[English] 日本語
Yorodumi
- PDB-1n1c: Crystal Structure Of The Dimeric TorD Chaperone From Shewanella M... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1n1c
TitleCrystal Structure Of The Dimeric TorD Chaperone From Shewanella Massilia
ComponentsTorA specific chaperone
KeywordsCHAPERONE / TORD / 3D-domain swapping
Function / homology
Function and homology information


protein complex oligomerization / protein folding / cytoplasm
Similarity search - Function
Four Helix Bundle (Hemerythrin (Met), subunit A) - #1820 / Chaperone TorD / HscB, C-terminal domain superfamily / HscB, C-terminal domain / : / DMSO/Nitrate reductase chaperone / TorD-like superfamily / Nitrate reductase delta subunit / Monooxygenase / Four Helix Bundle (Hemerythrin (Met), subunit A) ...Four Helix Bundle (Hemerythrin (Met), subunit A) - #1820 / Chaperone TorD / HscB, C-terminal domain superfamily / HscB, C-terminal domain / : / DMSO/Nitrate reductase chaperone / TorD-like superfamily / Nitrate reductase delta subunit / Monooxygenase / Four Helix Bundle (Hemerythrin (Met), subunit A) / Up-down Bundle / Mainly Alpha
Similarity search - Domain/homology
2,3-DIHYDROXY-1,4-DITHIOBUTANE / Chaperone protein TorD
Similarity search - Component
Biological speciesShewanella massilia (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.4 Å
AuthorsTranier, S. / Iobbi-Nivol, C. / Mortier-Barriere, I. / Birck, C. / Mejean, V. / Samama, J.-P.
Citation
Journal: Structure / Year: 2003
Title: A Novel Protein Fold and Extreme Domain Swapping in the Dimeric TorD Chaperone from Shewanella massilia
Authors: Tranier, S. / Iobbi-Nivol, C. / Birck, C. / Ilbert, M. / Mortier-Barriere, I. / Mejean, V. / Samama, J.P.
#1: Journal: Protein Sci. / Year: 2002
Title: Characterization And Multiple Molecular Forms Of TorD From Shewanella Massilia, The Putative Chaperone Of The Molybdoenzyme TorA
Authors: Tranier, S. / Mortier-Barriere, I. / Ilbert, M. / Birck, C. / Iobbi-Nivol, C. / Mejean, V. / Samama, J.-P.
#2: Journal: J.Biol.Chem. / Year: 1998
Title: TorD, a cytoplasmic chaperone that interacts with the unfolded trimethylamine N-oxide reductase enzyme (TorA) in Escherichia coli
Authors: Pommier, J. / Mejean, V. / Giordano, G. / Iobbi-Nivol, C.
History
DepositionOct 17, 2002Deposition site: RCSB / Processing site: PDBJ
Revision 1.0May 13, 2003Provider: repository / Type: Initial release
Revision 1.1Apr 28, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Nov 10, 2021Group: Data collection / Database references / Derived calculations
Category: database_2 / diffrn_source ...database_2 / diffrn_source / struct_conn / 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 / _diffrn_source.pdbx_synchrotron_site / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Oct 30, 2024Group: Data collection / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_entry_details / pdbx_modification_feature

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: TorA specific chaperone
B: TorA specific chaperone
hetero molecules


Theoretical massNumber of molelcules
Total (without water)49,6174
Polymers49,3092
Non-polymers3092
Water2,594144
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area10260 Å2
ΔGint-101 kcal/mol
Surface area19730 Å2
MethodPISA
Unit cell
Length a, b, c (Å)65.958, 93.441, 95.136
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

-
Components

#1: Protein TorA specific chaperone


Mass: 24654.322 Da / Num. of mol.: 2 / Mutation: H8P/F147C/F163V
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Shewanella massilia (bacteria) / Gene: torD / Plasmid: pet-22b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21-DE3-PLYSS / References: UniProt: O87949
#2: Chemical ChemComp-DTT / 2,3-DIHYDROXY-1,4-DITHIOBUTANE / 1,4-DITHIOTHREITOL


