[English] 日本語
Yorodumi
- PDB-1i8o: RHODOPSEUDOMONAS PALUSTRIS CYT C2 AMMONIA COMPLEX AT 1.15 ANGSTRO... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1i8o
TitleRHODOPSEUDOMONAS PALUSTRIS CYT C2 AMMONIA COMPLEX AT 1.15 ANGSTROM RESOLUTION
ComponentsCYTOCHROME C2
KeywordsELECTRON TRANSPORT / CYTOCHROME / HEME / AMMONIA / OXIDIZED
Function / homology
Function and homology information


photosynthesis / electron transfer activity / heme binding / metal ion binding
Similarity search - Function
Cytochrome c, class IA/ IB / Cytochrome c / Cytochrome c-like domain / Cytochrome Bc1 Complex; Chain D, domain 2 / Cytochrome c family profile. / Cytochrome c-like domain / Cytochrome c-like domain superfamily / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
HEME C / AMMONIA / Cytochrome c2
Similarity search - Component
Biological speciesRhodopseudomonas palustris (phototrophic)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.15 Å
AuthorsGarau, G. / Geremia, S.
Citation
Journal: Protein Sci. / Year: 2002
Title: Cleavage of the iron-methionine bond in c-type cytochromes: crystal structure of oxidized and reduced cytochrome c(2) from Rhodopseudomonas palustris and its ammonia complex.
Authors: Geremia, S. / Garau, G. / Vaccari, L. / Sgarra, R. / Viezzoli, M.S. / Calligaris, M. / Randaccio, L.
#1: Journal: Acta Crystallogr.,Sect.D / Year: 2000
Title: Crystallization and Preliminary X-Ray Analysis of Two Ph-Dependent Forms of Cytochrome C2 from Rhodopseudomonas Palustris
Authors: Garau, G. / Geremia, S. / Randaccio, L. / Vaccari, L. / Viezzoli, M.S.
#2: Journal: To be Published
Title: Crystal Structure of Oxidized and Reduced Cytochrome from Rhodopseudomonas Palustris: Relationship Between Hydrogen-Bonding Network of the Conservative Water Molecule and Reduction Potential
Authors: Geremia, S. / Calligaris, M. / Garau, G. / Vaccari, L. / Viezzoli, M.S. / Randaccio, L.
#3: Journal: Acta Crystallogr.,Sect.D / Year: 1994
Title: Crystallization and X-Ray Structure Determination O Cytochrome C2 Fromrhodobacter Sphaeroides in Three Crystal Forms
Authors: Axelrod, H. / Feher, G. / Allen, J.P. / Chirino, A.J. / Day, M.W. / Hsu, B.T. / Rees, D.C.
#4: Journal: Nature / Year: 1979
Title: Cytochrome C2 Sequence Variation Among the Recognised Species of Purple Nonsulphur Photosynthetic Bacteria
Authors: Ambler, R.P. / Daniel, M. / Hermoso, J. / Meyer, T.E. / Bartsch, R.G. / Kamen, M.D.
History
DepositionMar 15, 2001Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 4, 2001Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Oct 4, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 1.4Jan 31, 2018Group: Experimental preparation / Category: exptl_crystal_grow / Item: _exptl_crystal_grow.temp
Revision 2.0Dec 25, 2019Group: Database references / Derived calculations / Polymer sequence
Category: entity_poly / pdbx_struct_mod_residue ...entity_poly / pdbx_struct_mod_residue / pdbx_struct_special_symmetry / struct_conn / struct_ref_seq_dif
Item: _entity_poly.pdbx_seq_one_letter_code_can / _pdbx_struct_mod_residue.parent_comp_id / _struct_conn.pdbx_leaving_atom_flag
Revision 2.1Aug 9, 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_conn / struct_conn_type / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_conn_type.id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Remark 999SEQUENCE PCA 1: GLN 1 HAS BEEN CYCLIZED TO PYRROLIDONE CARBOXYLIC ACID. THIS PROTEIN WAS EXPRESSED ...SEQUENCE PCA 1: GLN 1 HAS BEEN CYCLIZED TO PYRROLIDONE CARBOXYLIC ACID. THIS PROTEIN WAS EXPRESSED FROM A DIFFERENT STRAIN THAN THE DATABASE PROTEIN SWISSPROT ENTRY P00091 AND HAS SEVERAL MUTATIONS: G29A, I64V, N65P, N68A, AND D80E.

