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- PDB-6co6: Crystal structure of Rhodococcus jostii RHA1 IpdAB -

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Basic information

Entry
Database: PDB / ID: 6co6
TitleCrystal structure of Rhodococcus jostii RHA1 IpdAB
Components
  • Probable CoA-transferase alpha subunit
  • Probable CoA-transferase beta subunit
KeywordsHYDROLASE / Cholesterol / Ring cleaving / virulence factor
Function / homology
Function and homology information


Lyases; Carbon-carbon lyases; Other carbon-carbon lyases / CoA-transferase activity / 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
Cholesterol ring-cleaving hydrolase IpdA subunit / Cholesterol ring-cleaving hydrolase IpdB subunit
Similarity search - Component
Biological speciesRhodococcus jostii (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.701 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: Probable CoA-transferase alpha subunit
B: Probable CoA-transferase beta subunit
hetero molecules


Theoretical massNumber of molelcules
Total (without water)62,94119
Polymers61,3312
Non-polymers1,60917
Water8,107450
1
A: Probable CoA-transferase alpha subunit
B: Probable CoA-transferase beta subunit
hetero molecules

A: Probable CoA-transferase alpha subunit
B: Probable CoA-transferase beta subunit
hetero molecules


Theoretical massNumber of molelcules
Total (without water)125,88138
Polymers122,6634
Non-polymers3,21934
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_556y,x,-z+11
Buried area20010 Å2
ΔGint-256 kcal/mol
Surface area37610 Å2
MethodPISA
Unit cell
Length a, b, c (Å)68.910, 68.910, 241.370
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number96
Space group name H-MP43212
Components on special symmetry positions
IDModelComponents
11B-405-

HOH

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Components

#1: Protein Probable CoA-transferase alpha subunit


Mass: 33793.266 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rhodococcus jostii (bacteria) / Strain: RHA1 / Gene: RHA1_ro04651 / Production host: Rhodococcus jostii RHA1 (bacteria) / References: UniProt: Q0S7P9
#2: Protein Probable CoA-transferase beta subunit


Mass: 27538.000 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rhodococcus jostii (strain RHA1) (bacteria)
Strain: RHA1 / Gene: RHA1_ro04650 / Production host: Rhodococcus jostii RHA1 (bacteria) / References: UniProt: Q0S7Q0
#3: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 11 / Source method: obtained synthetically / Formula: SO4
#4: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C3H8O3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 450 / 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: 2.43 Å3/Da / Density % sol: 49.35 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 1.9 M ammonium sulfate, 0.2 M sodium potassium tartrate

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: CLSI / Beamline: 08B1-1 / Wavelength: 0.97948 Å
DetectorType: RAYONIX MX300HE / Detector: CCD / Date: Feb 12, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97948 Å / Relative weight: 1
ReflectionResolution: 1.701→59.85 Å / Num. obs: 65095 / % possible obs: 100 % / Redundancy: 8 % / Biso Wilson estimate: 18.06 Å2 / Rmerge(I) obs: 0.09076 / Net I/σ(I): 16.54
Reflection shellResolution: 1.701→1.762 Å / Redundancy: 8 % / Mean I/σ(I) obs: 2.31 / Num. unique obs: 6374 / CC1/2: 0.818 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX1.13_2998refinement
Aimlessdata scaling
PDB_EXTRACT3.24data extraction
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1POI

