA-transferase subunit alpha
  • CoA-transferase subunit beta
KeywordsHYDROLASE / Cholesterol / Ring cleaving / virulence factor
Function / homology
Function and homology information


3-oxoadipate CoA-transferase / 3-oxoadipate CoA-transferase activity / glutaconate CoA-transferase / glutaconate CoA-transferase activity / Transferases; Transferring sulfur-containing groups; CoA-transferases / Lyases; Carbon-carbon lyases; Other carbon-carbon lyases / CoA-transferase activity / biological process involved in interaction with host / cholesterol catabolic process / lyase activity
Similarity search - Function
Coenzyme A transferase family I / Coenzyme A transferase / Coenzyme A transferase / NagB/RpiA transferase-like
Similarity search - Domain/homology
3-oxoadipate CoA-transferase subunit B / CoA-transferase (Alpha subunit) / Cholesterol ring-cleaving hydrolase IpdB subunit / Cholesterol ring-cleaving hydrolase IpdA subunit
Similarity search - Component
Biological speciesMycobacterium tuberculosis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å
AuthorsCrowe, A.M. / Workman, S.D. / Watanabe, N. / Worrall, L.J. / Strynadka, N.C.J. / Eltis, L.D.
CitationJournal: Proc. Natl. Acad. Sci. U.S.A. / Year: 2018
Title: IpdAB, a virulence factor inMycobacterium tuberculosis, is a cholesterol ring-cleaving hydrolase.
Authors: Crowe, A.M. / Workman, S.D. / Watanabe, N. / Worrall, L.J. / Strynadka, N.C.J. / Eltis, L.D.
History
DepositionMar 12, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 28, 2018Provider: repository / Type: Initial release
Revision 1.1Apr 11, 2018Group: Data collection / Database references / Category: citation
Item: _citation.journal_abbrev / _citation.pdbx_database_id_DOI ..._citation.journal_abbrev / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2Apr 25, 2018Group: Data collection / Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.3Jun 13, 2018Group: Data collection / Structure summary / Category: audit_author / Item: _audit_author.name
Revision 1.4Oct 4, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: CoA-transferase subunit alpha
B: CoA-transferase subunit beta
C: CoA-transferase subunit alpha
D: CoA-transferase subunit beta
E: CoA-transferase subunit alpha
F: CoA-transferase subunit beta
G: CoA-transferase subunit alpha
H: CoA-transferase subunit beta


Theoretical massNumber of molelcules
Total (without water)243,0078
Polymers243,0078
Non-polymers00
Water17,673981
1
A: CoA-transferase subunit alpha
B: CoA-transferase subunit beta
C: CoA-transferase subunit alpha
D: CoA-transferase subunit beta


Theoretical massNumber of molelcules
Total (without water)121,5034
Polymers121,5034
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area13770 Å2
ΔGint-50 kcal/mol
Surface area37000 Å2
MethodPISA
2
E: CoA-transferase subunit alpha
F: CoA-transferase subunit beta
G: CoA-transferase subunit alpha
H: CoA-transferase subunit beta


Theoretical massNumber of molelcules
Total (without water)121,5034
Polymers121,5034
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area13770 Å2
ΔGint-48 kcal/mol
Surface area36870 Å2
MethodPISA
Unit cell
Length a, b, c (Å)66.878, 133.823, 118.845
Angle α, β, γ (deg.)90.000, 90.230, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
CoA-transferase subunit alpha


Mass: 33325.703 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium tuberculosis (bacteria)
Gene: gctA, CRX58_09925, ERS007663_04080, ERS007665_02371, ERS023446_02783, ERS027646_00148, ERS027654_03521, ERS027656_00696, ERS124361_01188, SAMEA2682864_02618, SAMEA2683035_00650
Production host: Rhodococcus jostii RHA1 (bacteria)
References: UniProt: A0A045J8X5, UniProt: P9WPW1*PLUS, Transferases; Transferring sulfur-containing groups; CoA-transferases, glutaconate CoA-transferase
#2: Protein
CoA-transferase subunit beta


Mass: 27426.020 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium tuberculosis (bacteria)
Gene: catJ, CRX58_09930, ERS007657_01926, ERS007661_02237, ERS007665_02370, ERS007670_03185, ERS007672_03945, ERS007679_04090, ERS007681_03977, ERS007688_03438, ERS007703_04697, ERS007722_01813, ...Gene: catJ, CRX58_09930, ERS007657_01926, ERS007661_02237, ERS007665_02370, ERS007670_03185, ERS007672_03945, ERS007679_04090, ERS007681_03977, ERS007688_03438, ERS007703_04697, ERS007722_01813, ERS007741_03174, ERS023446_02782, ERS024213_01521, ERS024276_02483, ERS027644_04603, ERS027646_00147, ERS027656_00695, ERS027659_03102, ERS027661_03605, ERS027666_03707, ERS124361_01187, SAMEA2682864_02619, SAMEA2683035_00651
Production host: Rhodococcus jostii RHA1 (bacteria)
References: UniProt: A0A045H5Z8, UniProt: P9WPV9*PLUS, Transferases; Transferring sulfur-containing groups; CoA-transferases, 3-oxoadipate CoA-transferase
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 981 / 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: 2.25 Å3/Da / Density % sol: 45.37 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / Details: 25% PEG 3350, 0.5 M magnesium formate

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: CLSI / Beamline: 08B1-1 / Wavelength: 0.97777 Å
DetectorType: RAYONIX MX300HE / Detector: CCD / Date: Aug 7, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97777 Å / Relative weight: 1
ReflectionResolution: 2.1→88.86 Å / Num. obs: 119998 / % possible obs: 98.7 % / Redundancy: 3.8 % / CC1/2: 0.995 / Rmerge(I) obs: 0.07 / Rpim(I) all: 0.041 / Rrim(I) all: 0.081 / Net I/σ(I): 12.2 / Num. measured all: 456667 / Scaling rejects: 38
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. measured allNum. unique obsCC1/2Rpim(I) allRrim(I) allNet I/σ(I) obs% possible all
2.1-2.143.40.1851692750230.9460.1160.2194.884.3
11.5-88.863.60.03127817790.9980.020.0371999.5

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Processing

Software
NameVersionClassification
REFMAC5.8.0189refinement
Aimless0.5.32data scaling
PDB_EXTRACT3.24data extraction
DIALSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6CO6

6co6


Resolution: 2.1→88.86 Å / Cor.coef. Fo:Fc: 0.869 / Cor.coef. Fo:Fc free: 0.854 / WRfactor Rfree: 0.2764 / WRfactor Rwork: 0.2523 / FOM work R set: 0.8159 / SU B: 0.002 / SU ML: 0 / SU R Cruickshank DPI: 0.2117 / SU Rfree: 0.2313 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.212 / ESU R Free: 0.231 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2743 5983 5 %RANDOM
Rwork0.251 ---
obs0.2522 113984 98.61 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 100.33 Å2 / Biso mean: 25.566 Å2 / Biso min: 9.71 Å2
Baniso -1Baniso -2Baniso -3
1--0.13 Å20 Å2-0.54 Å2
2--0.57 Å20 Å2
3----0.43 Å2
Refinement stepCycle: final / Resolution: 2.1→88.86 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms16612 0 0 982 17594
Biso mean---31.62 -
Num. residues----2164
LS refinement shellResolution: 2.1→2.155 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.29 356 -
Rwork0.244 7436 -
all-7792 -
obs--86.87 %

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