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- PDB-6h95: AlbA, albicidin resistance protein -

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Basic information

Entry
Database: PDB / ID: 6h95
TitleAlbA, 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 / SAD / Resolution: 1.9 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 / pdbx_seq_map_depositor_info
Item: _citation.journal_abbrev / _citation.journal_volume ..._citation.journal_abbrev / _citation.journal_volume / _citation.page_first / _citation.page_last / _pdbx_seq_map_depositor_info.one_letter_code_mod
Revision 1.2Oct 23, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature
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)27,0921
Polymers27,0921
Non-polymers00
Water1,49583
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 area13070 Å2
MethodPISA
Unit cell
Length a, b, c (Å)70.579, 70.579, 95.095
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: 27091.553 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: Selenomethione / 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.: 83 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 2.24 Å3/Da / Density % sol: 45.01 %
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: ID29 / Wavelength: 0.97264 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Sep 16, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97264 Å / Relative weight: 1
ReflectionResolution: 1.9→44.19 Å / Num. obs: 19572 / % possible obs: 99.63 % / Redundancy: 2 % / Rmerge(I) obs: 0.03281 / Net I/σ(I): 19.41
Reflection shellResolution: 1.9→1.968 Å / Rmerge(I) obs: 0.3075

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Processing

Software
NameVersionClassification
PHENIX(1.13_2998: ???)refinement
xia2data reduction
xia2data scaling
PHASERphasing
RefinementMethod to determine structure: SAD / Resolution: 1.9→44.195 Å / SU ML: 0.19 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 22.03 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2065 922 4.73 %
Rwork0.1934 --
obs0.1941 19504 99.63 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.9→44.195 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1848 0 0 83 1931
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0081893
X-RAY DIFFRACTIONf_angle_d0.8722560
X-RAY DIFFRACTIONf_dihedral_angle_d15.3231151
X-RAY DIFFRACTIONf_chiral_restr0.041259
X-RAY DIFFRACTIONf_plane_restr0.007342
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.9-2.00020.29651390.25212600X-RAY DIFFRACTION100
2.0002-2.12550.26191120.2222621X-RAY DIFFRACTION100
2.1255-2.28960.24521270.20492612X-RAY DIFFRACTION100
2.2896-2.520.23531330.1992644X-RAY DIFFRACTION100
2.52-2.88460.21461200.2012650X-RAY DIFFRACTION100
2.8846-3.6340.20691150.19952689X-RAY DIFFRACTION99
3.634-44.20680.18351760.17562766X-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)
12.5048-2.0757-2.3851.69472.07073.9880.2280.62160.6342-0.3799-0.0522-0.2613-0.2667-0.3929-0.11340.5672-0.03130.05140.3730.10620.451101.793985.7321101.21
24.36613.6622-2.45213.3091-1.31257.33190.31590.31650.10570.1451-0.20360.2795-0.7359-0.46330.09250.35330.1205-0.02180.4580.06480.445589.5374.726291.9054
31.31371.59460.97454.9440.45173.20370.08870.23860.16590.14240.02820.43760.0614-0.1912-0.05270.26720.00550.00440.37870.03090.343693.131265.231593.348
43.0234-0.8503-1.3452.35431.33983.7220.11930.06010.35280.0271-0.05490.1218-0.4039-0.25330.03840.3780.02120.01490.31440.03820.333596.972377.3147104.7675
55.6927-3.1617-1.47773.69592.2933.9219-0.0758-0.3257-0.24380.19320.18160.38670.2356-0.13820.09320.309-0.03480.00250.35310.05580.304594.874459.464498.6446
63.2820.13830.23673.63162.91184.66110.2643-0.3649-0.56460.4096-0.13090.25440.9971-0.5635-0.0950.4232-0.0102-0.00240.36080.07540.4767100.156245.6995102.67
74.05071.4919-0.09763.7164-0.90892.7521-0.0513-0.25240.33180.23310.00740.0131-0.2158-0.13350.16510.28820.0432-0.01380.35480.00060.3317113.833362.116107.741
83.3601-1.14470.51975.4898-4.55044.160.19680.1317-0.253-0.0003-0.0858-0.22960.11030.6546-0.01020.43930.1193-0.01710.4569-0.0280.4135111.184547.377998.4939
91.71933.08270.9527.62824.00183.84450.0144-0.3721-0.05410.39360.2092-0.68610.37111.0265-0.13910.26160.0236-0.03810.43370.03990.3318107.824661.838695.0281
105.2253-2.31571.19786.8551-0.81796.11120.31180.65680.1282-0.7875-0.4095-0.36320.0064-0.1079-0.08580.30650.03530.0030.48010.02510.3328120.552161.52499.8301
111.0324-1.4644-1.48374.01253.7823.6946-0.02730.4211-0.06030.1139-0.02980.540.0666-0.5853-0.1170.41320.0285-0.04640.47330.03680.4644125.852948.4889103.1819
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 127 )
7X-RAY DIFFRACTION7chain 'A' and (resid 128 through 172 )
8X-RAY DIFFRACTION8chain 'A' and (resid 173 through 188 )
9X-RAY DIFFRACTION9chain 'A' and (resid 189 through 199 )
10X-RAY DIFFRACTION10chain 'A' and (resid 200 through 211 )
11X-RAY DIFFRACTION11chain 'A' and (resid 212 through 223 )

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