[English] 日本語
Yorodumi
- PDB-6co6: Crystal structure of Rhodococcus jostii RHA1 IpdAB -

+
Open data


ID or keywords:

Loading...

-
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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
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

-
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

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
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

-
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

-
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

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbjlvh1.pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more