[English] 日本語
Yorodumi
- PDB-1c52: THERMUS THERMOPHILUS CYTOCHROME-C552: A NEW HIGHLY THERMOSTABLE C... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1c52
TitleTHERMUS THERMOPHILUS CYTOCHROME-C552: A NEW HIGHLY THERMOSTABLE CYTOCHROME-C STRUCTURE OBTAINED BY MAD PHASING
ComponentsCYTOCHROME-C552
KeywordsELECTRON TRANSPORT PROTEIN / CYTOCHROME-C552 / MAD / THERMOSTABILITY
Function / homology
Function and homology information


electron transfer activity / heme binding / metal ion binding
Similarity search - Function
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
PROTOPORPHYRIN IX CONTAINING FE / Cytochrome c-552
Similarity search - Component
Biological speciesThermus thermophilus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.28 Å
AuthorsThan, M.E. / Hof, P. / Huber, R. / Bourenkov, G.P. / Bartunik, H.D. / Buse, G. / Soulimane, T.
Citation
Journal: J.Mol.Biol. / Year: 1997
Title: Thermus thermophilus cytochrome-c552: A new highly thermostable cytochrome-c structure obtained by MAD phasing.
Authors: Than, M.E. / Hof, P. / Huber, R. / Bourenkov, G.P. / Bartunik, H.D. / Buse, G. / Soulimane, T.
#1: Journal: Biochem.Biophys.Res.Commun. / Year: 1985
Title: Amino Acid Sequence of Cytochrome C-552 from Thermus Thermophilus Hb8
Authors: Titani, K. / Ericsson, L.H. / Hon-Nami, K. / Miyazawa, T.
#2: Journal: J.Mol.Biol. / Year: 1978
Title: Reversible Thermal Unfolding of Thermostable Cytochrome C-552
Authors: Nojima, H. / Hon-Nami, K. / Oshima, T. / Noda, H.
#3: Journal: J.Biochem.(Tokyo) / Year: 1977
Title: Purification and Some Properties of Cytochrome C-552 from an Extreme Thermophile, Thermus Thermophilus Hb8
Authors: Hon-Nami, K. / Oshima, T.
History
DepositionJun 23, 1997Processing site: BNL
Revision 1.0Jun 24, 1998Provider: repository / Type: Initial release
Revision 1.1Mar 24, 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-C552
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,8112
Polymers14,1951
Non-polymers6161
Water3,531196
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)47.100, 47.100, 68.820
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number76
Space group name H-MP41

-
Components

#1: Protein CYTOCHROME-C552


Mass: 14194.575 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: OXIDIZED STATE (FE+++) / Source: (natural) Thermus thermophilus (bacteria) / Cellular location: PERIPLASM / References: UniProt: P04164
#2: Chemical ChemComp-HEM / PROTOPORPHYRIN IX CONTAINING FE / HEME / Heme B


Mass: 616.487 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C34H32FeN4O4
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 196 / 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: 2.58 Å3/Da / Density % sol: 52.3 %
Crystal growpH: 8.2
Details: PROTEIN WAS CRYSTALLIZED FROM 2.8 M AMMONIUM SULFATE, 100 MM TRIS/HCL, PH 8.2
Crystal grow
*PLUS
Method: unknown
Details: drop consists of 8 microlitter protein and 2 microlitter reservoir solution
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
110 mg/mlprotein1drop
210 mMTris/HCl1drop
3100 mMTris-HCl1reservoir
42.0 Mammonium sulfate1reservoir

-
Data collection

DiffractionMean temperature: 90 K
Diffraction sourceSource: SYNCHROTRON / Site: MPG/DESY, HAMBURG / Beamline: BW6 / Wavelength: 1.05
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Oct 1, 1996 / Details: MIRROR
RadiationMonochromator: DOUBLE CRYSTAL SI(111) / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.05 Å / Relative weight: 1
ReflectionResolution: 1.28→14.6 Å / Num. obs: 36004 / % possible obs: 93.6 % / Redundancy: 4.6 % / Biso Wilson estimate: 12.7 Å2 / Rsym value: 0.033 / Net I/σ(I): 14.1
Reflection shellResolution: 1.28→1.31 Å / Redundancy: 2.5 % / Mean I/σ(I) obs: 1.6 / Rsym value: 0.357 / % possible all: 78.2
Reflection
*PLUS
Num. measured all: 165576 / Rmerge(I) obs: 0.033
Reflection shell
*PLUS
% possible obs: 78.2 % / Rmerge(I) obs: 0.357

-
Processing

Software
NameVersionClassification
MADPRBmodel building
MADSYSphasing
X-PLOR3.851model building
X-PLOR3.851refinement
DENZOdata reduction
MOSFLMdata reduction
SCALEPACKdata scaling
CCP4(AGROVATAdata scaling
ROTAVATAdata scaling
TRUNCATE)data scaling
MADPRBphasing
X-PLOR3.851phasing
RefinementMethod to determine structure: MAD / Resolution: 1.28→8 Å / Data cutoff high absF: 100000 / Data cutoff low absF: 0.1 / Isotropic thermal model: RESTRAINED
Details: OCCUPANCY AND B-FACTOR ARE SET TO ZERO FOR ALL ATOMS THAT ARE NOT DEFINED IN THE FINAL 2FO-FC ELECTRON DENSITY.
RfactorNum. reflection% reflectionSelection details
Rfree0.224 1825 4.7 %RANDOM
Rwork0.191 ---
obs0.191 35906 93.3 %-
Displacement parametersBiso mean: 15.1 Å2
Refinement stepCycle: LAST / Resolution: 1.28→8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1040 0 43 196 1279
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_deg1.453
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d23.15
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d1.263
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
LS refinement shellResolution: 1.28→1.29 Å / Total num. of bins used: 30
RfactorNum. reflection% reflection
Rfree0.304 34 2.66 %
Rwork0.327 748 -
obs--61.1 %
Software
*PLUS
Name: X-PLOR / Version: 3.851 / Classification: refinement
Refinement
*PLUS
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_deg23.15
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg1.263
LS refinement shell
*PLUS
Rfactor obs: 0.327

+
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