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- PDB-6h97: AlbAT99V mutant , albicidin resistance protein -

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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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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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

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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

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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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

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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

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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

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)
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 )

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