[English] 日本語
Yorodumi
- PDB-3cni: Crystal structure of a domain of a putative ABC type-2 transporte... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 3cni
TitleCrystal structure of a domain of a putative ABC type-2 transporter from Thermotoga maritima MSB8
ComponentsPutative ABC type-2 transporter
KeywordsTRANSPORT PROTEIN / STRUCTURAL GENOMICS / ABC TYPE-2 TRANSPORTER / THERMOTOGA MARITIMA / PSI-2 / Protein Structure Initiative / Midwest Center for Structural Genomics / MCSG
Function / homology
Function and homology information


transmembrane transporter activity / ATP-binding cassette (ABC) transporter complex / transmembrane transport / metal ion binding / plasma membrane
Similarity search - Function
abc type-2 transporter like fold / abc type-2 transporter like domain / ABC-2 transporter / ABC transporter integral membrane type-2 domain profile. / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Uncharacterized protein
Similarity search - Component
Biological speciesThermotoga maritima MSB8 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.3 Å
AuthorsFilippova, E.V. / Shumilin, I. / Tkaczuk, K.L. / Cymborowski, M. / Chruszcz, M. / Xu, X. / Que, Q. / Savchenko, A. / Edwards, A.M. / Joachimiak, A. ...Filippova, E.V. / Shumilin, I. / Tkaczuk, K.L. / Cymborowski, M. / Chruszcz, M. / Xu, X. / Que, Q. / Savchenko, A. / Edwards, A.M. / Joachimiak, A. / Minor, W. / Midwest Center for Structural Genomics (MCSG)
CitationJournal: J.Struct.Funct.Genom. / Year: 2014
Title: Structural characterization of the putative ABC-type 2 transporter from Thermotoga maritima MSB8.
Authors: Filippova, E.V. / Tkaczuk, K.L. / Chruszcz, M. / Xu, X. / Savchenko, A. / Edwards, A. / Minor, W.
History
DepositionMar 25, 2008Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 8, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2Oct 5, 2011Group: Structure summary
Revision 1.3Oct 29, 2014Group: Database references
Revision 1.4Feb 4, 2015Group: Database references
Revision 1.5Apr 13, 2022Group: Database references / Derived calculations / Structure summary
Category: audit_author / citation_author ...audit_author / citation_author / database_2 / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _audit_author.identifier_ORCID / _citation_author.identifier_ORCID ..._audit_author.identifier_ORCID / _citation_author.identifier_ORCID / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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.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.pdbx_leaving_atom_flag / _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_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_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: Putative ABC type-2 transporter
hetero molecules


Theoretical massNumber of molelcules
Total (without water)17,2173
Polymers17,1371
Non-polymers802
Water55831
1
A: Putative ABC type-2 transporter
hetero molecules

A: Putative ABC type-2 transporter
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,4356
Polymers34,2752
Non-polymers1604
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_655-x+1,-y,z1
Buried area2260 Å2
ΔGint-23.2 kcal/mol
Surface area12900 Å2
MethodPISA
Unit cell
Length a, b, c (Å)65.598, 65.598, 141.192
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number181
Space group name H-MP6422
Components on special symmetry positions
IDModelComponents
11A-202-

CA

-
Components

#1: Protein Putative ABC type-2 transporter


Mass: 17137.287 Da / Num. of mol.: 1 / Fragment: Domain: Residues 37-192
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermotoga maritima MSB8 (bacteria) / Species: Thermotoga maritima / Strain: MSB8 / DSM 3109 / JCM 10099 / Gene: TM_0543 / Plasmid: p15TV LIC / Production host: Escherichia coli (E. coli) / Strain (production host): BL21-CODONPLUS(DE3)-RIPL / References: UniProt: Q9WZ13
#2: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ca
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 31 / 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: 2.56 Å3/Da / Density % sol: 51.93 %
Crystal growTemperature: 273 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 0.1M Na Hepes, 0.2M CaCl2, 28% PEG 400, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 273K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-BM / Wavelength: 0.97934 Å
DetectorType: APS-1 / Detector: CCD / Date: Feb 24, 2008 / Details: Mirror
RadiationMonochromator: SI(111) CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97934 Å / Relative weight: 1
ReflectionResolution: 2.3→56.8 Å / Num. obs: 8587 / % possible obs: 99.6 % / Observed criterion σ(I): -3 / Redundancy: 13.4 % / Biso Wilson estimate: 64.88 Å2 / Rmerge(I) obs: 0.05 / Rsym value: 0.05 / Net I/σ(I): 65.696
Reflection shellResolution: 2.3→2.34 Å / Redundancy: 10.6 % / Rmerge(I) obs: 0.713 / Mean I/σ(I) obs: 3.4 / Rsym value: 0.713 / % possible all: 99.2

-
Processing

Software
NameVersionClassification
HKL-3000phasing
MLPHAREphasing
DMmodel building
SHELXDphasing
ARP/wARPmodel building
SHELXEmodel building
RESOLVEmodel building
Cootmodel building
CCP4model building
REFMAC5.4.0069refinement
HKL-3000data reduction
HKL-2000data scaling
DMphasing
RESOLVEphasing
CCP4phasing
RefinementMethod to determine structure: SAD / Resolution: 2.3→56.8 Å / Cor.coef. Fo:Fc: 0.961 / Cor.coef. Fo:Fc free: 0.959 / SU B: 15.17 / SU ML: 0.181 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.271 / ESU R Free: 0.199 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.227 403 4.7 %RANDOM
Rwork0.204 ---
obs0.205 8537 99.44 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 51.47 Å2
Baniso -1Baniso -2Baniso -3
1--1.22 Å2-0.61 Å20 Å2
2---1.22 Å20 Å2
3---1.84 Å2
Refinement stepCycle: LAST / Resolution: 2.3→56.8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1092 0 2 31 1125
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0220.0221125
X-RAY DIFFRACTIONr_bond_other_d0.0020.02741
X-RAY DIFFRACTIONr_angle_refined_deg1.8021.9811528
X-RAY DIFFRACTIONr_angle_other_deg1.51731837
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.995148
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.28725.95242
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.37515199
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.184152
X-RAY DIFFRACTIONr_chiral_restr0.0920.2184
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.021241
X-RAY DIFFRACTIONr_gen_planes_other0.0030.02204
X-RAY DIFFRACTIONr_mcbond_it0.911.5726
X-RAY DIFFRACTIONr_mcbond_other0.2111.5295
X-RAY DIFFRACTIONr_mcangle_it1.65521171
X-RAY DIFFRACTIONr_scbond_it2.5793399
X-RAY DIFFRACTIONr_scangle_it4.2214.5355
LS refinement shellResolution: 2.3→2.36 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.408 26 -
Rwork0.283 591 -
obs--99.2 %
Refinement TLS params.Method: refined / Origin x: 22.089 Å / Origin y: 5.2863 Å / Origin z: 15.0134 Å
111213212223313233
T-0.105 Å2-0.0211 Å20.0208 Å2--0.2293 Å20.0126 Å2---0.1311 Å2
L4.6499 °20.8844 °2-1.7092 °2-3.8027 °2-0.7341 °2--3.4212 °2
S0.2674 Å °-0.0722 Å °0.4007 Å °-0.3023 Å °0.0747 Å °0.7186 Å °-0.2668 Å °-0.2069 Å °-0.342 Å °

+
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