[English] 日本語
Yorodumi
- PDB-1kng: Crystal structure of CcmG reducing oxidoreductase at 1.14 A -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1kng
TitleCrystal structure of CcmG reducing oxidoreductase at 1.14 A
ComponentsTHIOL:DISULFIDE INTERCHANGE PROTEIN CYCY
KeywordsOXIDOREDUCTASE / thioredoxin fold / cytochrome c maturation / atomic resolution
Function / homology
Function and homology information


cytochrome complex assembly / disulfide oxidoreductase activity / cell redox homeostasis / outer membrane-bounded periplasmic space
Similarity search - Function
Periplasmic protein thiol:disulphide oxidoreductase DsbE / Redoxin / Redoxin / Thioredoxin, conserved site / Thioredoxin family active site. / Thioredoxin domain profile. / Thioredoxin domain / Glutaredoxin / Glutaredoxin / Thioredoxin-like superfamily ...Periplasmic protein thiol:disulphide oxidoreductase DsbE / Redoxin / Redoxin / Thioredoxin, conserved site / Thioredoxin family active site. / Thioredoxin domain profile. / Thioredoxin domain / Glutaredoxin / Glutaredoxin / Thioredoxin-like superfamily / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Thiol:disulfide interchange protein CycY
Similarity search - Component
Biological speciesBradyrhizobium japonicum (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.14 Å
AuthorsEdeling, M.A. / Guddat, L.W. / Fabianek, R.A. / Thony-Meyer, L. / Martin, J.L.
Citation
Journal: Structure / Year: 2002
Title: Structure of CcmG/DsbE at 1.14 A resolution: high-fidelity reducing activity in an indiscriminately oxidizing environment
Authors: Edeling, M.A. / Guddat, L.W. / Fabianek, R.A. / Thony-Meyer, L. / Martin, J.L.
#1: Journal: Acta Crystallogr.,Sect.D / Year: 2001
Title: Crystallization and preliminary diffraction studies of native and selenomethionine CcmG (CycY, DsbE)
Authors: Edeling, M.A. / Guddat, L.W. / Fabianek, R.A. / Halliday, J.A. / Jones, A. / Thony-Meyer, L. / Martin, J.L.
#2: Journal: J.Biol.Chem. / Year: 1997
Title: Characterization of the Bradyrhizobium japonicum CycY protein, a membrane-anchored periplasmic thioredoxin that may play a role as a reductant in the biogenesis of c-type cytochromes
Authors: Fabianek, R.A. / Huber-Wunderlich, M. / Glockshuber, R. / Kunzler, P. / Hennecke, H. / Thony-Meyer, L.
#3: Journal: J.BACTERIOL. / Year: 1998
Title: The active-site cysteines of the periplasmic thioredoxin-like protein CcmG of Escherichia coli are important but not essential for cytochrome c maturation in vivo.
Authors: Fabianek, R.A. / Hennecke, H. / Thony-Meyer, L.
History
DepositionDec 18, 2001Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 17, 2002Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: THIOL:DISULFIDE INTERCHANGE PROTEIN CYCY


Theoretical massNumber of molelcules
Total (without water)16,8931
Polymers16,8931
Non-polymers00
Water2,774154
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)35.1, 48.2, 90.2
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

-
Components

#1: Protein THIOL:DISULFIDE INTERCHANGE PROTEIN CYCY / thioredoxin-like protein CcmG


Mass: 16893.371 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bradyrhizobium japonicum (bacteria) / Gene: cycy / Plasmid: pRJ2766 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P30960
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 154 / 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: 2.2 Å3/Da / Density % sol: 45 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 0.1M HEPES pH 6.5, 2% PEG 400, 2M ammonium sulfate, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal grow
*PLUS
Details: Edeling, M.A., (2001) Acta Crystallogr., Sect.D, 57, 1293.
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
140 mg/mlprotein1drop
20.1 MHEPES1reservoirpH6.5
32 %(v/v)PEG4001reservoir
42.0 Mammonium sulfate1reservoir

-
Data collection

Diffraction
IDMean temperature (K)Crystal-ID
12771
21
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL7-1 / Wavelength: 1.08 Å
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Feb 1, 1998
Radiation
IDMonochromatorProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
158 cm long, Pt-coated, fused silica, vertical focussing mirror, Cylindrically bent triangular Si(111) asymmetric cut, horizontal focus monochromatorSINGLE WAVELENGTHMx-ray1
2bent cylindrical Si-mirror (Rh coating), Si(111) double-crystal monochromatorMADMx-ray1
Radiation wavelengthWavelength: 1.08 Å / Relative weight: 1
ReflectionResolution: 1.14→20 Å / Num. all: 50056 / Num. obs: 50056 / % possible obs: 88.4 % / Observed criterion σ(I): 0 / Redundancy: 3.49 % / Rmerge(I) obs: 0.062 / Net I/σ(I): 17.6
Reflection shellResolution: 1.14→1.18 Å / Rmerge(I) obs: 0.291 / Mean I/σ(I) obs: 2.64 / Num. unique all: 4512 / % possible all: 80.8
Reflection
*PLUS
Lowest resolution: 20 Å
Reflection shell
*PLUS
% possible obs: 80.3 % / Mean I/σ(I) obs: 2.6

-
Processing

Software
NameClassification
DENZOdata reduction
SCALEPACKdata scaling
SOLVEphasing
SHARPphasing
SOLOMONphasing
SHELXL-97refinement
RefinementMethod to determine structure: MAD / Resolution: 1.14→20 Å / Num. parameters: 11353 / Num. restraintsaints: 7075 / Isotropic thermal model: anisotropic / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
Details: HYDROGENS WERE GENERATED ACCORDING TO THE RIDING MODEL WHICH IS BASED ON GEOMETRIC CRITERIA. TO GENERATE THE HYDROGENS REFER TO THE LYSOZYME TUTORIAL ON THE SHELX HOMEPAGE.
RfactorNum. reflection% reflectionSelection details
Rfree0.151 5037 10 %random
all-50042 --
obs-50042 88.4 %-
Solvent computationSolvent model: MOEWS & KRETSINGER
Refine analyzeNum. disordered residues: 8 / Occupancy sum hydrogen: 1018 / Occupancy sum non hydrogen: 1195
Refinement stepCycle: LAST / Resolution: 1.14→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1077 0 0 154 1231
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONs_bond_d0.014
X-RAY DIFFRACTIONs_angle_d0.03
X-RAY DIFFRACTIONs_zero_chiral_vol0.09
X-RAY DIFFRACTIONs_non_zero_chiral_vol0.082
X-RAY DIFFRACTIONs_anti_bump_dis_restr0.019
X-RAY DIFFRACTIONs_approx_iso_adps0.11
X-RAY DIFFRACTIONs_from_restr_planes0.029
X-RAY DIFFRACTIONs_similar_dist
X-RAY DIFFRACTIONs_rigid_bond_adp_cmpnt0.006
Software
*PLUS
Name: SHELXL / Version: 97 / Classification: refinement
Refinement
*PLUS
Highest resolution: 2.1 Å / Lowest resolution: 20 Å / Num. reflection obs: 45005 / % reflection Rfree: 10 % / Rfactor Rwork: 0.118
Solvent computation
*PLUS
Displacement parameters
*PLUS

+
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