[English] 日本語
Yorodumi
- PDB-4q7m: Structure of NBD288-Avi of TM287/288 -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 4q7m
TitleStructure of NBD288-Avi of TM287/288
ComponentsUncharacterized ABC transporter ATP-binding protein TM_0288
KeywordsMETAL BINDING PROTEIN / ABC-type Nucleotide Binding Domain (NBD)
Function / homology
Function and homology information


ATPase-coupled transmembrane transporter activity / ABC-type transporter activity / transmembrane transport / ATP hydrolysis activity / ATP binding / plasma membrane
Similarity search - Function
Type 1 protein exporter / ABC transporter transmembrane region / ABC transporter type 1, transmembrane domain / ABC transporter integral membrane type-1 fused domain profile. / ABC transporter type 1, transmembrane domain superfamily / ABC transporter / ABC transporter-like, ATP-binding domain / ATP-binding cassette, ABC transporter-type domain profile. / P-loop containing nucleotide triphosphate hydrolases / ATPases associated with a variety of cellular activities ...Type 1 protein exporter / ABC transporter transmembrane region / ABC transporter type 1, transmembrane domain / ABC transporter integral membrane type-1 fused domain profile. / ABC transporter type 1, transmembrane domain superfamily / ABC transporter / ABC transporter-like, ATP-binding domain / ATP-binding cassette, ABC transporter-type domain profile. / 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 / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Uncharacterized ABC transporter ATP-binding protein TM_0288
Similarity search - Component
Biological speciesThermotoga maritima (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
AuthorsBukowska, M.A. / Hohl, M. / Gruetter, M.G. / Seeger, M.A.
CitationJournal: Biochemistry / Year: 2015
Title: A Transporter Motor Taken Apart: Flexibility in the Nucleotide Binding Domains of a Heterodimeric ABC Exporter.
Authors: Bukowska, M.A. / Hohl, M. / Geertsma, E.R. / Hurlimann, L.M. / Grutter, M.G. / Seeger, M.A.
History
DepositionApr 25, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 20, 2015Provider: repository / Type: Initial release
Revision 1.1Jun 3, 2015Group: Database references
Revision 1.2Nov 22, 2017Group: Refinement description / Category: software
Revision 1.3Feb 28, 2024Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
B: Uncharacterized ABC transporter ATP-binding protein TM_0288


Theoretical massNumber of molelcules
Total (without water)30,6911
Polymers30,6911
Non-polymers00
Water2,306128
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)58.300, 58.300, 208.690
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Space group name H-MP3221
Components on special symmetry positions
IDModelComponents
11B-701-

HOH

21B-822-

HOH

-
Components

#1: Protein Uncharacterized ABC transporter ATP-binding protein TM_0288


Mass: 30691.256 Da / Num. of mol.: 1 / Fragment: unp residues 353-598
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermotoga maritima (bacteria) / Strain: ATCC 43589 / MSB8 / DSM 3109 / JCM 10099 / Gene: TM_0288 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9WYC4
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 128 / 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: 3.34 Å3/Da / Density % sol: 63.13 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, sitting drop / pH: 5.5
Details: 100 mM Sodium acetate, 6 % PEG550 MME, 6 % PEG20000, 200 mM MgCl2, pH 5.5, VAPOR DIFFUSION, SITTING DROP, temperature 293.15K

-
Data collection

DiffractionMean temperature: 90 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 0.9999 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Sep 14, 2012
RadiationMonochromator: mirror / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9999 Å / Relative weight: 1
ReflectionResolution: 2.3→50.489 Å / Num. all: 19151 / Num. obs: 19132 / % possible obs: 99.9 % / Observed criterion σ(F): -3

-
Processing

Software
NameVersionClassification
PHASERphasing
PHENIX(phenix.refine: 1.9_1678)refinement
XDSdata reduction
XSCALEdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.3→50.489 Å / SU ML: 0.24 / σ(F): 1.36 / Phase error: 23.19 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.236 957 5 %random
Rwork0.1806 ---
obs0.1834 19132 99.9 %-
all-19151 --
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.3→50.489 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2020 0 0 128 2148
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0062069
X-RAY DIFFRACTIONf_angle_d0.9442790
X-RAY DIFFRACTIONf_dihedral_angle_d13.922782
X-RAY DIFFRACTIONf_chiral_restr0.039322
X-RAY DIFFRACTIONf_plane_restr0.003355
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.3003-2.42160.27091340.22812550X-RAY DIFFRACTION100
2.4216-2.57330.26561330.20872521X-RAY DIFFRACTION100
2.5733-2.7720.26051340.20112557X-RAY DIFFRACTION100
2.772-3.05090.25431360.20792575X-RAY DIFFRACTION100
3.0509-3.49230.25291350.19362575X-RAY DIFFRACTION100
3.4923-4.39950.22231380.16022617X-RAY DIFFRACTION99
4.3995-50.50140.21661470.16372780X-RAY DIFFRACTION100
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)
11.2564-0.6636-0.46750.96960.02791.6548-0.19920.1072-0.1984-0.50460.3175-0.27610.21710.28620.02230.26120.1222-0.00140.30540.01240.286611.7594-8.6443-14.1806
20.51870.4306-0.71351.102-0.22531.0430.069-0.2083-0.0879-0.1292-0.08060.08240.12250.00310.00050.27070.1086-0.00750.2907-0.01660.29356.9143-4.0564-9.7194
32.6548-1.462-1.17592.5105-0.82612.26010.35910.29140.0539-0.2937-0.18250.0911-0.3461-0.31680.01940.39090.16030.00630.3067-0.00230.3093-8.569818.3722-11.7646
41.35570.1606-0.10.38870.30970.26270.230.65220.044-0.41040.0561-0.22230.11540.20350.02410.44550.06880.04550.46590.06020.3131.904813.2847-20.0931
52.47930.08790.43390.59220.61092.3040.02450.3330.229-0.34260.06780.1237-0.14740.4040.00010.3970.07480.01430.41410.01510.283611.60320.3413-27.1048
60.3814-0.2363-0.04770.00960.31390.7502-0.09090.0217-0.0271-0.04210.0443-0.0167-0.44220.4598-0.00180.4882-0.04810.04640.3119-0.0820.35387.5935-0.9453-55.0333
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(chain B and resid 352:383)
2X-RAY DIFFRACTION2(chain B and resid 384:436)
3X-RAY DIFFRACTION3(chain B and resid 437:506)
4X-RAY DIFFRACTION4(chain B and resid 507:538)
5X-RAY DIFFRACTION5(chain B and resid 539:580)
6X-RAY DIFFRACTION6(chain B and resid 581:609)

+
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