[English] 日本語
Yorodumi
- PDB-6o14: Crystal structure of the Aquifex aeolicus Wzt Carbohydrate Bindin... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6o14
TitleCrystal structure of the Aquifex aeolicus Wzt Carbohydrate Binding Domain
ComponentsABC transporter
KeywordsMEMBRANE PROTEIN / ABC transporter / Wzt / Wzm / O antigen / Carbohydrate Binding Domain
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 VF5 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.65 Å
AuthorsBi, Y. / Zimmer, J.
Citation
Journal: Structure / Year: 2020
Title: Structure and Ligand-Binding Properties of the O Antigen ABC Transporter Carbohydrate-Binding Domain.
Authors: Bi, Y. / Zimmer, J.
#1: Journal: Nature / Year: 2018
Title: Architecture of a channel-forming O-antigen polysaccharide ABC transporter.
Authors: Bi, Y. / Mann, E. / Whitfield, C. / Zimmer, J.
History
DepositionFeb 17, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 15, 2020Provider: repository / Type: Initial release
Revision 1.1Feb 19, 2020Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.year
Revision 1.2Oct 11, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: ABC transporter
B: ABC transporter
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,5874
Polymers35,4032
Non-polymers1842
Water32418
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: light scattering
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4750 Å2
ΔGint-34 kcal/mol
Surface area14710 Å2
MethodPISA
2
A: ABC transporter
B: ABC transporter
hetero molecules

A: ABC transporter
B: ABC transporter
hetero molecules

A: ABC transporter
B: ABC transporter
hetero molecules


Theoretical massNumber of molelcules
Total (without water)106,76112
Polymers106,2096
Non-polymers5536
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_545-y,x-y-1,z1
crystal symmetry operation3_655-x+y+1,-x,z1
Buried area17610 Å2
ΔGint-103 kcal/mol
Surface area40800 Å2
MethodPISA
Unit cell
Length a, b, c (Å)128.345, 128.345, 45.158
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number173
Space group name H-MP63
Components on special symmetry positions
IDModelComponents
11A-603-

HOH

-
Components

#1: Protein ABC transporter


Mass: 17701.443 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Aquifex aeolicus VF5 (bacteria) / Strain: VF5 / Gene: abcT4, aq_1094 / Production host: Escherichia coli (E. coli) / References: UniProt: O67181
#2: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 18 / 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: 3.01 Å3/Da / Density % sol: 59.15 %
Crystal growTemperature: 300 K / Method: vapor diffusion, sitting drop / Details: 0.1 M MOPS pH 7, 1.5 M sodium acetate

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: NSLS-II / Beamline: 17-ID-1 / Wavelength: 0.987 Å
DetectorType: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Mar 15, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.987 Å / Relative weight: 1
ReflectionResolution: 2.65→28.65 Å / Num. obs: 12535 / % possible obs: 99.8 % / Redundancy: 9.2 % / CC1/2: 0.989 / Rmerge(I) obs: 0.2 / Rpim(I) all: 0.06 / Net I/av σ(I): 6.9 / Net I/σ(I): 6.9
Reflection shellResolution: 2.65→2.78 Å / Rmerge(I) obs: 1.14 / Mean I/σ(I) obs: 1.5 / Num. unique obs: 2392 / CC1/2: 0.731 / Rpim(I) all: 0.36

-
Processing

Software
NameVersionClassification
PHENIX(1.14_3260: ???)refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2R5O

