[English] 日本語
Yorodumi
- PDB-3r9s: Structure of a carnitinyl-CoA dehydratase from Mycobacterium avium 104 -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 3r9s
TitleStructure of a carnitinyl-CoA dehydratase from Mycobacterium avium 104
ComponentsCarnitinyl-CoA dehydratase
KeywordsLYASE / SSGCID / Seattle Structural Genomics Center for Infectious Disease / carnitinyl-CoA dehydratase
Function / homology
Function and homology information


Lyases; Carbon-oxygen lyases; Hydro-lyases / enoyl-CoA hydratase activity
Similarity search - Function
Lyase 2-enoyl-coa Hydratase, Chain A, domain 2 / Lyase 2-enoyl-coa Hydratase; Chain A, domain 2 / Enoyl-CoA hydratase, C-terminal / Enoyl-CoA hydratase/isomerase, conserved site / Enoyl-CoA hydratase/isomerase signature. / Enoyl-CoA hydratase/isomerase / Enoyl-CoA hydratase/isomerase / 2-enoyl-CoA Hydratase; Chain A, domain 1 / 2-enoyl-CoA Hydratase; Chain A, domain 1 / ClpP/crotonase-like domain superfamily ...Lyase 2-enoyl-coa Hydratase, Chain A, domain 2 / Lyase 2-enoyl-coa Hydratase; Chain A, domain 2 / Enoyl-CoA hydratase, C-terminal / Enoyl-CoA hydratase/isomerase, conserved site / Enoyl-CoA hydratase/isomerase signature. / Enoyl-CoA hydratase/isomerase / Enoyl-CoA hydratase/isomerase / 2-enoyl-CoA Hydratase; Chain A, domain 1 / 2-enoyl-CoA Hydratase; Chain A, domain 1 / ClpP/crotonase-like domain superfamily / Alpha-Beta Complex / Orthogonal Bundle / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
BENZOIC ACID / Carnitinyl-CoA dehydratase / Carnitinyl-CoA dehydratase
Similarity search - Component
Biological speciesMycobacterium avium (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.2 Å
AuthorsSeattle Structural Genomics Center for Infectious Disease (SSGCID)
CitationJournal: Tuberculosis (Edinb) / Year: 2015
Title: Increasing the structural coverage of tuberculosis drug targets.
Authors: Baugh, L. / Phan, I. / Begley, D.W. / Clifton, M.C. / Armour, B. / Dranow, D.M. / Taylor, B.M. / Muruthi, M.M. / Abendroth, J. / Fairman, J.W. / Fox, D. / Dieterich, S.H. / Staker, B.L. / ...Authors: Baugh, L. / Phan, I. / Begley, D.W. / Clifton, M.C. / Armour, B. / Dranow, D.M. / Taylor, B.M. / Muruthi, M.M. / Abendroth, J. / Fairman, J.W. / Fox, D. / Dieterich, S.H. / Staker, B.L. / Gardberg, A.S. / Choi, R. / Hewitt, S.N. / Napuli, A.J. / Myers, J. / Barrett, L.K. / Zhang, Y. / Ferrell, M. / Mundt, E. / Thompkins, K. / Tran, N. / Lyons-Abbott, S. / Abramov, A. / Sekar, A. / Serbzhinskiy, D. / Lorimer, D. / Buchko, G.W. / Stacy, R. / Stewart, L.J. / Edwards, T.E. / Van Voorhis, W.C. / Myler, P.J.
History
DepositionMar 25, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 13, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Apr 22, 2015Group: Database references
Revision 1.3Nov 8, 2017Group: Refinement description / Category: software
Revision 1.4Sep 13, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Carnitinyl-CoA dehydratase
B: Carnitinyl-CoA dehydratase
C: Carnitinyl-CoA dehydratase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)84,9849
Polymers84,4923
Non-polymers4936
Water8,161453
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area10020 Å2
ΔGint-15 kcal/mol
Surface area27570 Å2
MethodPISA
Unit cell
Length a, b, c (Å)76.740, 74.961, 76.982
Angle α, β, γ (deg.)90.00, 112.76, 90.00
Int Tables number4
Space group name H-MP1211

-
Components

#1: Protein Carnitinyl-CoA dehydratase


Mass: 28163.941 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium avium (bacteria) / Strain: 104 / Gene: MAV_1277 / Production host: Escherichia coli (E. coli)
References: UniProt: A0QC84, UniProt: A0A0H2ZTH2*PLUS, Lyases; Carbon-oxygen lyases; Hydro-lyases
#2: Chemical ChemComp-BEZ / BENZOIC ACID