1poi


Resolution: 1.701→48.727 Å / SU ML: 0.15 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 18.16 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1923 3311 5.09 %
Rwork0.1645 61710 -
obs0.1659 65021 99.86 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 144.38 Å2 / Biso mean: 23.3913 Å2 / Biso min: 10.8 Å2
Refinement stepCycle: final / Resolution: 1.701→48.727 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4148 0 91 450 4689
Biso mean--69.43 34.18 -
Num. residues----541
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 24 / % reflection obs: 100 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all
1.701-1.72530.25051550.244625322687
1.7253-1.75110.26341380.220724892627
1.7511-1.77840.25341300.206425202650
1.7784-1.80760.20731440.202225342678
1.8076-1.83870.27721030.199425402643
1.8387-1.87220.22221260.1925492675
1.8722-1.90820.24251160.186925272643
1.9082-1.94710.2321550.18225332688
1.9471-1.98950.23721430.184325072650
1.9895-2.03580.22151460.168425372683
2.0358-2.08670.18751510.157825322683
2.0867-2.14310.17481070.159225432650
2.1431-2.20620.19031470.159125742721
2.2062-2.27740.19521310.157925382669
2.2774-2.35880.16751430.161625482691
2.3588-2.45320.19991300.159725772707
2.4532-2.56480.20221530.166225792732
2.5648-2.70010.21831430.16325532696
2.7001-2.86920.19011490.172525942743
2.8692-3.09070.20891270.164425842711
3.0907-3.40170.16961390.152926192758
3.4017-3.89370.17711440.140226492793
3.8937-4.90490.15391520.13426812833
4.9049-48.74670.17411390.18328713010
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)
15.91391.1735-2.00980.5812-0.96163.35950.08790.26590.3628-0.03160.03720.2226-0.161-0.5484-0.13620.1481-0.005-0.02010.1922-0.01150.165-4.474718.147199.8721
22.129-0.35640.45681.627-1.16663.0557-0.00620.1593-0.0367-0.0835-0.04050.02460.15970.01220.04720.1406-0.0310.01180.1308-0.01180.104911.02548.055695.7666
31.0246-0.3027-0.20350.68260.58360.61450.0190.05110.0447-0.06560.0075-0.0384-0.03520.0359-0.02530.1471-0.02410.00660.14430.00690.149820.191913.1932105.3745
41.39840.81633.62651.29362.59099.7470.02090.10460.0556-0.03480.0493-0.0703-0.23210.5214-0.04030.1054-0.05220.0310.17450.00210.156129.178519.4823115.7999
51.2951-0.26560.14990.3506-0.11990.8541-0.0453-0.0237-0.0988-0.02580.02010.09790.0822-0.17080.01790.1247-0.03970.00750.1353-0.00810.11284.980510.5872109.3094
66.62322.1071-1.90491.391-0.27744.2722-0.00180.0482-0.0288-0.0108-0.14030.28170.4132-0.60610.10350.1753-0.0593-0.01830.2206-0.02850.1454-7.52538.5211108.3384
71.4707-0.8555-1.37860.63680.46091.8373-0.11820.0813-0.14240.0159-0.0130.09670.2895-0.18850.14260.1888-0.0794-0.00940.1984-0.00810.1417-1.98943.968105.9908
82.11791.1687-1.74751.66-2.93296.7295-0.11490.2574-0.2154-0.45940.0324-0.00950.9094-0.28640.06030.3086-0.06960.01780.2004-0.0670.18088.0459-0.831583.7163
95.86530.10270.74264.33121.7675.38520.00440.4819-0.54210.0947-0.24950.3930.5635-0.58770.26940.4358-0.25440.02670.4186-0.0860.229-3.2822-4.150786.7763
103.8374-0.2526-1.29112.89012.17936.0962-0.06780.0424-0.23260.05710.1461-0.27220.2710.215-0.09130.0802-0.0036-0.02110.0910.01770.167233.7745-20.789111.6746
110.46120.1227-0.25150.5894-0.07930.93820.0012-0.0002-0.04090.07530.00950.00630.06630.0093-0.00770.1592-0.0217-0.00530.1331-00.160222.0469-7.3846115.4249
129.0151.6214-6.22535.3999-2.90715.0699-0.24610.4181-0.3294-0.47790.0342-0.13560.41270.09450.23860.1546-0.002-0.00930.1669-0.01680.103927.4765.627396.0153
130.70330.4126-0.10851.7512-0.04640.4294-0.0019-0.0184-0.04810.0549-0.0037-0.29630.00830.19840.00560.0977-0.0122-0.01640.17420.00480.155438.5046-6.728110.681
149.79126.7756-7.90792.1477-6.69126.7096-0.09450.25220.12780.03680.2907-0.03270.04660.0671-0.16180.170.00830.02050.1611-0.02680.195725.3881-21.7446104.2834
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 2 through 26 )A2 - 26
2X-RAY DIFFRACTION2chain 'A' and (resid 27 through 86 )A27 - 86
3X-RAY DIFFRACTION3chain 'A' and (resid 87 through 131 )A87 - 131
4X-RAY DIFFRACTION4chain 'A' and (resid 132 through 155 )A132 - 155
5X-RAY DIFFRACTION5chain 'A' and (resid 156 through 196 )A156 - 196
6X-RAY DIFFRACTION6chain 'A' and (resid 197 through 217 )A197 - 217
7X-RAY DIFFRACTION7chain 'A' and (resid 218 through 252 )A218 - 252
8X-RAY DIFFRACTION8chain 'A' and (resid 253 through 280 )A253 - 280
9X-RAY DIFFRACTION9chain 'A' and (resid 281 through 294 )A281 - 294
10X-RAY DIFFRACTION10chain 'B' and (resid 6 through 22 )B6 - 22
11X-RAY DIFFRACTION11chain 'B' and (resid 23 through 110 )B23 - 110
12X-RAY DIFFRACTION12chain 'B' and (resid 111 through 127 )B111 - 127
13X-RAY DIFFRACTION13chain 'B' and (resid 128 through 239 )B128 - 239
14X-RAY DIFFRACTION14chain 'B' and (resid 240 through 253 )B240 - 253

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