[English] 日本語
Yorodumi
- PDB-1nbb: N-BUTYLISOCYANIDE BOUND RHODOBACTER CAPSULATUS CYTOCHROME C' -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1nbb
TitleN-BUTYLISOCYANIDE BOUND RHODOBACTER CAPSULATUS CYTOCHROME C'
ComponentsCYTOCHROME C'
KeywordsELECTRON TRANSPORT (HEME PROTEIN) / ELECTRON TRANSPORT / CYTOCHROME / HEME PROTEIN
Function / homology
Function and homology information


electron transfer activity / periplasmic space / iron ion binding / heme binding
Similarity search - Function
Cytochrome c prime, subgroup / Cytochrome c prime / Cytochrome c class II profile. / Cytochrome c, class II / Cytochrome C' / Cytochrome c/b562 / Cytochrome c/b562 / Four Helix Bundle (Hemerythrin (Met), subunit A) / Up-down Bundle / Mainly Alpha
Similarity search - Domain/homology
PROTOPORPHYRIN IX CONTAINING FE / N-BUTYL ISOCYANIDE / Cytochrome c'
Similarity search - Component
Biological speciesRhodobacter capsulatus (bacteria)
MethodX-RAY DIFFRACTION / Resolution: 2.4 Å
AuthorsTahirov, T.H. / Misaki, S. / Meyer, T.E. / Cusanovich, M.A. / Higuchi, Y. / Yasuoka, N.
Citation
Journal: Nat.Struct.Biol. / Year: 1996
Title: Concerted movement of side chains in the haem vicinity observed on ligand binding in cytochrome c' from rhodobacter capsulatus.
Authors: Tahirov, T.H. / Misaki, S. / Meyer, T.E. / Cusanovich, M.A. / Higuchi, Y. / Yasuoka, N.
#1: Journal: To be Published
Title: Crystal Structures of Cytochrome C' from Rhodobacter Capsulatus Strain St. Louis
Authors: Tahirov, T.H. / Misaki, S. / Meyer, T.E. / Cusanovich, M.A. / Yasuoka, N.
#2: Journal: J.Mol.Biol. / Year: 1996
Title: High-Resolution Crystal Structures of Two Polymorphs of Cytochrome C' from the Purple Phototrophic Bacterium Rhodobacter Capsulatus
Authors: Tahirov, T.H. / Misaki, S. / Meyer, T.E. / Cusanovich, M.A. / Higuchi, Y. / Yasuoka, N.
History
DepositionMar 18, 1996-
Revision 1.0Aug 17, 1996Provider: repository / Type: Initial release
Revision 1.1Mar 3, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: CYTOCHROME C'
B: CYTOCHROME C'
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,7096
Polymers26,3092
Non-polymers1,3994
Water1,820101
1
A: CYTOCHROME C'
hetero molecules


Theoretical massNumber of molelcules
Total (without water)13,8543
Polymers13,1551
Non-polymers7002
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: CYTOCHROME C'
hetero molecules


Theoretical massNumber of molelcules
Total (without water)13,8543
Polymers13,1551
Non-polymers7002
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)47.734, 70.535, 89.652
Angle α, β, γ (deg.)90.00, 87.02, 90.00
Int Tables number5
Space group name H-MI121

-
Components

#1: Protein CYTOCHROME C'


Mass: 13154.733 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Details: N-BUTYLISOCYANIDE BOUND TO HEME IRON / Source: (natural) Rhodobacter capsulatus (bacteria) / Strain: M110 / References: UniProt: P00147
#2: Chemical ChemComp-HEM / PROTOPORPHYRIN IX CONTAINING FE / HEME / Heme B


Mass: 616.487 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C34H32FeN4O4
#3: Chemical ChemComp-NBN / N-BUTYL ISOCYANIDE


Mass: 83.132 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C5H9N
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 101 / 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: 2.86 Å3/Da / Density % sol: 53 %
Crystal growpH: 6.5 / Details: pH 6.5
Crystal grow
*PLUS
Method: vapor diffusion, sitting drop / Details: Tahirov, T.H., (1996) J.Mol.Biol., 259, 467.
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
120 mg/mlprotein1drop
21.5 Msodium citrate1reservoir

-
Data collection

DiffractionMean temperature: 283 K
Diffraction sourceWavelength: 1.5418
DetectorDetector: IMAGE PLATE / Date: Sep 15, 1995 / Details: DOUBLE MIRROR
RadiationMonochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.4→30 Å / Num. obs: 49034 / % possible obs: 92 % / Observed criterion σ(I): 1 / Redundancy: 4.44 % / Rmerge(I) obs: 0.129 / Net I/σ(I): 9.28
Reflection shellResolution: 2.4→2.49 Å / Mean I/σ(I) obs: 3.1 / % possible all: 73
Reflection
*PLUS
Num. obs: 11056 / Num. measured all: 49034
Reflection shell
*PLUS
% possible obs: 73 % / Rmerge(I) obs: 0.261

-
Processing

Software
NameVersionClassification
X-PLOR2.1model building
X-PLOR2.1refinement
DENZOdata reduction
SCALEPACKdata scaling
X-PLOR2.1phasing
RefinementResolution: 2.4→6 Å / σ(F): 1
RfactorNum. reflection% reflection
Rwork0.174 --
obs0.174 9841 89.9 %
Displacement parametersBiso mean: 29.87 Å2
Refinement stepCycle: LAST / Resolution: 2.4→6 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1845 0 98 101 2044
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.012
X-RAY DIFFRACTIONx_bond_d_na
X-RAY DIFFRACTIONx_bond_d_prot
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_angle_d_na
X-RAY DIFFRACTIONx_angle_d_prot
X-RAY DIFFRACTIONx_angle_deg1.62
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d21.22
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d1.81
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it
X-RAY DIFFRACTIONx_mcangle_it
X-RAY DIFFRACTIONx_scbond_it
X-RAY DIFFRACTIONx_scangle_it
Software
*PLUS
Name: X-PLOR / Version: 2.1 / Classification: refinement
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_deg21.22
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg1.81

+
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