[English] 日本語
Yorodumi
- PDB-5fje: CU(I)-CSP1 (COPPER STORAGE PROTEIN 1) FROM METHYLOSINUS TRICHOSPO... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 5fje
TitleCU(I)-CSP1 (COPPER STORAGE PROTEIN 1) FROM METHYLOSINUS TRICHOSPORIUM OB3B
ComponentsCOPPER STORAGE PROTEIN 1
KeywordsCOPPER BINDING PROTEIN / METHANE OXIDATION / COPPER STORAGE / METHANOTROPHS / PARTICULATE METHANE MONOOXYGENASE
Function / homologyTwin-arginine translocation signal, Cys-rich four helix bundle protein / metal ion binding / COPPER (I) ION / Copper storage protein 1
Function and homology information
Biological speciesMETHYLOSINUS TRICHOSPORIUM OB3B (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.9 Å
AuthorsVita, N. / Platsaki, S. / Basle, A. / Allen, S.J. / Paterson, N.G. / Crombie, A.T. / Murrell, J.C. / Waldron, K.J. / Dennison, C.
CitationJournal: Nature / Year: 2015
Title: A Four-Helix Bundle Stores Copper for Methane Oxidation.
Authors: Vita, N. / Platsaki, S. / Basle, A. / Allen, S.J. / Paterson, N.G. / Crombie, A.T. / Murrell, J.C. / Waldron, K.J. / Dennison, C.
History
DepositionOct 7, 2015Deposition site: PDBE / Processing site: PDBE
SupersessionNov 18, 2015ID: 5AJF
Revision 1.0Nov 18, 2015Provider: repository / Type: Initial release
Revision 1.1May 8, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_struct_conn_angle / struct_conn / struct_site
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_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_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.ptnr2_auth_comp_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr2_label_atom_id / _pdbx_struct_conn_angle.ptnr2_label_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_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_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 / _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: COPPER STORAGE PROTEIN 1
B: COPPER STORAGE PROTEIN 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,91730
Polymers25,2192
Non-polymers1,69828
Water2,090116
1
A: COPPER STORAGE PROTEIN 1
B: COPPER STORAGE PROTEIN 1
hetero molecules

A: COPPER STORAGE PROTEIN 1
B: COPPER STORAGE PROTEIN 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)53,83460
Polymers50,4384
Non-polymers3,39656
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_656-x+1,y,-z+11
Buried area11400 Å2
ΔGint-382.5 kcal/mol
Surface area16040 Å2
MethodPISA
Unit cell
Length a, b, c (Å)44.410, 41.420, 53.130
Angle α, β, γ (deg.)90.00, 92.96, 90.00
Int Tables number3
Space group name H-MP121
Components on special symmetry positions
IDModelComponents
11A-2017-

HOH

21A-2019-

HOH

31B-2010-

HOH

41B-2016-

HOH

-
Components

#1: Protein COPPER STORAGE PROTEIN 1


Mass: 12609.529 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) METHYLOSINUS TRICHOSPORIUM OB3B (bacteria)
Plasmid: PET29A / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: A0A0M3KL60*PLUS
#2: Chemical...
ChemComp-CU1 / COPPER (I) ION


Mass: 63.546 Da / Num. of mol.: 26 / Source method: obtained synthetically / Formula: Cu
#3: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Na
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 116 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION

-
Sample preparation

CrystalDensity Matthews: 1.94 Å3/Da / Density % sol: 36 % / Description: NONE
Crystal growDetails: 0.03 M MGCL2, 0.03 M CACL2, 0.1 M TRIS PH 8.5, 12.5% V/V MPD (RACEMIC), 12.5% PEG 1000, 12.5% PEG 3350

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I24 / Wavelength: 1.3777
DetectorType: MARRESEARCH / Detector: CCD / Date: Aug 10, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.3777 Å / Relative weight: 1
ReflectionResolution: 1.9→53.06 Å / Num. obs: 15212 / % possible obs: 99.1 % / Observed criterion σ(I): 2 / Redundancy: 2.8 % / Rmerge(I) obs: 0.09 / Net I/σ(I): 5.6
Reflection shellResolution: 1.9→1.95 Å / Redundancy: 2.4 % / Rmerge(I) obs: 0.43 / Mean I/σ(I) obs: 2.1 / % possible all: 97.1

-
Processing

Software
NameVersionClassification
XDSdata reduction
Aimlessdata scaling
SHELXCDphasing
PHASEREPphasing
REFMAC5.8.0103refinement
RefinementMethod to determine structure: SAD
Starting model: NONE

Resolution: 1.9→53.06 Å / Cor.coef. Fo:Fc: 0.967 / Cor.coef. Fo:Fc free: 0.956 / SU B: 6.514 / SU ML: 0.164 / Cross valid method: THROUGHOUT / ESU R: 0.183 / ESU R Free: 0.155 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.23166 722 4.7 %RANDOM
Rwork0.19819 ---
obs0.19988 14489 99.04 %-
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: 40.332 Å2
Baniso -1Baniso -2Baniso -3
1-1.78 Å20 Å20.03 Å2
2---1.38 Å20 Å2
3----0.4 Å2
Refinement stepCycle: LAST / Resolution: 1.9→53.06 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1556 0 28 116 1700
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.0191598
X-RAY DIFFRACTIONr_bond_other_d0.0060.021496
X-RAY DIFFRACTIONr_angle_refined_deg1.5941.9562155
X-RAY DIFFRACTIONr_angle_other_deg1.24333478
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.8385222
X-RAY DIFFRACTIONr_dihedral_angle_2_deg28.26225.6653
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.99915266
X-RAY DIFFRACTIONr_dihedral_angle_4_deg35.572152
X-RAY DIFFRACTIONr_chiral_restr0.0890.2249
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.021846
X-RAY DIFFRACTIONr_gen_planes_other0.0040.02322
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_it3.1493.741888
X-RAY DIFFRACTIONr_mcbond_other3.0993.736887
X-RAY DIFFRACTIONr_mcangle_it4.0785.61110
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it4.2724.277710
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
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: 1.9→1.95 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.499 46 -
Rwork0.53 1050 -
obs--97.08 %

+
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