[English] 日本語
Yorodumi
- PDB-6amx: Crystal Structure of Nucelotide Binding Domain of O-antigen polys... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6amx
TitleCrystal Structure of Nucelotide Binding Domain of O-antigen polysaccharide ABC-transporter
ComponentsABC transporter
KeywordsTRANSPORT PROTEIN / Nucleotide Binding Domain from abcT4
Function / homology
Function and homology information


ABC-type transporter activity / ATP hydrolysis activity / ATP binding / membrane
Similarity search - Function
Wzt, C-terminal / Wzt C-terminal domain / ABC transporter, teichoic acids export TagH-like / 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. / ATPases associated with a variety of cellular activities / AAA+ ATPase domain / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
Biological speciesAquifex aeolicus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.05 Å
AuthorsZimmer, J. / Bi, Y.
CitationJournal: Nature / Year: 2018
Title: Architecture of a channel-forming O-antigen polysaccharide ABC transporter.
Authors: Bi, Y. / Mann, E. / Whitfield, C. / Zimmer, J.
History
DepositionAug 11, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 29, 2017Provider: repository / Type: Initial release
Revision 1.1Jan 24, 2018Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Jan 31, 2018Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.3Mar 13, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: ABC transporter
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,0517
Polymers27,6601
Non-polymers2,3916
Water70339
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2050 Å2
ΔGint10 kcal/mol
Surface area13230 Å2
MethodPISA
Unit cell
Length a, b, c (Å)96.220, 96.220, 60.930
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number152
Space group name H-MP3121

-
Components

#1: Protein ABC transporter


Mass: 27660.098 Da / Num. of mol.: 1 / Fragment: Nucelotide Binding Domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Aquifex aeolicus (strain VF5) (bacteria)
Strain: VF5 / Gene: abcT4, aq_1094 / Plasmid: pETDuet / Production host: Escherichia coli (E. coli) / Strain (production host): C43 / References: UniProt: O67181
#2: Chemical
ChemComp-PE5 / 3,6,9,12,15,18,21,24-OCTAOXAHEXACOSAN-1-OL / 2-(2-{2-[2-(2-{2-[2-(2-ETHOXY-ETHOXY)-ETHOXY]-ETHOXY}-ETHOXY)-ETHOXY]-ETHOXY}-ETHOXY)-ETHANOL / POLYETHYLENE GLYCOL PEG400


Mass: 398.489 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C18H38O9 / Comment: precipitant*YM
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 39 / 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: 2.99 Å3/Da / Density % sol: 58.84 % / Mosaicity: 0.58 °
Crystal growTemperature: 290 K / Method: vapor diffusion, sitting drop / pH: 5.4
Details: 41% PEG400, 0.05 M sodium acetate, 0.15 M magnesium acetate, 47 mM octyl-glucoside

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Apr 24, 2016 / Details: 4*4 mosiac
RadiationMonochromator: double crystal - liquid nitrogen cooled / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.05→31.5 Å / Num. obs: 20289 / % possible obs: 98.3 % / Redundancy: 4.8 % / CC1/2: 0.997 / Rmerge(I) obs: 0.078 / Rpim(I) all: 0.039 / Rrim(I) all: 0.088 / Net I/σ(I): 9.5 / Num. measured all: 96755 / Scaling rejects: 8
Reflection shell

Diffraction-ID: 1 / Resolution: 2.05→2.11 Å

Redundancy (%)Num. unique obsCC1/2Rpim(I) allRrim(I) all% possible allRmerge(I) obs
4.716070.8240.6141.3799.3
3.71970.9990.0160.03470.80.03

-
Processing

Software
NameVersionClassification
Aimless0.5.32data scaling
PHENIX1.11.1_2575refinement
PDB_EXTRACT3.22data extraction
Aimlessdata reduction
PHENIXphasing
RefinementResolution: 2.05→27.776 Å / SU ML: 0.29 / Cross valid method: FREE R-VALUE / σ(F): 0.02 / Phase error: 30.5
RfactorNum. reflection% reflection
Rfree0.2343 1004 4.65 %
Rwork0.2024 --
obs0.204 20289 95.83 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 175.12 Å2 / Biso mean: 67.4949 Å2 / Biso min: 32.69 Å2
Refinement stepCycle: final / Resolution: 2.05→27.776 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1919 0 63 39 2021
Biso mean--77.82 59.02 -
Num. residues----239
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0082015
X-RAY DIFFRACTIONf_angle_d0.8592682
X-RAY DIFFRACTIONf_chiral_restr0.052291
X-RAY DIFFRACTIONf_plane_restr0.006331
X-RAY DIFFRACTIONf_dihedral_angle_d6.4371210
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Highest resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.0502-2.10560.4363143284297
2.1056-2.16750.3382160275697
2.1675-2.23750.306598290197
2.2375-2.31740.3201120282997
2.3174-2.41010.2895151276996
2.4101-2.51970.2427164274795
2.5197-2.65250.2798134280196
2.6525-2.81850.2583140278997
2.8185-3.03590.2335134278196
3.0359-3.3410.2416127280796
3.341-3.82330.2009126277795
3.8233-4.81290.18831410.1561275495
4.81290.22611280.18262390
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)
12.32220.2859-0.3094.15030.9143.46960.2515-0.48870.85030.1229-0.1028-0.1492-1.93660.1194-0.07160.979-0.1362-0.02090.5407-0.02230.706633.926-10.24084.9775
23.62210.5838-1.10351.1187-0.7583.9786-0.12220.31970.182-0.24510.18420.34370.3173-0.7786-0.04550.3929-0.0823-0.06590.4339-0.00210.32214.7277-32.1079-2.4176
32.39152.9926-0.36796.21091.06231.59940.1193-0.2583-0.76350.7022-0.1583-0.00620.94540.2730.09280.6472-0.08440.00670.63060.05230.430121.2296-37.6995-2.3135
49.74431.7303-2.95866.3913-2.39198.0006-0.15890.2082-1.15160.32050.0964-0.04871.0511-0.28250.05870.6829-0.1468-0.0240.3595-0.0650.52319.5022-45.0262-7.8345
58.65261.55170.36363.77540.13463.33710.2320.015-0.25340.0663-0.1701-0.29780.66990.35760.02330.39860.0444-0.00690.44210.02630.227835.7111-35.7217-5.9843
6-0.03250.02340.05991.33212.82518.19080.2139-0.1201-0.56360.0247-0.4661-0.85180.6951.4675-0.33950.51570.1146-0.11480.80470.10.476646.5589-36.2292-0.1087
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 2 through 40 )A2 - 40
2X-RAY DIFFRACTION2chain 'A' and (resid 41 through 157 )A41 - 157
3X-RAY DIFFRACTION3chain 'A' and (resid 158 through 175 )A158 - 175
4X-RAY DIFFRACTION4chain 'A' and (resid 176 through 189 )A176 - 189
5X-RAY DIFFRACTION5chain 'A' and (resid 190 through 224 )A190 - 224
6X-RAY DIFFRACTION6chain 'A' and (resid 225 through 240 )A225 - 240

+
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