[English] 日本語
Yorodumi
- PDB-5jve: L16I mutant of cytochrome c prime from Alcaligenes xylosoxidans: ... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 5jve
TitleL16I mutant of cytochrome c prime from Alcaligenes xylosoxidans: Ferrous state
ComponentsCytochrome c'
KeywordsELECTRON TRANSPORT / gas sensor / cytochrome / nitric oxide
Function / homology
Function and homology information


electron transport chain / electron transfer activity / periplasmic space / iron ion binding / heme binding
Similarity search - Function
Cytochrome c prime, subgroup / Cytochrome c, class II / Cytochrome c prime / Cytochrome C' / Cytochrome c class II profile. / Cytochrome c/b562 / Cytochrome c/b562 / Four Helix Bundle (Hemerythrin (Met), subunit A) / Up-down Bundle / Mainly Alpha
Similarity search - Domain/homology
HEME C / Cytochrome c'
Similarity search - Component
Biological speciesAlcaligenes xylosoxydans xylosoxydans (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.12 Å
AuthorsKekilli, D. / Strange, R.W. / Hough, M.A.
CitationJournal: Chem Sci / Year: 2017
Title: Engineering proximal vs. distal heme-NO coordination via dinitrosyl dynamics: implications for NO sensor design.
Authors: Kekilli, D. / Petersen, C.A. / Pixton, D.A. / Ghafoor, D.D. / Abdullah, G.H. / Dworkowski, F.S.N. / Wilson, M.T. / Heyes, D.J. / Hardman, S.J.O. / Murphy, L.M. / Strange, R.W. / Scrutton, N. ...Authors: Kekilli, D. / Petersen, C.A. / Pixton, D.A. / Ghafoor, D.D. / Abdullah, G.H. / Dworkowski, F.S.N. / Wilson, M.T. / Heyes, D.J. / Hardman, S.J.O. / Murphy, L.M. / Strange, R.W. / Scrutton, N.S. / Andrew, C.R. / Hough, M.A.
History
DepositionMay 11, 2016Deposition site: RCSB / Processing site: PDBE
Revision 1.0Mar 8, 2017Provider: repository / Type: Initial release
Revision 1.1Dec 6, 2017Group: Advisory / Database references / Refinement description
Category: citation / pdbx_unobs_or_zero_occ_atoms / software
Item: _citation.journal_id_ISSN / _citation.journal_volume ..._citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _software.name
Revision 2.0Mar 11, 2020Group: Derived calculations / Polymer sequence / Category: entity_poly / pdbx_struct_special_symmetry / Item: _entity_poly.pdbx_seq_one_letter_code_can
Revision 2.1Jan 10, 2024Group: Advisory / Data collection ...Advisory / 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 / pdbx_unobs_or_zero_occ_atoms
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 2.2Nov 13, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Cytochrome c'
hetero molecules


Theoretical massNumber of molelcules
Total (without water)13,9922
Polymers13,3731
Non-polymers6191
Water3,207178
1
A: Cytochrome c'
hetero molecules

A: Cytochrome c'
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,9834
Polymers26,7462
Non-polymers1,2372
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation10_665-y+1,-x+1,-z+1/61
Buried area3520 Å2
ΔGint-52 kcal/mol
Surface area12280 Å2
MethodPISA
Unit cell
Length a, b, c (Å)53.520, 53.520, 179.682
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number179
Space group name H-MP6522
Components on special symmetry positions
IDModelComponents
11A-1369-

HOH

-
Components

#1: Protein Cytochrome c'


Mass: 13373.082 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Alcaligenes xylosoxydans xylosoxydans (bacteria)
Plasmid: pet26b+ / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P00138
#2: Chemical ChemComp-HEC / HEME C


Mass: 618.503 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C34H34FeN4O4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 178 / 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: 2.02 Å3/Da / Density % sol: 55.72 %
Crystal growTemperature: 294 K / Method: vapor diffusion, hanging drop / pH: 7.5 / Details: 2.2M Ammonium sulfate, 0.1 M HEPES pH 7.5

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 0.9 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Jul 10, 2015
RadiationMonochromator: Silicon / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9 Å / Relative weight: 1
ReflectionResolution: 1.1→44.8 Å / Num. obs: 61939 / % possible obs: 98.7 % / Redundancy: 5.5 % / CC1/2: 0.998 / Rmerge(I) obs: 0.064 / Net I/σ(I): 9.6
Reflection shellResolution: 1.1→1.12 Å / Redundancy: 4.5 % / Rmerge(I) obs: 0.652 / Mean I/σ(I) obs: 1.5 / % possible all: 94.8

-
Processing

Software
NameVersionClassification
Aimless0.5.8data scaling
SHELXDEphasing
PDB_EXTRACT3.2data extraction
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2YLI

2yli


Resolution: 1.12→10 Å / Cross valid method: FREE R-VALUE / σ(F): 0
Details: ANISOTROPIC REFINEMENT REDUCED FREE R (NO CUTOFF) BY ?
RfactorNum. reflection% reflectionSelection details
Rfree0.181 --RANDOM
Rwork0.153 ---
obs-51996 42.5 %-
Displacement parametersBiso max: 68.89 Å2 / Biso mean: 18.1983 Å2 / Biso min: 8.7 Å2
Refinement stepCycle: final / Resolution: 1.12→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms940 0 43 183 1166
Biso mean--12.24 30.22 -
Num. residues----125
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONs_bond_d0.015
X-RAY DIFFRACTIONs_angle_d325
X-RAY DIFFRACTIONs_similar_dist0
X-RAY DIFFRACTIONs_from_restr_planes0.004
X-RAY DIFFRACTIONs_zero_chiral_vol53
X-RAY DIFFRACTIONs_non_zero_chiral_vol8
X-RAY DIFFRACTIONs_anti_bump_dis_restr0.035
X-RAY DIFFRACTIONs_rigid_bond_adp_cmpnt0
X-RAY DIFFRACTIONs_similar_adp_cmpnt0.041
X-RAY DIFFRACTIONs_approx_iso_adps0.121

+
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