[English] 日本語
Yorodumi
- PDB-1h21: A novel iron centre in the split-Soret cytochrome c from Desulfov... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1h21
TitleA novel iron centre in the split-Soret cytochrome c from Desulfovibrio desulfuricans ATCC 27774
ComponentsSPLIT-SORET CYTOCHROME C
KeywordsCYTOCHROME / DIMERIC DI-HEME CYTOCHROME / STACKED HEME ARRANGEMENT / NOVEL FOLD / NOVEL IRON-SULFUR CENTRE / ELECTRON TRANSPORT / SULFATE RESPIRATION
Function / homology
Function and homology information


anaerobic respiration / 2 iron, 2 sulfur cluster binding / metal ion binding
Similarity search - Function
CGCAxxGCC motif / Putative redox-active protein (C_GCAxxG_C_C) / Multiheme cytochrome superfamily / Twin arginine translocation (Tat) signal profile. / Twin-arginine translocation pathway, signal sequence
Similarity search - Domain/homology
HEME C / Split-Soret cytochrome c
Similarity search - Component
Biological speciesDESULFOVIBRIO DESULFURICANS (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.5 Å
AuthorsAbreu, I.A. / Lourenco, A.I. / Xavier, A.V. / Legall, J. / Coelho, A.V. / Matias, P.M. / Pinto, D.M. / Carrondo, M.A. / Teixeira, M. / Saraiva, L.M.
Citation
Journal: J.Biol.Inorg.Chem. / Year: 2003
Title: A Novel Iron Centre in the Split-Soret Cytochrome C from Desulfovibrio Desulfuricans Atcc 27774
Authors: Abreu, I.A. / Lourenco, A.I. / Xavier, A.V. / Legall, J. / Coelho, A.V. / Matias, P.M. / Pinto, D.M. / Armenia Carrondo, M. / Teixeira, M. / Saraiva, L.M.
#1: Journal: J.Biol.Inorg.Chem. / Year: 1997
Title: A Preliminary Analysis of the Three Dimensional Structure of Dimeric Di-Haem Split-Soret Cytochrome C from Desulfovibrio Desulfuricans Atcc 27774 at 2.5 A Resolution Using the MAD Phasing ...Title: A Preliminary Analysis of the Three Dimensional Structure of Dimeric Di-Haem Split-Soret Cytochrome C from Desulfovibrio Desulfuricans Atcc 27774 at 2.5 A Resolution Using the MAD Phasing Method: A Novel Cytochrome Fold with a Stacked Haem Arrangement
Authors: Matias, P.M. / Morais, J. / Coelho, A.V. / Meijers, R. / Gonzalez, A. / Thompson, A.W. / Sieker, L. / Legall, J. / Carrondo, M.A.
History
SupersessionJul 30, 2002ID: 1DDC
DepositionJul 30, 2002Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 20, 2003Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: SPLIT-SORET CYTOCHROME C
B: SPLIT-SORET CYTOCHROME C
C: SPLIT-SORET CYTOCHROME C
D: SPLIT-SORET CYTOCHROME C
hetero molecules


Theoretical massNumber of molelcules
Total (without water)112,70612
Polymers107,7584
Non-polymers4,9488
Water3,387188
1
A: SPLIT-SORET CYTOCHROME C
B: SPLIT-SORET CYTOCHROME C
hetero molecules


Theoretical massNumber of molelcules
Total (without water)56,3536
Polymers53,8792
Non-polymers2,4744
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
2
C: SPLIT-SORET CYTOCHROME C
D: SPLIT-SORET CYTOCHROME C
hetero molecules


Theoretical massNumber of molelcules
Total (without water)56,3536
Polymers53,8792
Non-polymers2,4744
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)96.060, 100.130, 109.300
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS oper:
IDCodeMatrixVector
1given(-0.93011, 0.05726, 0.36279), (0.0154, -0.98082, 0.19428), (0.36696, 0.18629, 0.91139)129.47571, -13.45994, -23.49785
2given(-0.93141, 0.05568, 0.35969), (0.01592, -0.98105, 0.19311), (0.36362, 0.18559, 0.91287)129.6824, -13.46635, -23.31216

-
Components

#1: Protein
SPLIT-SORET CYTOCHROME C / DIMERIC DI-HEME SPLIT-SORET CYTOCHROME C


Mass: 26939.469 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Source: (natural) DESULFOVIBRIO DESULFURICANS (bacteria) / References: UniProt: P81040
#2: Chemical
ChemComp-HEC / HEME C / Heme C


Mass: 618.503 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C34H34FeN4O4
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 188 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsGENBANK ENTRY AF465622 IS ON HOLD PENDING MANUSCRIPT ACCEPTANCE FOR PUBLICATION. SEQADV RECORDS ...GENBANK ENTRY AF465622 IS ON HOLD PENDING MANUSCRIPT ACCEPTANCE FOR PUBLICATION. SEQADV RECORDS BELOW ARE DUE TO ERRORS IN SWS P81040 THAT WERE CORRECTED IN AF465622

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
Sample preparation

CrystalDensity Matthews: 2.59 Å3/Da / Density % sol: 53 %
Crystal growpH: 5
Details: PROTEIN WAS CRYSTALLIZED FROM A SOLUTION CONTAINING 0.1-0.2 % (W/V) AGAROSE IN 12-15 % PEG 8K, 0.1M SODIUM ACETATE BUFFER PH 5.0
Crystal grow
*PLUS
Method: vapor diffusion, sitting drop / Details: Matias, P.M., (1997) J.Biol.Inorg.Chem., 2, 507.
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
115 mg/mlprotein1drop
217-19 %(w/v)PEG80001drop
30.1 Msodium acetate1droppH5.0
40.1-0.2 %(w/v)agarose1reservoir
512-15 %PEG80001reservoir
60.1 Msodium acetate1reservoirpH5.0

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: BM14 / Wavelength: 1.7401
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Feb 15, 1996 / Details: MIRRORS
RadiationMonochromator: SI (111) / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.7401 Å / Relative weight: 1
ReflectionResolution: 2.5→20 Å / Num. obs: 34228 / % possible obs: 93 % / Redundancy: 6.2 % / Rmerge(I) obs: 0.038 / Net I/σ(I): 9.7
Reflection shellResolution: 2.5→2.56 Å / Rmerge(I) obs: 0.074 / Mean I/σ(I) obs: 9.7 / % possible all: 86

-
Processing

Software
NameVersionClassification
DENZOdata reduction
SCALEPACKdata scaling
MLPHAREphasing
DMphasing
X-PLOR3.1refinement
RefinementMethod to determine structure: MAD / Resolution: 2.5→20 Å / Data cutoff high absF: 100000 / Data cutoff low absF: 0.1 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 2 / Details: FIRST 7 RESIDUES NOT VISIBLE IN ELECTRON DENSITY.
RfactorNum. reflection% reflectionSelection details
Rfree0.264 1681 5 %RANDOM
Rwork0.199 ---
obs0.199 34127 92.8 %-
Displacement parametersBiso mean: 35.04 Å2
Refine analyzeLuzzati d res low obs: 10 Å / Luzzati sigma a obs: 0.35 Å
Refinement stepCycle: LAST / Resolution: 2.5→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7384 0 344 188 7916
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.013
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_deg1.65
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d24.5
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d1.76
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
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PARHCSDX.PROTOPHCSDX.PRO
X-RAY DIFFRACTION2PARAM19X.HEMETOPH19X.HEME
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_deg24.5
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg1.76

+
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