[English] 日本語
Yorodumi
- PDB-5xec: Heterodimer constructed from PA cyt c551-HT cyt c552 and HT cyt c... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 5xec
TitleHeterodimer constructed from PA cyt c551-HT cyt c552 and HT cyt c552-PA cyt c551 chimeric proteins
Components
  • Cytochrome c-551,Cytochrome c-552
  • Cytochrome c-552,Cytochrome c-551
KeywordsELECTRON TRANSPORT / Chimeric protein
Function / homology
Function and homology information


periplasmic space / electron transfer activity / iron ion binding / heme binding
Similarity search - Function
Cytochrome c, class ID / 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 / Cytochrome c-551 / Cytochrome c-552
Similarity search - Component
Biological speciesHydrogenobacter thermophilus (bacteria)
Pseudomonas aeruginosa (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.1 Å
AuthorsZhang, M. / Nakanishi, T. / Yamanaka, M. / Nagao, S. / Yanagisawa, S. / Shomura, Y. / Shibata, N. / Ogura, T. / Higuchi, Y. / Hirota, S.
Funding support Japan, 3items
OrganizationGrant numberCountry
JSPS26288080 Japan
JSPS15K13744 Japan
JSPS15H00945 Japan
CitationJournal: Chembiochem / Year: 2017
Title: Rational Design of Domain-Swapping-Based c-Type Cytochrome Heterodimers by Using Chimeric Proteins.
Authors: Zhang, M. / Nakanishi, T. / Yamanaka, M. / Nagao, S. / Yanagisawa, S. / Shomura, Y. / Shibata, N. / Ogura, T. / Higuchi, Y. / Hirota, S.
History
DepositionApr 4, 2017Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Aug 9, 2017Provider: repository / Type: Initial release
Revision 1.1Dec 6, 2017Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.2Nov 22, 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
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_asym_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_asym_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
Revision 1.3Nov 13, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
C: Cytochrome c-552,Cytochrome c-551
A: Cytochrome c-551,Cytochrome c-552
hetero molecules


Theoretical massNumber of molelcules
Total (without water)18,5284
Polymers17,2912
Non-polymers1,2372
Water4,342241
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5440 Å2
ΔGint-70 kcal/mol
Surface area9120 Å2
MethodPISA
Unit cell
Length a, b, c (Å)31.350, 72.540, 35.010
Angle α, β, γ (deg.)90.00, 106.07, 90.00
Int Tables number4
Space group name H-MP1211

-
Components

#1: Protein Cytochrome c-552,Cytochrome c-551 / Cytochrome c552 / Cytochrome C8 / Cytochrome c551


Mass: 8504.748 Da / Num. of mol.: 1 / Fragment: UNP RESIDUES 19-36,UNP RESIDUES 43-104
Source method: isolated from a genetically manipulated source
Details: The chimeric protein of Cytochrome c-552 (19-36) and Cytochrome c-551 (43-104)
Source: (gene. exp.) Hydrogenobacter thermophilus (bacteria), (gene. exp.) Pseudomonas aeruginosa (bacteria)
Strain: DSM 6534 / IAM 12695 / TK-6, ATCC 15692 / DSM 22644 / CIP 104116 / JCM 14847 / LMG 12228 / 1C / PRS 101 / PAO1
Gene: HTH_0988, Hydth_0984, nirM, PA0518 / Production host: Escherichia coli (E. coli) / Strain (production host): JCB387 / References: UniProt: P15452, UniProt: P00099
#2: Protein Cytochrome c-551,Cytochrome c-552 / Cytochrome C8 / Cytochrome c551 / Cytochrome c552


