[English] 日本語
Yorodumi
- PDB-2onk: ABC transporter ModBC in complex with its binding protein ModA -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 2onk
TitleABC transporter ModBC in complex with its binding protein ModA
Components
  • (Molybdate/tungstate ABC transporter, ...) x 2
  • Molybdate/tungstate binding protein
KeywordsMEMBRANE PROTEIN
Function / homology
Function and homology information


ABC-type tungstate transporter / ABC-type tungstate transporter activity / tungstate binding / transmembrane transport / membrane => GO:0016020 / ATP hydrolysis activity / ATP binding / metal ion binding / plasma membrane
Similarity search - Function
Tungstate ABC transporter, substrate-binding protein WtpA / MetI-like fold / MetI-like / Bacterial extracellular solute-binding protein / ABC transporter type 1, transmembrane domain MetI-like / MetI-like superfamily / Binding-protein-dependent transport system inner membrane component / ABC transporter integral membrane type-1 domain profile. / Bacterial extracellular solute-binding protein / ABC transporter-like, conserved site ...Tungstate ABC transporter, substrate-binding protein WtpA / MetI-like fold / MetI-like / Bacterial extracellular solute-binding protein / ABC transporter type 1, transmembrane domain MetI-like / MetI-like superfamily / Binding-protein-dependent transport system inner membrane component / ABC transporter integral membrane type-1 domain profile. / Bacterial extracellular solute-binding protein / ABC transporter-like, conserved site / ABC transporters family signature. / Periplasmic binding protein-like II / ABC transporter / ABC transporter-like, ATP-binding domain / ATP-binding cassette, ABC transporter-type domain profile. / D-Maltodextrin-Binding Protein; domain 2 / P-loop containing nucleotide triphosphate hydrolases / ATPases associated with a variety of cellular activities / AAA+ ATPase domain / P-loop containing nucleoside triphosphate hydrolase / Rossmann fold / Orthogonal Bundle / 3-Layer(aba) Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
PHOSPHATE ION / TUNGSTATE(VI)ION / Molybdate/tungstate-binding protein WtpA / Molybdate/tungstate transport system permease protein WtpB / Molybdate/tungstate import ATP-binding protein WtpC
Similarity search - Component
Biological speciesArchaeoglobus fulgidus (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 3.1 Å
AuthorsHollenstein, K. / Frei, D.C. / Locher, K.P.
CitationJournal: Nature / Year: 2007
Title: Structure of an ABC transporter in complex with its binding protein.
Authors: Hollenstein, K. / Frei, D.C. / Locher, K.P.
History
DepositionJan 24, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 6, 2007Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Dec 27, 2023Group: 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_asym_id / _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_asym_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_asym_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_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 / _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: Molybdate/tungstate ABC transporter, ATP-binding protein
B: Molybdate/tungstate ABC transporter, ATP-binding protein
F: Molybdate/tungstate ABC transporter, ATP-binding protein
G: Molybdate/tungstate ABC transporter, ATP-binding protein
C: Molybdate/tungstate ABC transporter, permease protein
D: Molybdate/tungstate ABC transporter, permease protein
H: Molybdate/tungstate ABC transporter, permease protein
I: Molybdate/tungstate ABC transporter, permease protein
E: Molybdate/tungstate binding protein
J: Molybdate/tungstate binding protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)303,30922
Polymers302,28710
Non-polymers1,02112
Water0
1
A: Molybdate/tungstate ABC transporter, ATP-binding protein
B: Molybdate/tungstate ABC transporter, ATP-binding protein
C: Molybdate/tungstate ABC transporter, permease protein
D: Molybdate/tungstate ABC transporter, permease protein
E: Molybdate/tungstate binding protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)151,65411
Polymers151,1445
Non-polymers5116
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area17640 Å2
ΔGint-179 kcal/mol
Surface area52070 Å2
MethodPISA
2
F: Molybdate/tungstate ABC transporter, ATP-binding protein
G: Molybdate/tungstate ABC transporter, ATP-binding protein
H: Molybdate/tungstate ABC transporter, permease protein
I: Molybdate/tungstate ABC transporter, permease protein
J: Molybdate/tungstate binding protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)151,65411
Polymers151,1445
Non-polymers5116
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)93.032, 171.203, 158.470
Angle α, β, γ (deg.)90.00, 98.79, 90.00
Int Tables number4
Space group name H-MP1211

-
Components

-
Molybdate/tungstate ABC transporter, ... , 2 types, 8 molecules ABFGCDHI

#1: Protein
Molybdate/tungstate ABC transporter, ATP-binding protein / CysA / AF0092 / ModC


Mass: 27069.809 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Archaeoglobus fulgidus (archaea) / Production host: Escherichia coli (E. coli) / References: UniProt: O30144
#2: Protein
Molybdate/tungstate ABC transporter, permease protein / CysT / AF0093 / ModB


Mass: 30643.141 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Archaeoglobus fulgidus (archaea) / Production host: Escherichia coli (E. coli) / References: UniProt: O30143

-
Protein , 1 types, 2 molecules EJ

#3: Protein Molybdate/tungstate binding protein


Mass: 35717.785 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Archaeoglobus fulgidus (archaea) / Production host: Escherichia coli (E. coli) / References: UniProt: O30142

-
Non-polymers , 3 types, 12 molecules

#4: Chemical
ChemComp-PO4 / PHOSPHATE ION / Phosphate


Mass: 94.971 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: PO4
#5: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Mg
#6: Chemical ChemComp-WO4 / TUNGSTATE(VI)ION


Mass: 247.838 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: WO4

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 4.12 Å3/Da / Density % sol: 70.17 %

-
Data collection

Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06SA
RadiationProtocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthRelative weight: 1
ReflectionResolution: 3.1→30 Å / Num. obs: 88979

-
Processing

Software
NameVersionClassificationNB
CNSrefinement
PDB_EXTRACT2data extraction
RefinementMethod to determine structure: MAD / Resolution: 3.1→30 Å / σ(F): 0
RfactorNum. reflection% reflection
Rfree0.283 4387 4.9 %
Rwork0.256 --
obs0.256 88712 100 %
all-93099 -
Solvent computationBsol: 48.43 Å2
Displacement parametersBiso mean: 99.93 Å2
Baniso -1Baniso -2Baniso -3
1--4.647 Å20 Å2-1.735 Å2
2--3.504 Å20 Å2
3---1.144 Å2
Refinement stepCycle: LAST / Resolution: 3.1→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms20182 0 36 0 20218
Xplor file
Refine-IDSerial noParam file
X-RAY DIFFRACTION1PROTEIN_REP.PARAM
X-RAY DIFFRACTION2ION.PARAM
X-RAY DIFFRACTION3PO4.PARAM

+
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