[English] 日本語
Yorodumi
- PDB-2bh4: X-ray structure of the M100K variant of ferric cyt c-550 from Par... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 2bh4
TitleX-ray structure of the M100K variant of ferric cyt c-550 from Paracoccus versutus determined at 100 K.
ComponentsCYTOCHROME C-550
KeywordsELECTRON TRANSFER / C-TYPE CYTOCHROME / HEME / AXIAL LIGAND / PYRROLIDONE CARBOXYLIC ACID
Function / homology
Function and homology information


electron transfer activity / heme binding / metal ion binding
Similarity search - Function
Cytochrome c, class IA/ IB / 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 / Cytochrome c-550
Similarity search - Component
Biological speciesPARACOCCUS VERSUTUS (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / OTHER / Resolution: 1.55 Å
AuthorsWorrall, J.A.R. / Van Roon, A.-M.M. / Ubbink, M. / Canters, G.W.
CitationJournal: FEBS J. / Year: 2005
Title: The Effect of Replacing the Axial Methionine Ligand with a Lysine Residue in Cytochrome C-550 from Paracoccus Versutus Assessed by X-Ray Crystallography and Unfolding.
Authors: Worrall, J.A.R. / Van Roon, A.-M.M. / Ubbink, M. / Canters, G.W.
History
DepositionJan 7, 2005Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 11, 2005Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Nov 13, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_entry_details / pdbx_modification_feature / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _pdbx_entry_details.has_protein_modification / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.pdbx_ptnr1_label_alt_id / _struct_conn.pdbx_ptnr2_label_alt_id / _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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
X: CYTOCHROME C-550
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,7732
Polymers14,1551
Non-polymers6191
Water2,522140
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)30.868, 42.880, 87.480
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

-
Components

#1: Protein CYTOCHROME C-550


Mass: 14154.857 Da / Num. of mol.: 1 / Mutation: YES
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) PARACOCCUS VERSUTUS (bacteria) / Plasmid: PUC19_M100K/PEC86 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): MV1190 / References: UniProt: Q00499
#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.: 140 / Source method: isolated from a natural source / Formula: H2O
Compound detailsENGINEERED MUTATION IN CHAIN X MET 100 TO LYS
Has protein modificationY
Sequence detailsWILD-TYPE GENE ACCESSION NUMBER

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2 Å3/Da / Density % sol: 37 %
Description: STRUCTURE WAS ALREADY SOLVED FOR A CRYSTAL MEASURED AT 295 K.
Crystal growpH: 9 / Details: 3.2 M AMMONIUM SULFATE, 0.1 M BICINE PH9, pH 9.00

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: BM30A / Wavelength: 0.98
DetectorType: MARRESEARCH / Detector: CCD / Date: Nov 28, 2003 / Details: MIRRORS
RadiationMonochromator: SI(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 1.55→43.85 Å / Num. obs: 17450 / % possible obs: 97.7 % / Observed criterion σ(I): 2 / Redundancy: 3.7 % / Rmerge(I) obs: 0.04 / Net I/σ(I): 20.6
Reflection shellResolution: 1.55→1.58 Å / Redundancy: 1.9 % / Rmerge(I) obs: 0.05 / Mean I/σ(I) obs: 11.7 / % possible all: 82.6

-
Processing

Software
NameVersionClassification
REFMAC5.2.0005refinement
HKL-2000data reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: OTHER / Resolution: 1.55→43.85 Å / Cor.coef. Fo:Fc: 0.971 / Cor.coef. Fo:Fc free: 0.957 / SU ML: 0.045 / Cross valid method: THROUGHOUT / ESU R: 0.103 / ESU R Free: 0.085 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. RESIDUES 1 AND 122-134 ARE NOT OBSERVED. RESIDUES 97-101 ARE MODELED IN A DOUBLE MAIN-CHAIN CONFORMATION.
RfactorNum. reflection% reflectionSelection details
Rfree0.202 836 4.9 %RANDOM
Rwork0.147 ---
obs0.15 16211 97.7 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 17.18 Å2
Baniso -1Baniso -2Baniso -3
1-0.76 Å20 Å20 Å2
2--0.74 Å20 Å2
3----1.51 Å2
Refinement stepCycle: LAST / Resolution: 1.55→43.85 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms911 0 43 140 1094
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0221033
X-RAY DIFFRACTIONr_bond_other_d0.0010.02911
X-RAY DIFFRACTIONr_angle_refined_deg1.4382.0981407
X-RAY DIFFRACTIONr_angle_other_deg0.82632145
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.9165125
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.1926.4139
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.66615179
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.069151
X-RAY DIFFRACTIONr_chiral_restr0.0870.2144
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.021130
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02173
X-RAY DIFFRACTIONr_nbd_refined0.290.3255
X-RAY DIFFRACTIONr_nbd_other0.180.3871
X-RAY DIFFRACTIONr_nbtor_refined0.1830.5498
X-RAY DIFFRACTIONr_nbtor_other0.0880.5505
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1470.5166
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1580.33
X-RAY DIFFRACTIONr_symmetry_vdw_other0.1680.328
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.190.526
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it2.6251.5806
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it3.08921001
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it4.293503
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it5.3894.5404
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.55→1.59 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.166 63
Rwork0.118 996

+
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