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- PDB-6coj: Crystal structure of Rhodococcus jostii RHA1 IpdAB E105A COCHEA-C... -

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Basic information

Entry
Database: PDB / ID: 6coj
TitleCrystal structure of Rhodococcus jostii RHA1 IpdAB E105A COCHEA-COA complex
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
Chem-F8G / 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: 1.4 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)62,5376
Polymers61,2732
Non-polymers1,2644
Water12,755708
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)125,07412
Polymers122,5464
Non-polymers2,5288
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_555y,x,-z1
Buried area14630 Å2
ΔGint-83 kcal/mol
Surface area37510 Å2
MethodPISA
Unit cell
Length a, b, c (Å)69.172, 69.172, 241.873
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
11A-740-

HOH

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Components

#1: Protein Probable CoA-transferase alpha subunit


Mass: 33735.230 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_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 (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.: 3 / Source method: obtained synthetically / Formula: SO4
#4: Chemical ChemComp-F8G / S-{(3R,5R,9R)-1-[(2R,3S,4R,5R)-5-(6-amino-9H-purin-9-yl)-4-hydroxy-3-(phosphonooxy)tetrahydrofuran-2-yl]-3,5,9-trihydroxy-8,8-dimethyl-3,5-dioxido-10,14-dioxo-2,4,6-trioxa-11,15-diaza-3lambda~5~,5lambda~5~-diphosphaheptadecan-17-yl} (5R,10R)-7-hydroxy-10-methyl-2-oxo-1-oxaspiro[4.5]dec-6-ene-6-carbothioate (non-preferred name)


Mass: 975.745 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C32H48N7O20P3S / Feature type: SUBJECT OF INVESTIGATION
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 708 / 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: 2.45 Å3/Da / Density % sol: 49.72 %
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: 0.97874 Å
DetectorType: RAYONIX MX300HE / Detector: CCD / Date: Dec 16, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97874 Å / Relative weight: 1
ReflectionResolution: 1.4→48.912 Å / Num. obs: 116084 / % possible obs: 100 % / Redundancy: 7.1 % / Biso Wilson estimate: 16.09 Å2 / CC1/2: 1 / Rmerge(I) obs: 0.0541 / Net I/σ(I): 20.62
Reflection shellResolution: 1.4→1.45 Å / Rmerge(I) obs: 1.336 / Num. unique obs: 11331 / CC1/2: 0.624

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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: 6CO6

6co6


Resolution: 1.4→48.912 Å / SU ML: 0.14 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 17.75 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1735 5804 5 %
Rwork0.1525 110245 -
obs0.1535 116049 99.57 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 203.96 Å2 / Biso mean: 24.6529 Å2 / Biso min: 10.96 Å2
Refinement stepCycle: final / Resolution: 1.4→48.912 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4152 0 78 716 4946
Biso mean--65.8 39.74 -
Num. residues----543
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 30

