[English] 日本語
Yorodumi
- PDB-3skx: Crystal structure of the ATP binding domain of Archaeoglobus fulg... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 3skx
TitleCrystal structure of the ATP binding domain of Archaeoglobus fulgidus COPB
ComponentsCopper-exporting P-type ATPase B
KeywordsHYDROLASE / P1B-ATPase / ATP binding domain / copper(II) transporter / membrane protein
Function / homology
Function and homology information


P-type Cu2+ transporter / P-type divalent copper transporter activity / ATP hydrolysis activity / ATP binding / metal ion binding / plasma membrane
Similarity search - Function
P-type ATPase, subfamily IB / Calcium-transporting ATPase, cytoplasmic domain N / Calcium-transporting ATPase, cytoplasmic domain N / E1-E2 ATPase / P-type ATPase, haloacid dehalogenase domain / 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 ...P-type ATPase, subfamily IB / Calcium-transporting ATPase, cytoplasmic domain N / Calcium-transporting ATPase, cytoplasmic domain N / E1-E2 ATPase / P-type ATPase, haloacid dehalogenase domain / 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 / P-type ATPase, transmembrane domain superfamily / HAD superfamily/HAD-like / haloacid dehalogenase-like hydrolase / HAD superfamily / HAD-like superfamily / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
ACETATE ION / Copper-exporting P-type ATPase B
Similarity search - Component
Biological speciesArchaeoglobus fulgidus (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.59 Å
AuthorsJayakanthan, S. / Roberts, S.A. / Weichsel, A. / Arguello, J.M. / McEvoy, M.M.
CitationJournal: Biosci.Rep. / Year: 2012
Title: Conformations of the apo-, substrate-bound and phosphate-bound ATP-binding domain of the Cu(II) ATPase CopB illustrate coupling of domain movement to the catalytic cycle.
Authors: Jayakanthan, S. / Roberts, S.A. / Weichsel, A. / Arguello, J.M. / McEvoy, M.M.
History
DepositionJun 23, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 20, 2012Provider: repository / Type: Initial release
Revision 1.1Sep 26, 2012Group: Database references
Revision 1.2Feb 28, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / 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 / _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: Copper-exporting P-type ATPase B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,8413
Polymers30,7231
Non-polymers1182
Water4,648258
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)36.052, 62.682, 106.059
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP22121

-
Components

#1: Protein Copper-exporting P-type ATPase B


Mass: 30723.006 Da / Num. of mol.: 1 / Fragment: ATP binding domain (UNP residues 372-636)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Archaeoglobus fulgidus (archaea) / Strain: DSM 4304 / Gene: AF_0152, copB / Plasmid: pPR-IBAI / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta 2(DE3)pLysS / References: UniProt: O30085, Cu2+-exporting ATPase
#2: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H3O2
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 258 / 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: 1.95 Å3/Da / Density % sol: 36.93 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: 0.2M Sodium acetate, 0.1M TRIS.HCl pH 8.5, 30% PEG 4000, 0.01M Magnesium chloride, VAPOR DIFFUSION, HANGING DROP, temperature 298K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL9-2 / Wavelength: 0.97920, 0.9792, 0.9116, 0.9793
DetectorType: MARMOSAIC 325 mm CCD / Detector: CCD / Date: Apr 20, 2011
RadiationProtocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.97921
20.97921
30.91161
40.97931
ReflectionResolution: 1.59→106.06 Å / Num. all: 31479 / Num. obs: 31479 / % possible obs: 95.3 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 5.63 % / Rmerge(I) obs: 0.033 / Net I/σ(I): 25
Reflection shellResolution: 1.59→1.65 Å / Redundancy: 4.61 % / Rmerge(I) obs: 0.237 / Mean I/σ(I) obs: 4.9 / % possible all: 93.8

-
Processing

Software
NameVersionClassification
Blu-Icedata collection
SOLVEphasing
REFMAC5.5.0109refinement
CrystalCleardata reduction
CrystalCleardata scaling
RefinementMethod to determine structure: MAD / Resolution: 1.59→106.06 Å / Cor.coef. Fo:Fc: 0.962 / Cor.coef. Fo:Fc free: 0.944 / SU B: 4.24 / SU ML: 0.068 / Cross valid method: THROUGHOUT / ESU R: 0.112 / ESU R Free: 0.107 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.23316 1604 5.1 %RANDOM
Rwork0.20095 ---
obs0.2026 29875 95.26 %-
all-31479 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 23.933 Å2
Baniso -1Baniso -2Baniso -3
1-0.85 Å20 Å20 Å2
2--0.42 Å20 Å2
3----1.28 Å2
Refinement stepCycle: LAST / Resolution: 1.59→106.06 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1971 0 8 258 2237
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0222108
X-RAY DIFFRACTIONr_bond_other_d0.0010.021437
X-RAY DIFFRACTIONr_angle_refined_deg1.2251.9722860
X-RAY DIFFRACTIONr_angle_other_deg0.78633528
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.8085286
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.10824.94795
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.5115385
X-RAY DIFFRACTIONr_dihedral_angle_4_deg11.6271515
X-RAY DIFFRACTIONr_chiral_restr0.0710.2326
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.022422
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02408
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_it0.6581.51350
X-RAY DIFFRACTIONr_mcbond_other0.1651.5556
X-RAY DIFFRACTIONr_mcangle_it1.22822172
X-RAY DIFFRACTIONr_scbond_it2.0773758
X-RAY DIFFRACTIONr_scangle_it3.5354.5681
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.593→1.634 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.339 118 -
Rwork0.372 2100 -
obs--92.61 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
14.3971-0.33823.97371.3281-0.33318.30880.33740.0833-0.3596-0.4216-0.09310.1030.5691-0.5863-0.24440.1897-0.0139-0.05120.1463-0.03080.103534.58210.09262.617
21.61890.52351.17733.57310.17383.24970.1487-0.3361-0.08930.6167-0.054-0.01030.0955-0.1276-0.09460.1738-0.02-0.00550.12050.02040.0446589.9892.831
32.95130.70721.70011.7330.24451.6899-0.0031-0.14670.16320.206-0.02440.1018-0.0558-0.08570.02750.10460.0099-0.00480.0868-0.01150.056856.93518.35485.852
41.49960.0854-0.18232.42831.0672.55810.01810.16460.0734-0.2096-0.07620.0911-0.0366-0.2160.05810.09040.0133-0.01170.11560.00420.048736.2716.33267.044
52.27660.50672.62644.51292.90057.82370.2497-0.2699-0.1262-0.0716-0.29520.32740.6469-0.61920.04550.2479-0.0692-0.00190.1681-0.05820.061832.6133.08959.716
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A375 - 398
2X-RAY DIFFRACTION2A399 - 483
3X-RAY DIFFRACTION3A484 - 514
4X-RAY DIFFRACTION4A515 - 600
5X-RAY DIFFRACTION5A601 - 635

+
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