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: CYTOCHROME C2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)13,0155
Polymers12,1871
Non-polymers8284
Water4,306239
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
2
A: CYTOCHROME C2
hetero molecules

A: CYTOCHROME C2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,02910
Polymers24,3742
Non-polymers1,6558
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation6_555-x,-x+y,-z+2/31
Buried area4280 Å2
ΔGint-101 kcal/mol
Surface area11050 Å2
MethodPISA
Unit cell
Length a, b, c (Å)64.950, 64.950, 68.670
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Space group name H-MP3221
Components on special symmetry positions
IDModelComponents
11A-421-

HOH

-
Components

#1: Protein CYTOCHROME C2


Mass: 12186.983 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Rhodopseudomonas palustris (phototrophic) / Strain: 42 OL / References: UniProt: P00091
#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-HEC / HEME C


Mass: 618.503 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C34H34FeN4O4
#4: Chemical ChemComp-NH3 / AMMONIA


Mass: 17.031 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: NH3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 239 / 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: 3.2 Å3/Da / Density % sol: 61 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: 60% AMMONIUM SULPHATE, 0.1 M TRIS PH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 20K
Crystal grow
*PLUS
pH: 6
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
19.0 mg/mlprotein1droppH6.0
220 mMphosphate1drop
342-44 %satammonium sulfate1reservoir
40.1 Mcitrate1reservoirpH4.4

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ELETTRA / Beamline: 5.2R / Wavelength: 1 / Wavelength: 1 Å
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Jul 8, 2000 / Details: MIRRORS
RadiationMonochromator: SI 111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
111
211
ReflectionResolution: 1.15→15.2 Å / Num. all: 59295 / Num. obs: 55707 / % possible obs: 99.1 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 0 / Redundancy: 6.3 % / Biso Wilson estimate: 9.3 Å2 / Rmerge(I) obs: 0.054 / Net I/σ(I): 7.1
Reflection shellResolution: 1.15→1.21 Å / Redundancy: 5.9 % / Rmerge(I) obs: 0.412 / Mean I/σ(I) obs: 5.9 / % possible all: 99.1
Reflection
*PLUS
Num. obs: 57362 / % possible obs: 99.3 % / Num. measured all: 364867
Reflection shell
*PLUS
% possible obs: 96.7 % / Mean I/σ(I) obs: 4.1

-
Processing

Software
NameVersionClassification
AMoREphasing
SHELXVERSION 97-1refinement
MOSFLMdata reduction
CCP4(SCALA)data scaling
SHELXL-97refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1HH7

1hh7


Resolution: 1.15→15.2 Å / Num. parameters: 10378 / Num. restraintsaints: 11837 / Cross valid method: FREE R / σ(F): 0 / σ(I): 2 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.1616 2972 5 %RANDOM
Rwork0.1345 ---
all0.1402 58679 --
obs0.1401 55707 99.1 %-
Refine analyzeNum. disordered residues: 1
Refinement stepCycle: LAST / Resolution: 1.15→15.2 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms855 0 54 239 1148
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONs_bond_d0.014
X-RAY DIFFRACTIONs_angle_d2.1
Software
*PLUS
Name: SHELX / Version: VERSION 97-1 / Classification: refinement
Refinement
*PLUS
Lowest resolution: 20 Å / % reflection Rfree: 5 % / Rfactor obs: 0.139 / Rfactor Rfree: 0.167 / Rfactor Rwork: 0.151
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.01
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_angle_deg1.6

+
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