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.4-1.41590.2941880.29043573376198
1.4159-1.43260.28951890.27933582377199
1.4326-1.450.25421900.26143605379599
1.45-1.46840.25731890.25063592378199
1.4684-1.48770.27281890.24143602379199
1.4877-1.50810.25251910.22673618380999
1.5081-1.52970.24261900.22133610380099
1.5297-1.55250.24141900.19793613380399
1.5525-1.57670.22291920.19163636382899
1.5767-1.60260.21481890.18753606379599
1.6026-1.63020.23161920.171836353827100
1.6302-1.65990.19251900.16823613380399
1.6599-1.69180.18641920.160536403832100
1.6918-1.72630.18971910.162736323823100
1.7263-1.76390.18271920.154936483840100
1.7639-1.80490.16541920.152336463838100
1.8049-1.85010.19221930.153936673860100
1.8501-1.90010.18961920.156236583850100
1.9001-1.9560.21571940.165636703864100
1.956-2.01910.15271930.14536693862100
2.0191-2.09130.16731950.139437053900100
2.0913-2.1750.15571950.14336953890100
2.175-2.2740.16171920.152436693861100
2.274-2.39390.16451960.145337213917100
2.3939-2.54390.17941960.146937223918100
2.5439-2.74030.16681970.14437363933100
2.7403-3.0160.18991970.147937573954100
3.016-3.45230.15012000.138837983998100
3.4523-4.34920.13012030.115838464049100
4.3492-48.94180.15572150.144540814296100
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)
12.66420.59970.60370.58910.65742.3083-00.2974-0.2414-0.04950.0259-0.11870.05090.3006-0.04140.1775-0.04870.02490.2204-0.00790.1493.9898-18.0623-21.4491
21.49520.114-0.09150.73770.01221.3794-0.02950.2795-0.0505-0.1640.01350.0139-0.0702-0.10390.0050.1792-0.0514-0.00410.213-0.00870.0886-13.9376-8.6497-25.5276
33.4196-2.21140.69782.1795-1.12140.7261-0.0077-0.0434-0.097-0.02370.03870.06690.0686-0.0892-0.0120.1513-0.0754-0.00070.1611-0.00390.0983-19.5373-15.9218-6.8383
42.39240.6216-1.81821.242-2.14569.06610.0208-0.0692-0.0554-0.03990.06820.07250.245-0.4321-0.0810.1667-0.1135-0.0260.2103-0.00050.1489-29.6323-19.4886-4.0646
51.0618-0.0042-0.0220.54450.07770.8284-0.02460.01340.0132-0.03290.009-0.054-0.02290.07220.01530.1485-0.06310.00390.15740.00270.0854-5.1853-10.7133-11.4319
66.26731.26751.24480.80060.10864.16220.04340.13920.0345-0.0795-0.1142-0.2172-0.37450.60350.0430.1438-0.11420.04030.21750.02330.09577.8705-8.4987-12.5159
71.1121-0.84370.21871.2327-0.35612.0175-0.0309-0.0477-0.02790.16940.0105-0.0529-0.16210.07070.03440.1672-0.07260.01080.22510.01360.13093.6142-10.0781-6.132
82.3944-2.0050.6023.3889-1.08091.31480.01160.15150.2241-0.156-0.0564-0.2429-0.22690.19780.06610.2197-0.10370.00920.21330.01730.1250.18580.5935-21.3205
92.10840.89772.12281.76091.05554.0161-0.26240.3946-0.0865-0.91590.21150.0181-0.5430.130.05410.4551-0.15520.01920.35750.01050.1438-9.05461.3155-37.2091
107.9968-5.8994-1.13972.0097-0.7522.6014-0.05380.50960.4451-0.1489-0.2652-0.5591-0.14010.18230.34360.3234-0.1515-0.02280.33320.03920.18161.80215.6613-34.0055
113.8856-0.63671.90213.4886-3.52365.7464-0.038-0.07070.10510.23010.1270.2825-0.2179-0.3523-0.0830.14270.01140.02780.1923-0.0130.1692-33.583320.1909-8.761
120.48960.0670.27670.83380.05860.97620.02760.06660.02330.04660.00610.04150.0198-0.0919-0.02710.1248-0.04490.01020.16050.00890.1139-23.89594.5578-8.2135
132.7547-0.92130.58974.67550.85980.37960.08490.1647-0.1199-0.2819-0.12480.44730.1824-0.26320.02740.119-0.0875-0.01390.3142-0.00790.1462-38.3009-0.4395-17.6934
140.6425-0.26630.06832.3383-0.6530.46030.026-0.0703-0.07480.11990.00050.27890.149-0.251-0.01920.176-0.10010.02550.3067-0.00090.1706-39.1848-0.3896-5.2598
151.71070.76350.41473.97370.36592.0212-0.01380.14810.2956-0.1221-0.04960.6956-0.1264-0.71980.0430.0944-0.0262-0.00780.44180.01590.2951-47.199112.3595-14.5026
166.51363.9445-0.64333.8404-0.42731.9462-0.0895-0.24030.54530.2424-0.02520.4355-0.2729-0.37010.09630.16350.05580.01060.1736-0.03290.1866-32.641325.653-4.9809
172.75412.2893.57917.95872.97872.0264-0.13090.35570.0382-0.43750.25730.1213-0.3775-0.0732-0.17940.1476-0.01950.02890.19970.03140.1146-25.411221.3448-16.5383
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 104 )A27 - 104
3X-RAY DIFFRACTION3chain 'A' and (resid 105 through 131 )A105 - 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 231 )A218 - 231
8X-RAY DIFFRACTION8chain 'A' and (resid 232 through 252 )A232 - 252
9X-RAY DIFFRACTION9chain 'A' and (resid 253 through 280 )A253 - 280
10X-RAY DIFFRACTION10chain 'A' and (resid 281 through 296 )A281 - 296
11X-RAY DIFFRACTION11chain 'B' and (resid 6 through 22 )B6 - 22
12X-RAY DIFFRACTION12chain 'B' and (resid 23 through 141 )B23 - 141
13X-RAY DIFFRACTION13chain 'B' and (resid 142 through 163 )B142 - 163
14X-RAY DIFFRACTION14chain 'B' and (resid 164 through 195 )B164 - 195
15X-RAY DIFFRACTION15chain 'B' and (resid 196 through 222 )B196 - 222
16X-RAY DIFFRACTION16chain 'B' and (resid 223 through 239 )B223 - 239
17X-RAY DIFFRACTION17chain 'B' and (resid 240 through 253 )B240 - 253

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