2r5o


Resolution: 2.65→28.643 Å / SU ML: 0.36 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 30.38
RfactorNum. reflection% reflection
Rfree0.2391 614 4.9 %
Rwork0.1798 --
obs0.1828 12535 99.48 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.65→28.643 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2357 0 12 18 2387
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0082423
X-RAY DIFFRACTIONf_angle_d1.1383258
X-RAY DIFFRACTIONf_dihedral_angle_d5.4711440
X-RAY DIFFRACTIONf_chiral_restr0.059347
X-RAY DIFFRACTIONf_plane_restr0.006414
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.6503-2.91670.34151620.27752930X-RAY DIFFRACTION100
2.9167-3.33820.28251360.22042967X-RAY DIFFRACTION99
3.3382-4.20370.21771390.17162989X-RAY DIFFRACTION100
4.2037-28.6450.21811770.15013035X-RAY DIFFRACTION99
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)
12.46020.3058-1.70932.2776-1.67555.7777-0.22590.7594-0.6559-0.02620.40010.0670.5073-0.3003-0.12280.8151-0.0324-0.0740.74460.08440.279847.2113-38.9699-16.6055
25.6566-0.94571.70591.86163.26618.0594-0.36970.66410.499-0.29390.2896-0.23140.1270.7334-0.12030.4125-0.0364-0.05490.64240.10990.298661.6901-27.0574-7.3884
38.6691.58125.47551.67061.74167.50660.22141.0097-0.31320.0180.6361-0.52090.21210.4712-0.32940.5667-0.0357-0.04840.74490.01010.226851.5498-31.6317-16.051
43.6382-1.05870.07925.7857-0.15432.37430.68170.3402-0.5845-0.88260.19931.3298-0.1866-0.7233-0.40320.7769-0.1597-0.2691.03750.09470.512236.5177-34.8865-24.8272
53.17860.32952.58320.86431.64684.37630.2738-0.2043-0.2221-0.72630.2995-0.35320.5597-1.0984-0.97760.2137-0.0991-0.04040.68980.07260.321844.2275-32.0055-6.2519
61.90250.6472-2.68765.40663.00987.4001-0.6531-0.4211-0.53070.98030.4012-0.11541.0947-0.85050.26810.61950.00560.1010.7970.0470.217346.1981-31.56221.8725
70.7480.70540.84174.59132.28284.62520.17950.31530.303-0.8698-0.29530.4134-0.8262-1.80760.4810.70330.0026-0.06641.19150.02140.288138.62-26.5422-19.4524
81.1941-0.67662.45391.03840.20626.42030.00240.22010.0348-0.14920.18240.00130.1411-0.2018-0.06980.68810.02540.00480.6237-0.03240.205349.7429-30.2213-9.0447
96.02722.846-6.55971.6705-2.6357.8025-0.5177-0.03782.27211.52410.72461.87921.3701-1.5298-0.18130.847-0.1280.19721.392-0.06621.232229.6423-33.9947-12.6286
101.7540.16731.47731.18390.20641.11190.0318-0.0938-0.2129-0.60610.08-0.35041.5696-1.0733-0.17450.8012-0.2802-0.21051.0664-0.0134-0.288447.729-38.1534-7.2703
115.6464-2.5418-3.59872.81594.17366.22190.45590.00610.8794-0.07720.0384-0.2063-1.03860.3193-0.48760.65490.05350.02740.5340.00830.284860.2166-20.44465.2226
120.6398-0.5735-0.20668.54274.66093.27780.0832-0.09180.332-1.0068-0.0415-0.2469-1.2616-0.07220.17941.00640.0140.0980.6136-0.01480.403553.1745-2.85610.7959
132.82571.8906-1.66064.6272-0.40511.1263-0.2631-0.78470.11810.72970.0699-0.4508-1.72310.1487-0.06931.11390.08640.05170.7636-0.13390.436649.8646-3.940823.3789
146.11092.4629-0.04295.51151.13472.76740.19040.0890.455-0.19370.1180.4435-1.2368-0.3989-0.06720.92910.17510.00880.77450.03410.314542.4695-5.29339.9611
152.49191.37090.06034.65931.47294.00940.2777-0.41780.20430.1248-0.0943-0.2357-0.88880.1213-0.21780.7084-0.1002-0.00780.6079-0.05990.271656.3219-10.234616.4379
163.91473.60570.09667.90822.90575.25270.2282-0.29450.5467-0.1316-0.26610.1884-0.9587-0.2056-0.220.67150.06630.05660.703-0.01020.302548.7671-9.798813.4072
174.45480.6183-0.31644.57751.74685.4271-0.002-0.69521.47381.1939-0.4612-0.2486-0.9394-0.43-0.04991.0408-0.0525-0.06020.81310.07730.196247.2054-15.179514.1579
182.41140.8890.38434.16711.3758.7761-0.25580.4563-0.0184-0.3472-0.06970.159-0.1270.4597-0.0050.49670.0555-0.10070.64520.02030.238847.5619-24.8628-14.5421
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 253 through 265 )
2X-RAY DIFFRACTION2chain 'A' and (resid 266 through 278 )
3X-RAY DIFFRACTION3chain 'A' and (resid 279 through 288 )
4X-RAY DIFFRACTION4chain 'A' and (resid 289 through 295 )
5X-RAY DIFFRACTION5chain 'A' and (resid 296 through 302 )
6X-RAY DIFFRACTION6chain 'A' and (resid 303 through 313 )
7X-RAY DIFFRACTION7chain 'A' and (resid 314 through 325 )
8X-RAY DIFFRACTION8chain 'A' and (resid 326 through 350 )
9X-RAY DIFFRACTION9chain 'A' and (resid 351 through 358 )
10X-RAY DIFFRACTION10chain 'A' and (resid 359 through 371 )
11X-RAY DIFFRACTION11chain 'A' and (resid 372 through 381 )
12X-RAY DIFFRACTION12chain 'A' and (resid 382 through 397 )
13X-RAY DIFFRACTION13chain 'B' and (resid 253 through 265 )
14X-RAY DIFFRACTION14chain 'B' and (resid 266 through 288 )
15X-RAY DIFFRACTION15chain 'B' and (resid 289 through 325 )
16X-RAY DIFFRACTION16chain 'B' and (resid 326 through 351 )
17X-RAY DIFFRACTION17chain 'B' and (resid 352 through 381 )
18X-RAY DIFFRACTION18chain 'B' and (resid 382 through 395 )

+
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