Mass: 154.251 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C4H10O2S2
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 144 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 3.08 Å3/Da / Density % sol: 59.75 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 6.4
Details: ammonium sulfate 1.6M, MES 100mM; Crystals were obtained by mixing 1 microl (1.2mg.ml-1) of protein solution with an equal volume of reservoir solution; Crystal Size (300x200x100 microM3), ...Details: ammonium sulfate 1.6M, MES 100mM; Crystals were obtained by mixing 1 microl (1.2mg.ml-1) of protein solution with an equal volume of reservoir solution; Crystal Size (300x200x100 microM3), pH 6.4, VAPOR DIFFUSION, HANGING DROP, temperature 277K
Crystal grow
*PLUS
Temperature: 4 ℃ / pH: 8
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetailsChemical formula
11.2 mg/mlprotein1drop
220 mMTris-HCl1droppH8.0
3240 mM1dropNaCl
410 mMdithiothreitol1drop
51.7 Mammonium sulfate1reservoir
6100 mMMES1reservoirpH6.6

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: BW7A / Wavelength: 0.97856, 0.95370, 0.97872
DetectorType: MARRESEARCH / Detector: CCD / Date: Aug 21, 2000
RadiationMonochromator: DOUBLE CRYSTAL FOCUSSING MONOCHROMATOR / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.978561
20.95371
30.978721
ReflectionResolution: 2.4→54.2 Å / Num. all: 23325 / Num. obs: 23239 / % possible obs: 98.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.7 % / Biso Wilson estimate: 41.5 Å2 / Rmerge(I) obs: 0.033 / Net I/σ(I): 14
Reflection shellResolution: 2.4→2.53 Å / Redundancy: 3.7 % / Rmerge(I) obs: 0.177 / Mean I/σ(I) obs: 3.6 / Num. unique all: 3365 / % possible all: 98.9
Reflection
*PLUS
Highest resolution: 2.4 Å / Lowest resolution: 54.23 Å / Num. measured all: 85570
Reflection shell
*PLUS
% possible obs: 98.9 % / Mean I/σ(I) obs: 3.6

-
Processing

Software
NameVersionClassification
MOSFLMdata reduction
SCALAdata scaling
SOLVEphasing
CNS1refinement
CCP4(SCALA)data scaling
RefinementMethod to determine structure: MAD / Resolution: 2.4→19.96 Å / Rfactor Rfree error: 0.008 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.255 1119 4.8 %RANDOM
Rwork0.224 ---
obs0.224 23149 98.1 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 40.4924 Å2 / ksol: 0.341965 e/Å3
Displacement parametersBiso mean: 43.8 Å2
Baniso -1Baniso -2Baniso -3
1-10.14 Å20 Å20 Å2
2---1.81 Å20 Å2
3----8.32 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.35 Å0.31 Å
Luzzati d res low-5 Å
Luzzati sigma a0.32 Å0.28 Å
Refinement stepCycle: LAST / Resolution: 2.4→19.96 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3115 0 16 144 3275
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.007
X-RAY DIFFRACTIONc_angle_deg1.2
X-RAY DIFFRACTIONc_dihedral_angle_d19.7
X-RAY DIFFRACTIONc_improper_angle_d0.87
X-RAY DIFFRACTIONc_mcbond_it0.993
X-RAY DIFFRACTIONc_mcangle_it1.775
X-RAY DIFFRACTIONc_scbond_it2.767
X-RAY DIFFRACTIONc_scangle_it3.9810
LS refinement shellResolution: 2.4→2.55 Å / Rfactor Rfree error: 0.023 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.304 178 4.7 %
Rwork0.29 3646 -
obs--99 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2WATER_REP.PARAMWATER.TOP
X-RAY DIFFRACTION3ION.PARAMION.TOP
Refinement
*PLUS
Highest resolution: 2.4 Å
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg19.7
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg0.87

+
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