[English] 日本語
Yorodumi
- PDB-4m5c: Crystal Structure of an Truncated Transition metal Transporter -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 4m5c
TitleCrystal Structure of an Truncated Transition metal Transporter
ComponentsCobalamin biosynthesis protein CbiM
KeywordsMEMBRANE PROTEIN / transporter / Cobalt
Function / homology
Function and homology information


transition metal ion transport / plasma membrane
Similarity search - Function
Metal transport protein CbiM/NikMN / Cobalt uptake substrate-specific transmembrane region / Arp2/3 complex 21 kDa subunit ARPC3 - #20 / Arp2/3 complex 21 kDa subunit ARPC3 / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
: / HEXANE-1,6-DIOL / Cobalamin biosynthesis protein CbiM
Similarity search - Component
Biological speciesThermoanaerobacter tengcongensis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 Å
AuthorsYu, Y. / Zhou, M.Z. / Gu, J.K.
CitationJournal: Cell Res. / Year: 2014
Title: Planar substrate-binding site dictates the specificity of ECF-type nickel/cobalt transporters
Authors: Yu, Y. / Zhou, M.Z. / Kirsch, F. / Xu, C.Q. / Zhang, L. / Wang, Y. / Jiang, Z. / Wang, N. / Li, J. / Eitinger, T. / Yang, M.J.
History
DepositionAug 8, 2013Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Mar 26, 2014Provider: repository / Type: Initial release
Revision 1.1Mar 20, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_conn_angle / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Cobalamin biosynthesis protein CbiM
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,4167
Polymers22,7661
Non-polymers6506
Water73941
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)64.479, 103.820, 121.285
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221

-
Components

#1: Protein Cobalamin biosynthesis protein CbiM / TtNikM2


Mass: 22765.900 Da / Num. of mol.: 1 / Fragment: UNP residues 1-209
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermoanaerobacter tengcongensis (bacteria)
Strain: MB4 / Gene: CbiM2, TTE1695 / Production host: Escherichia coli (E. coli) / References: UniProt: Q8R9C0
#2: Chemical ChemComp-CO / COBALT (II) ION


Mass: 58.933 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Co
#3: Chemical
ChemComp-HEZ / HEXANE-1,6-DIOL


Mass: 118.174 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C6H14O2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 41 / 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: 4.46 Å3/Da / Density % sol: 72.41 %
Crystal growTemperature: 291.15 K / Method: vapor diffusion, hanging drop / pH: 9.8
Details: 30% PEG 400, 0.05M CAPSO, 0.05M magnesium acetate,, pH 9.8, VAPOR DIFFUSION, HANGING DROP, temperature 291.15K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 1.589 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jun 3, 2013
RadiationMonochromator: Si 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.589 Å / Relative weight: 1
ReflectionResolution: 2.5→50 Å / Num. all: 27318 / Num. obs: 27181 / % possible obs: 99.5 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1
Reflection shellHighest resolution: 2.5 Å

-
Processing

Software
NameVersionClassification
CBASSdata collection
PHASESphasing
PHENIX(phenix.refine: 1.8_1069)refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.5→47.723 Å / Occupancy max: 1 / Occupancy min: 0.09 / FOM work R set: 0.8401 / SU ML: 0.3 / σ(F): 1.36 / Phase error: 22.65 / Stereochemistry target values: ML
Details: SF FILE CONTAINS FRIEDEL PAIRS UNDER UNDER I_PLUS/MINUS AND F_PLUS/MINUS COLUMNS.
RfactorNum. reflection% reflection
Rfree0.241 721 5.01 %
Rwork0.2014 --
obs0.2034 14394 99.34 %
all-14466 -
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 93.44 Å2 / Biso mean: 27.0563 Å2 / Biso min: 7.44 Å2
Refinement stepCycle: LAST / Resolution: 2.5→47.723 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1562 0 41 41 1644
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0071677
X-RAY DIFFRACTIONf_angle_d1.0632285
X-RAY DIFFRACTIONf_dihedral_angle_d13.403594
X-RAY DIFFRACTIONf_chiral_restr0.067278
X-RAY DIFFRACTIONf_plane_restr0.006278
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 5

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.4974-2.69020.26961500.21082642279298
2.6902-2.96090.2611370.196227082845100
2.9609-3.38930.21791610.188427202881100
3.3893-4.26970.25581360.187427332869100
4.2697-47.73140.22861370.21652870300799

+
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