[English] 日本語
Yorodumi
- PDB-6h97: AlbAT99V mutant , albicidin resistance protein -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6h97
TitleAlbAT99V mutant , albicidin resistance protein
ComponentsAlbicidin resistance protein
Keywordsalbicidin binding protein / albicidin resistance protein
Function / homologyTipAS antibiotic-recognition domain / TipAS antibiotic-recognition domain / Albicidin resistance protein
Function and homology information
Biological speciesKlebsiella oxytoca (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.598 Å
AuthorsKoehnke, J. / Sikandar, A.
Funding support Germany, 1items
OrganizationGrant numberCountry
KO4116_3_1 Germany
CitationJournal: J.Am.Chem.Soc. / Year: 2018
Title: Adaptation of a Bacterial Multidrug Resistance System Revealed by the Structure and Function of AlbA.
Authors: Sikandar, A. / Cirnski, K. / Testolin, G. / Volz, C. / Bronstrup, M. / Kalinina, O.V. / Muller, R. / Koehnke, J.
History
DepositionAug 3, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 21, 2018Provider: repository / Type: Initial release
Revision 1.1Apr 24, 2019Group: Data collection / Database references / Category: citation / pdbx_database_proc
Item: _citation.journal_abbrev / _citation.journal_volume ..._citation.journal_abbrev / _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.2May 15, 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: Albicidin resistance protein


Theoretical massNumber of molelcules
Total (without water)26,4801
Polymers26,4801
Non-polymers00
Water905
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area13000 Å2
MethodPISA
Unit cell
Length a, b, c (Å)69.922, 69.922, 95.225
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212

-
Components

#1: Protein Albicidin resistance protein


Mass: 26479.945 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Klebsiella oxytoca (bacteria) / Gene: albA / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q8KRS7
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 5 / 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: 2.2 Å3/Da / Density % sol: 44.03 %
Crystal growTemperature: 293 K / Method: vapor diffusion
Details: 0.2-0.4 M Ammonium Sulfate, 0.8-1.2 M Lithium Sulfate, 0.1 M sodium citrate tribasic

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 0.97895 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: May 3, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97895 Å / Relative weight: 1
ReflectionResolution: 2.598→39.35 Å / Num. obs: 7698 / % possible obs: 99.56 % / Redundancy: 2 % / Rmerge(I) obs: 0.03635 / Net I/σ(I): 13.76
Reflection shellResolution: 2.598→2.691 Å / Rmerge(I) obs: 0.3768

-
Processing

Software
NameVersionClassification
PHENIX(1.13_2998: ???)refinement
xia2data reduction
xia2data scaling
PHASERphasing
RefinementResolution: 2.598→39.35 Å / SU ML: 0.32 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 27.14
RfactorNum. reflection% reflection
Rfree0.2576 385 5 %
Rwork0.2181 --
obs0.22 7697 99.6 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.598→39.35 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1848 0 0 5 1853
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0031893
X-RAY DIFFRACTIONf_angle_d0.5212560
X-RAY DIFFRACTIONf_dihedral_angle_d16.2981151
X-RAY DIFFRACTIONf_chiral_restr0.032259
X-RAY DIFFRACTIONf_plane_restr0.004342
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.5983-2.97420.33071310.29462352X-RAY DIFFRACTION99
2.9742-3.74670.28661180.23552412X-RAY DIFFRACTION100
3.7467-39.35940.22761360.19122548X-RAY DIFFRACTION100
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL112)L122)L132)L222)L232)L332)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T112)T122)T132)T222)T232)T332)Origin x (Å)Origin y (Å)Origin z (Å)
16.8177-0.1935-4.96424.1466-0.82389.16120.11021.15180.9808-0.04010.43020.2722-0.5295-0.6695-0.43290.6212-0.07840.08920.60550.10660.6326100.821485.2059101.4178
23.45930.3262-2.9324.1898-2.10398.4588-0.09660.97450.39570.27650.41930.1374-1.0681-1.0103-0.21420.6030.1001-0.05840.63480.04770.517688.49174.261891.7479
33.9693-0.60253.09628.40080.77287.39030.12260.5737-0.0565-0.02080.13120.5352-0.0679-0.4344-0.16430.30620.03830.01970.4608-0.03270.367992.020464.874293.4027
44.66532.08210.01472.74090.38187.7486-0.3352-0.1050.50610.23990.11630.0065-0.3765-0.56090.34650.51510.0658-0.03720.31320.01730.462195.843176.7441104.6645
54.9138-4.54760.10949.33320.14271.96460.0592-0.186-0.6304-0.0284-0.04160.9182-0.1322-0.2349-0.02830.3296-0.0090.02380.48340.02670.421393.90958.799798.7638
65.4051-1.46310.50773.84732.13677.55090.0938-0.6357-0.4809-0.23340.04820.31880.2031-0.4218-0.09650.4992-0.04190.08280.55160.13880.615899.063248.3096104.4472
78.457-3.2595-1.41494.5272-1.25255.36950.0746-0.86620.3901-0.0079-0.171-0.6606-0.20590.64430.00990.42220.059-0.03140.5709-0.02010.4815115.441866.7073106.3987
88.68736.6851-2.40767.4694-0.76192.55680.426-0.7302-0.24590.8891-0.5245-0.1035-0.1127-0.4731-0.00080.54230.05260.02720.57460.02970.3629113.231856.4811109.2992
93.71850.05190.52895.0965-0.35478.11570.09790.071-0.42310.4630.0172-0.17970.89410.88620.01040.68360.11720.04250.4775-0.0650.6146109.88246.531998.7917
105.6525-2.32241.26121.3137-0.80490.47280.19190.20080.09950.1048-0.0826-0.3687-0.00370.0186-0.05530.4602-0.02590.0170.5790.01740.4355113.934860.050798.4416
112.7255-1.39271.76135.14374.5957.9999-0.9651-0.42180.44051.09780.73550.1728-2.1087-0.90280.16150.86540.1745-0.0130.76220.06570.548126.31845.9507101.3027
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid -1 through 22 )
2X-RAY DIFFRACTION2chain 'A' and (resid 23 through 41 )
3X-RAY DIFFRACTION3chain 'A' and (resid 42 through 65 )
4X-RAY DIFFRACTION4chain 'A' and (resid 66 through 93 )
5X-RAY DIFFRACTION5chain 'A' and (resid 94 through 114 )
6X-RAY DIFFRACTION6chain 'A' and (resid 115 through 131 )
7X-RAY DIFFRACTION7chain 'A' and (resid 132 through 154 )
8X-RAY DIFFRACTION8chain 'A' and (resid 155 through 172 )
9X-RAY DIFFRACTION9chain 'A' and (resid 173 through 188 )
10X-RAY DIFFRACTION10chain 'A' and (resid 189 through 214 )
11X-RAY DIFFRACTION11chain 'A' and (resid 215 through 223 )

+
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