[English] 日本語
Yorodumi
- PDB-1e83: Cytochrome c' from Alcaligenes xylosoxidans - oxidized structure -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1.0E+83
TitleCytochrome c' from Alcaligenes xylosoxidans - oxidized structure
ComponentsCYTOCHROME C'
KeywordsELECTRON TRANSPORT / HEME / 4-HELIX BUNDLE
Function / homology
Function and homology information


electron transport chain / periplasmic space / electron transfer activity / 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 XYLOSOXIDANS (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.05 Å
AuthorsLawson, D.M. / Stevenson, C.E.M. / Andrew, C.R. / Eady, R.R.
Citation
Journal: Embo J. / Year: 2000
Title: Unprecedented Proximal Binding of Nitric Oxide to Heme: Implications for Guanylate Cyclase
Authors: Lawson, D.M. / Stevenson, C.E.M. / Andrew, C.R. / Eady, R.R.
#1: Journal: Acta Crystallogr.,Sect.D / Year: 1996
Title: Three-Dimensional Structure of Cytochrome C' from Two Alcaligenes Species and the Implications for Four-Helix Bundle Structures.
Authors: Dobbs, A.J. / Anderson, B.F. / Faber, H.R. / Baker, E.N.
History
DepositionSep 15, 2000Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 6, 2000Provider: repository / Type: Initial release
Revision 1.1Feb 19, 2014Group: Database references / Derived calculations ...Database references / Derived calculations / Non-polymer description / Other / Structure summary / Version format compliance
Revision 1.2May 8, 2019Group: Data collection / Derived calculations ...Data collection / Derived calculations / Experimental preparation / Other
Category: database_PDB_rev / database_PDB_rev_record ...database_PDB_rev / database_PDB_rev_record / exptl_crystal_grow / pdbx_database_proc / pdbx_database_status / struct_conn
Item: _exptl_crystal_grow.method / _pdbx_database_status.recvd_author_approval / _struct_conn.pdbx_leaving_atom_flag
Revision 1.3Oct 23, 2019Group: Data collection / Database references / Other / Category: pdbx_database_status / struct_ref_seq_dif
Item: _pdbx_database_status.status_code_sf / _struct_ref_seq_dif.details
Revision 2.0Mar 11, 2020Group: Polymer sequence / Category: entity_poly / Item: _entity_poly.pdbx_seq_one_letter_code_can
Revision 2.1Dec 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_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 2.2Nov 13, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: CYTOCHROME C'
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,2502
Polymers13,6311
Non-polymers6191
Water2,756153
1
A: CYTOCHROME C'
hetero molecules

A: CYTOCHROME C'
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,5004
Polymers27,2632
Non-polymers1,2372
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation11_555-x+y,y,-z+1/21
Buried area2850 Å2
ΔGint-15 kcal/mol
Surface area14760 Å2
MethodPQS
Unit cell
Length a, b, c (Å)52.946, 52.946, 182.346
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number179
Space group name H-MP6522

-
Components

#1: Protein CYTOCHROME C'


Mass: 13631.442 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: FORMERLY KNOWN AS ALCALIGENES SP. / Source: (natural) ALCALIGENES XYLOSOXIDANS (bacteria) / Cellular location: PERIPLASM / Strain: NCIB 11015 / 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.: 153 / Source method: isolated from a natural source / Formula: H2O
Compound detailsCYTOCHROME C' IS THE MOST WIDELY OCCURRING BACTERIAL C-TYPE CYTOCHROME. CYTOCHROMES C'
Has protein modificationY
Sequence detailsN-TERMINAL RESIDUE IS PYRROLIDONE CARBOXYLIC ACID (PCA)

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 2

-
Sample preparation

CrystalDensity Matthews: 2.71 Å3/Da / Density % sol: 54.3 %
Crystal growMethod: vapor diffusion, hanging drop / pH: 7.5
Details: HANGING DROP VAPOUR DIFFUSION. PROTEIN AT CONCENTRATION 8 MG/ML WAS MIXED WITH AN EQUAL VOLUME OF WELL SOLUTION CONSISTING OF 55-65% SATURATED AMMONIUM SULFATE IN 100 MM HEPES BUFFER AT PH 7.5
Crystal grow
*PLUS
Temperature: 4 ℃ / pH: 7.2 / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
18 mg/mlprotein1drop
220 mMTris-HCl1drop
355-65 %satammonium sulfate1reservoir
4100 mMHEPES1reservoir

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SRS / Beamline: PX7.2 / Wavelength: 1.488
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Nov 15, 1997 / Details: MIRRORS
RadiationMonochromator: GE(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.488 Å / Relative weight: 1
ReflectionResolution: 2.05→40 Å / Num. obs: 10205 / % possible obs: 99 % / Observed criterion σ(I): -3 / Redundancy: 8.1 % / Biso Wilson estimate: 23 Å2 / Rmerge(I) obs: 0.109 / Net I/σ(I): 18.8
Reflection shellResolution: 2.05→2.12 Å / Rmerge(I) obs: 0.349 / Mean I/σ(I) obs: 5.2 / % possible all: 98.9
Reflection shell
*PLUS
% possible obs: 98.9 %

-
Processing

Software
NameClassification
REFMACrefinement
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1CGO

1cgo


Resolution: 2.05→40 Å / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.18 / ESU R Free: 0.18
Details: FE ATOM OF HEME REFINED WITH ANISOTROPIC THERMAL PARAMETERS
RfactorNum. reflection% reflectionSelection details
Rfree0.252 497 5 %RANDOM
Rwork0.192 ---
obs-10205 99 %-
Displacement parametersBiso mean: 23 Å2
Refinement stepCycle: LAST / Resolution: 2.05→40 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms935 0 43 153 1131
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONp_bond_d0.0170.02
X-RAY DIFFRACTIONp_angle_d0.0370.04
X-RAY DIFFRACTIONp_angle_deg
X-RAY DIFFRACTIONp_planar_d0.0390.05
X-RAY DIFFRACTIONp_hb_or_metal_coord
X-RAY DIFFRACTIONp_mcbond_it2.8133
X-RAY DIFFRACTIONp_mcangle_it3.1515
X-RAY DIFFRACTIONp_scbond_it5.9916
X-RAY DIFFRACTIONp_scangle_it6.548
X-RAY DIFFRACTIONp_plane_restr0.03270.04
X-RAY DIFFRACTIONp_chiral_restr0.1340.15
X-RAY DIFFRACTIONp_singtor_nbd0.1760.3
X-RAY DIFFRACTIONp_multtor_nbd0.2660.3
X-RAY DIFFRACTIONp_xhyhbond_nbd
X-RAY DIFFRACTIONp_xyhbond_nbd0.2030.3
X-RAY DIFFRACTIONp_planar_tor5.57
X-RAY DIFFRACTIONp_staggered_tor13.715
X-RAY DIFFRACTIONp_orthonormal_tor
X-RAY DIFFRACTIONp_transverse_tor28.720
X-RAY DIFFRACTIONp_special_tor
Software
*PLUS
Name: REFMAC / Classification: refinement
Refinement
*PLUS
Rfactor obs: 0.192
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://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