[English] 日本語
Yorodumi
- PDB-2yz2: Crystal structure of the ABC transporter in the cobalt transport ... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 2yz2
TitleCrystal structure of the ABC transporter in the cobalt transport system
ComponentsPutative ABC transporter ATP-binding protein TM_0222
KeywordsHYDROLASE / ABC Transporter / Cobalt transport / ATP-binding protein / TM0222 / Inner membrane / Membrane / Nucleotide-binding / Structural Genomics / NPPSFA / National Project on Protein Structural and Functional Analyses / RIKEN Structural Genomics/Proteomics Initiative / RSGI
Function / homology
Function and homology information


Translocases / riboflavin transport / riboflavin transmembrane transporter activity / ATPase-coupled transmembrane transporter activity / ATP-binding cassette (ABC) transporter complex / ATP hydrolysis activity / ATP binding / plasma membrane
Similarity search - Function
ABC transporter, CbiO/EcfA subunit / : / ABC transporter-like, conserved site / ABC transporters family signature. / 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 ...ABC transporter, CbiO/EcfA subunit / : / ABC transporter-like, conserved site / ABC transporters family signature. / 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 / Rossmann fold / P-loop containing nucleoside triphosphate hydrolase / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Energy-coupling factor transporter ATP-binding protein EcfA2
Similarity search - Component
Biological speciesThermotoga maritima (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.3 Å
AuthorsEthayathullah, A.S. / Bessho, Y. / Padmanabhan, B. / Singh, T.P. / Kaur, P. / Yokoyama, S. / RIKEN Structural Genomics/Proteomics Initiative (RSGI)
CitationJournal: To be Published
Title: Crystal structure of the ABC transporter in the cobalt transport system
Authors: Ethayathullah, A.S. / Bessho, Y. / Padmanabhan, B. / Singh, T.P. / Kaur, P. / Yokoyama, S.
History
DepositionMay 2, 2007Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Nov 6, 2007Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Source and taxonomy / Version format compliance
Revision 1.2Mar 13, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Putative ABC transporter ATP-binding protein TM_0222
B: Putative ABC transporter ATP-binding protein TM_0222


Theoretical massNumber of molelcules
Total (without water)60,5522
Polymers60,5522
Non-polymers00
Water8,575476
1
A: Putative ABC transporter ATP-binding protein TM_0222
B: Putative ABC transporter ATP-binding protein TM_0222

A: Putative ABC transporter ATP-binding protein TM_0222
B: Putative ABC transporter ATP-binding protein TM_0222

A: Putative ABC transporter ATP-binding protein TM_0222
B: Putative ABC transporter ATP-binding protein TM_0222

A: Putative ABC transporter ATP-binding protein TM_0222
B: Putative ABC transporter ATP-binding protein TM_0222


Theoretical massNumber of molelcules
Total (without water)242,2088
Polymers242,2088
Non-polymers00
Water1448
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_665-x+1,-y+1,z1
crystal symmetry operation7_555y,x,-z+1/31
crystal symmetry operation10_665-y+1,-x+1,-z+1/31
Buried area20054.1 Å2
MethodPISA
2
A: Putative ABC transporter ATP-binding protein TM_0222
B: Putative ABC transporter ATP-binding protein TM_0222

A: Putative ABC transporter ATP-binding protein TM_0222
B: Putative ABC transporter ATP-binding protein TM_0222


Theoretical massNumber of molelcules
Total (without water)121,1044
Polymers121,1044
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_665-x+1,-y+1,z1
Buried area8043.2 Å2
MethodPISA
Unit cell
Length a, b, c (Å)148.499, 148.499, 106.967
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number181
Space group name H-MP6422

-
Components

#1: Protein Putative ABC transporter ATP-binding protein TM_0222 / Putative cobalt import ATP-binding protein cbiO 1


Mass: 30276.000 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermotoga maritima (bacteria) / Strain: MSB8 / Plasmid: pET-21a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21-CodonPlus (DE3)-RIL-X
References: UniProt: Q9WY65, Hydrolases; Acting on acid anhydrides; Acting on acid anhydrides to catalyse transmembrane movement of substances
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 476 / 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: 2.81 Å3/Da / Density % sol: 56.25 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8
Details: 0.2M potassium flouride, 20% (w/v) PEG 3350 (PEG/ION-2), pH 8.0, VAPOR DIFFUSION, SITTING DROP, temperature 293K

-
Data collection

DiffractionMean temperature: 120 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL26B1 / Wavelength: 0.97891, 0.90000, 0.97934
DetectorType: RIGAKU JUPITER 210 / Detector: CCD
RadiationMonochromator: Si double crystal monochromator / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.978911
20.91
30.979341
ReflectionResolution: 2.3→50 Å / Num. all: 31565 / Num. obs: 31555 / % possible obs: 100 % / Observed criterion σ(F): -3 / Redundancy: 21.3 % / Rmerge(I) obs: 0.117
Reflection shellResolution: 2.3→2.38 Å / Redundancy: 17.8 % / Rmerge(I) obs: 0.49 / Num. unique all: 3095 / % possible all: 100

-
Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
ADSCQuantumdata collection
HKL-2000data reduction
SCALEPACKdata scaling
SOLVEphasing
RefinementMethod to determine structure: MAD / Resolution: 2.3→20 Å / Cor.coef. Fo:Fc: 0.906 / Cor.coef. Fo:Fc free: 0.83 / SU B: 7.397 / SU ML: 0.189 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.38 / ESU R Free: 0.292 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.29403 1467 5 %RANDOM
Rwork0.21352 ---
obs0.21751 27606 92.77 %-
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: 42.895 Å2
Baniso -1Baniso -2Baniso -3
1-0.87 Å20.44 Å20 Å2
2--0.87 Å20 Å2
3----1.31 Å2
Refinement stepCycle: LAST / Resolution: 2.3→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4223 0 0 476 4699
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0240.0224345
X-RAY DIFFRACTIONr_angle_refined_deg1.9991.9825859
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.5835532
X-RAY DIFFRACTIONr_dihedral_angle_2_deg40.73823.695203
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.07215812
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.8291536
X-RAY DIFFRACTIONr_chiral_restr0.1420.2663
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.023242
X-RAY DIFFRACTIONr_nbd_refined0.2360.22308
X-RAY DIFFRACTIONr_nbtor_refined0.3160.22992
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2080.2347
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2050.292
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2370.224
X-RAY DIFFRACTIONr_mcbond_it1.2641.52745
X-RAY DIFFRACTIONr_mcangle_it1.93424306
X-RAY DIFFRACTIONr_scbond_it3.12531801
X-RAY DIFFRACTIONr_scangle_it4.6684.51552
LS refinement shellResolution: 2.3→2.359 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.295 92 -
Rwork0.18 1525 -
obs--71.45 %

+
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