[English] 日本語
Yorodumi
- PDB-2yj4: Conformational changes in the catalytic domain of the CPx-ATPase ... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 2yj4
TitleConformational changes in the catalytic domain of the CPx-ATPase CopB- B upon nucleotide binding
ComponentsCOPPER-TRANSPORTING ATPASE
KeywordsHYDROLASE / P-TYPE ATPASE / COPB / HEAVY METAL TRANSLOCATION
Function / homology
Function and homology information


H+/K+-exchanging ATPase / ATPase-coupled monoatomic cation transmembrane transporter activity / transmembrane transporter activity / transmembrane transport / ATP hydrolysis activity / ATP binding / metal ion binding / membrane
Similarity search - Function
: / Hypothetical cof family signature 2. / P-type ATPase, subfamily IB / Heavy-metal-associated domain / Heavy metal-associated domain superfamily / Calcium-transporting ATPase, cytoplasmic domain N / Calcium-transporting ATPase, cytoplasmic domain N / Heavy-metal-associated domain profile. / Heavy metal-associated domain, HMA / P-type ATPase actuator domain ...: / Hypothetical cof family signature 2. / P-type ATPase, subfamily IB / Heavy-metal-associated domain / Heavy metal-associated domain superfamily / Calcium-transporting ATPase, cytoplasmic domain N / Calcium-transporting ATPase, cytoplasmic domain N / Heavy-metal-associated domain profile. / Heavy metal-associated domain, HMA / P-type ATPase actuator domain / HAD superfamily/HAD-like / P-type ATPase, phosphorylation site / P-type ATPase, cytoplasmic domain N / E1-E2 ATPases phosphorylation site. / P-type ATPase, A domain superfamily / P-type ATPase / haloacid dehalogenase-like hydrolase / HAD superfamily / HAD-like superfamily / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
ADENOSINE MONOPHOSPHATE / ADENOSINE-5'-TRIPHOSPHATE / PHOSPHATE ION / Copper-transporting ATPase
Similarity search - Component
Biological speciesSULFOLOBUS SOLFATARICUS (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.4 Å
AuthorsVoellmecke, C. / Schlicker, C. / Luebben, M. / Hofmann, E.
CitationJournal: To be Published
Title: Conformational Changes in the Catalytic Domain of the Cpx-ATPase Copb-B Upon Nucleotide Binding
Authors: Voellmecke, C. / Schlicker, C. / Luebben, M. / Hofmann, E.
History
DepositionMay 18, 2011Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 30, 2012Provider: repository / Type: Initial release
Revision 1.1Dec 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / 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 / _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-TRANSPORTING ATPASE
B: COPPER-TRANSPORTING ATPASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)58,6005
Polymers57,6512
Non-polymers9493
Water19811
1
A: COPPER-TRANSPORTING ATPASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,2683
Polymers28,8251
Non-polymers4422
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: COPPER-TRANSPORTING ATPASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,3332
Polymers28,8251
Non-polymers5071
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)52.120, 75.150, 133.920
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

-
Components

#1: Protein COPPER-TRANSPORTING ATPASE


Mass: 28825.393 Da / Num. of mol.: 2 / Fragment: RESIDUES 383-645 / Mutation: YES
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) SULFOLOBUS SOLFATARICUS (archaea) / Strain: P2 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3)
References: UniProt: Q97UU7, EC: 3.6.1.36, H+/K+-exchanging ATPase
#2: Chemical ChemComp-AMP / ADENOSINE MONOPHOSPHATE


Mass: 347.221 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H14N5O7P / Comment: AMP*YM
#3: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: PO4
#4: Chemical ChemComp-ATP / ADENOSINE-5'-TRIPHOSPHATE


Mass: 507.181 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H16N5O13P3 / Comment: ATP, energy-carrying molecule*YM
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 11 / Source method: isolated from a natural source / Formula: H2O
Compound detailsENGINEERED RESIDUE IN CHAIN A, ASP 416 TO ASN ENGINEERED RESIDUE IN CHAIN B, ASP 416 TO ASN

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.34 Å3/Da / Density % sol: 47.51 % / Description: NONE
Crystal growDetails: 0.1 M NA ACETATE PH 4.5, 0.2 M NA CHLORIDE, 10% PEG 4000.

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 1
DetectorType: DECTRIS PILATUS / Detector: PIXEL
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.4→48.57 Å / Num. obs: 21225 / % possible obs: 99.8 % / Observed criterion σ(I): 2 / Redundancy: 6.5 % / Biso Wilson estimate: 49.48 Å2 / Rmerge(I) obs: 0.06 / Net I/σ(I): 18.68
Reflection shellResolution: 2.4→2.5 Å / Redundancy: 6.5 % / Rmerge(I) obs: 0.37 / Mean I/σ(I) obs: 4.47 / % possible all: 100

-
Processing

Software
NameVersionClassification
PHENIX(PHENIX.REFINE)refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2IYE

2iye


Resolution: 2.4→48.571 Å / SU ML: 0.34 / σ(F): 2.02 / Phase error: 29.92 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2731 1061 5 %
Rwork0.2202 --
obs0.2229 21214 99.79 %
Solvent computationShrinkage radii: 0.83 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 45.398 Å2 / ksol: 0.3 e/Å3
Displacement parametersBiso mean: 51.9 Å2
Baniso -1Baniso -2Baniso -3
1-7.9542 Å20 Å20 Å2
2---8.9978 Å20 Å2
3---1.0437 Å2
Refinement stepCycle: LAST / Resolution: 2.4→48.571 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3729 0 59 11 3799
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0083829
X-RAY DIFFRACTIONf_angle_d1.265187
X-RAY DIFFRACTIONf_dihedral_angle_d17.9451417
X-RAY DIFFRACTIONf_chiral_restr0.077632
X-RAY DIFFRACTIONf_plane_restr0.004647
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.4-2.50920.33971300.26612463X-RAY DIFFRACTION100
2.5092-2.64150.36321300.27552466X-RAY DIFFRACTION100
2.6415-2.8070.37071310.27412483X-RAY DIFFRACTION100
2.807-3.02370.29011300.25722505X-RAY DIFFRACTION100
3.0237-3.32790.31641320.24382501X-RAY DIFFRACTION100
3.3279-3.80930.27471330.21412522X-RAY DIFFRACTION100
3.8093-4.79870.21521340.18012553X-RAY DIFFRACTION100
4.7987-48.58110.25651410.21122660X-RAY DIFFRACTION99

+
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