Mass: 8786.158 Da / Num. of mol.: 1 / Fragment: UNP RESIDUES 23-42,UNP RESIDUES 37-98
Source method: isolated from a genetically manipulated source
Details: The chimeric protein of Cytochrome c-551 (23-42) and Cytochrome c-552 (37-98)
Source: (gene. exp.) Pseudomonas aeruginosa (bacteria), (gene. exp.) Hydrogenobacter thermophilus (bacteria)
Strain: ATCC 15692 / DSM 22644 / CIP 104116 / JCM 14847 / LMG 12228 / 1C / PRS 101 / PAO1, DSM 6534 / IAM 12695 / TK-6
Gene: nirM, PA0518, HTH_0988, Hydth_0984 / Production host: Escherichia coli (E. coli) / Strain (production host): JCB387 / References: UniProt: P00099, UniProt: P15452
#3: Chemical ChemComp-HEC / HEME C


Mass: 618.503 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C34H34FeN4O4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 241 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.21 Å3/Da / Density % sol: 44.4 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: 100 mM Tris-HCl containing 200 mM sodium acetate, 30% w/v PEG 4000

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL38B1 / Wavelength: 1 Å
DetectorType: RAYONIX MX225HE / Detector: CCD / Date: Jan 12, 2015
RadiationMonochromator: Fixed exit Si (111) double crystal monochromator
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.1→20 Å / Num. obs: 60431 / % possible obs: 99.3 % / Redundancy: 3.5 % / CC1/2: 0.997 / Rmerge(I) obs: 0.078 / Net I/σ(I): 7.8
Reflection shellResolution: 1.1→1.16 Å / Redundancy: 3.5 % / Rmerge(I) obs: 0.389 / Mean I/σ(I) obs: 2.7 / Num. unique obs: 8875 / CC1/2: 0.843 / % possible all: 100

-
Processing

Software
NameVersionClassification
REFMAC5.8.0073refinement
iMOSFLMdata reduction
SCALAdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 351C, 1YNR

351c

1ynr


Resolution: 1.1→20 Å / Cor.coef. Fo:Fc: 0.96 / Cor.coef. Fo:Fc free: 0.956 / SU B: 1.295 / SU ML: 0.028 / Cross valid method: THROUGHOUT / ESU R: 0.038 / ESU R Free: 0.037 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.19731 2984 4.9 %RANDOM
Rwork0.17467 ---
obs0.17578 57400 99.2 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 12.396 Å2
Baniso -1Baniso -2Baniso -3
1-0.16 Å2-0 Å20.19 Å2
2---0.37 Å20 Å2
3---0.09 Å2
Refinement stepCycle: 1 / Resolution: 1.1→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1211 0 86 241 1538
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0191397
X-RAY DIFFRACTIONr_bond_other_d0.0020.021334
X-RAY DIFFRACTIONr_angle_refined_deg1.4082.0531923
X-RAY DIFFRACTIONr_angle_other_deg0.83933082
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.2295172
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.48826.12249
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.20415232
X-RAY DIFFRACTIONr_dihedral_angle_4_deg2.36153
X-RAY DIFFRACTIONr_chiral_restr0.1170.2189
X-RAY DIFFRACTIONr_gen_planes_refined0.0120.0211635
X-RAY DIFFRACTIONr_gen_planes_other0.010.02308
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.0241.065676
X-RAY DIFFRACTIONr_mcbond_other1.0231.064675
X-RAY DIFFRACTIONr_mcangle_it1.3381.601852
X-RAY DIFFRACTIONr_mcangle_other1.3381.601853
X-RAY DIFFRACTIONr_scbond_it1.611.206721
X-RAY DIFFRACTIONr_scbond_other1.6081.206719
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other1.8541.7071071
X-RAY DIFFRACTIONr_long_range_B_refined2.7899.7242006
X-RAY DIFFRACTIONr_long_range_B_other2.2929.0671840
X-RAY DIFFRACTIONr_rigid_bond_restr1.62832731
X-RAY DIFFRACTIONr_sphericity_free22.252533
X-RAY DIFFRACTIONr_sphericity_bonded8.22952894
LS refinement shellResolution: 1.1→1.128 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.261 235 -
Rwork0.244 4246 -
obs--99.96 %

+
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