Mass: 122.121 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C7H6O2
#3: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C2H6O2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 453 / 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: 2.42 Å3/Da / Density % sol: 49.1 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop
Details: 20% PEG3350, cryoprotectant: 25% ethylene glycol, VAPOR DIFFUSION, SITTING DROP, temperature 289K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.1 / Wavelength: 0.97
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Jan 23, 2011
RadiationMonochromator: asymmetric curved crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97 Å / Relative weight: 1
ReflectionResolution: 2.2→50 Å / Num. obs: 40794 / % possible obs: 99.5 % / Redundancy: 3.7 % / Rmerge(I) obs: 0.095 / Χ2: 1.008 / Net I/σ(I): 8
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
2.2-2.243.70.37420460.962199.8
2.24-2.283.70.33720051.06199.4
2.28-2.323.70.3120241.034199.7
2.32-2.373.70.28320341.055199.7
2.37-2.423.70.24720241.046199.8
2.42-2.483.70.23320551.069199.5
2.48-2.543.80.21819841.046199.8
2.54-2.613.80.19820541.034199.6
2.61-2.693.70.18220461.034199.6
2.69-2.773.70.16220241.007199.3
2.77-2.873.70.1420311.01199.4
2.87-2.993.70.12620541.017199.6
2.99-3.123.70.11420250.927199.7
3.12-3.293.70.09720480.93199.2
3.29-3.493.70.08820230.924198.9
3.49-3.763.70.08520220.953199
3.76-4.143.60.07720370.956198.9
4.14-4.743.60.07120620.949199
4.74-5.973.60.06120811.048199.6
5.97-503.70.04321151.0791100

-
Phasing

PhasingMethod: molecular replacement
Phasing MRRfactor: 40.48 / Model details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation2.5 Å48.68 Å
Translation2.5 Å48.68 Å

-
Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
PHASER2.1.4phasing
REFMACrefinement
PDB_EXTRACT3.1data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3R0O

3r0o


Resolution: 2.2→50 Å / Cor.coef. Fo:Fc: 0.952 / Cor.coef. Fo:Fc free: 0.931 / WRfactor Rfree: 0.2348 / WRfactor Rwork: 0.1789 / Occupancy max: 1 / Occupancy min: 0.5 / FOM work R set: 0.855 / SU B: 11.459 / SU ML: 0.133 / SU R Cruickshank DPI: 0.2531 / SU Rfree: 0.2012 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.253 / ESU R Free: 0.201 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : RESIDUAL ONLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2265 2051 5 %RANDOM
Rwork0.1742 ---
obs0.1768 40699 99.2 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso max: 88.72 Å2 / Biso mean: 43.6708 Å2 / Biso min: 22.72 Å2
Baniso -1Baniso -2Baniso -3
1-1.82 Å20 Å20.57 Å2
2---1.71 Å20 Å2
3---0.33 Å2
Refinement stepCycle: LAST / Resolution: 2.2→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5518 0 34 453 6005
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0225695
X-RAY DIFFRACTIONr_bond_other_d0.0010.023701
X-RAY DIFFRACTIONr_angle_refined_deg1.2411.9677767
X-RAY DIFFRACTIONr_angle_other_deg0.92139010
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.685780
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.85323.498223
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.57215813
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.7781548
X-RAY DIFFRACTIONr_chiral_restr0.0710.2901
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0216603
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021127
X-RAY DIFFRACTIONr_mcbond_it0.5381.53847
X-RAY DIFFRACTIONr_mcbond_other0.1191.51584
X-RAY DIFFRACTIONr_mcangle_it1.00226045
X-RAY DIFFRACTIONr_scbond_it1.73431848
X-RAY DIFFRACTIONr_scangle_it2.7974.51715
LS refinement shellResolution: 2.2→2.257 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.272 153 -
Rwork0.211 2798 -
all-2951 -
obs--98.43 %
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)
10.7764-0.0218-0.06430.2174-0.05540.76020.00120.03780.0074-0.03360.01410.06560.0164-0.075-0.01530.008-0.0055-0.01890.02430.00990.0487-19.0221-7.6007-31.2107
21.3021-0.1903-0.52610.6242-0.29410.7563-0.0392-0.12650.01590.10040.0111-0.0613-0.01250.10320.02810.0259-0.0048-0.00720.0419-0.00630.0072-2.5321-16.6684-3.8619
31.0532-0.16940.12990.9420.07030.6458-0.00360.07630.0133-0.1502-0.0094-0.019-0.00480.06560.0130.02530.00130.00370.03860.01350.005915.2195-11.7255-31.7657
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A4 - 263
2X-RAY DIFFRACTION2B4 - 263
3X-RAY DIFFRACTION3C4 - 263

+
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://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