PDB-6h95: AlbA, albicidin resistance protein

ID or keywords:

Entry

Database: PDB / ID: 6h95

Title

AlbA, albicidin resistance protein

Components

Albicidin resistance protein

Keywords

albicidin binding protein / albicidin resistance protein

Function / homology

TipAS antibiotic-recognition domain / TipAS antibiotic-recognition domain / Albicidin resistance protein

Function and homology information

Biological species

Klebsiella oxytoca (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

SAD / Resolution: 1.9 Å

Authors

Koehnke, J. / Sikandar, A.

Funding support

Germany, 1items

Citation

Journal: 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

Deposition	Aug 3, 2018	Deposition site: PDBE / Processing site: PDBE
Revision 1.0	Nov 21, 2018	Provider: repository / Type: Initial release
Revision 1.1	Apr 24, 2019	Group: 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

Structure viewer	Molecule: MolmilJmol/JSmol

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PDBx/mmCIF format	6h95.cif.gz	105.7 KB	Display	PDBx/mmCIF format
PDB format	pdb6h95.ent.gz	86.4 KB	Display	PDB format
PDBx/mmJSON format	6h95.json.gz		Tree view	PDBx/mmJSON format
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Validation report

Summary document	6h95_validation.pdf.gz	418.3 KB	Display	wwPDB validaton report
Full document	6h95_full_validation.pdf.gz	419.9 KB	Display
Data in XML	6h95_validation.xml.gz	10.7 KB	Display
Data in CIF	6h95_validation.cif.gz	14.2 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/h9/6h95 ftp://data.pdbj.org/pub/pdb/validation_reports/h9/6h95	HTTPS FTP

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Related structure data

Related structure data	6h96C 6h97C 6haiC C: citing same article (ref.)
Similar structure data	6h97-d 1j86-1 3p47-d 4k00-d 5ed0-3 3kpb-2 1j1y-d 4ap8-4 4noc-1 5uhm-d Search similar-shape structures by Omokage search (details) Similarity search - Function & homologyF&H Search Similarity search - HomologyF&H Search

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Links

PDB pages	PDBj / wwPDB / NCBI

Deposited unit

A: Albicidin resistance protein

27.1 kDa, 1 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

Idetical with deposited unit
defined by author&software
Evidence: gel filtration

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 number	96
Space group name H-M	P4₃2₁2

#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

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Experiment

Experiment	Method: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

Crystal	Density Matthews: 2.24 Å³/Da / Density % sol: 45.01 %
Crystal grow	Temperature: 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

Diffraction	Mean temperature: 100 K
Diffraction source	Source: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.97264 Å
Detector	Type: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Sep 16, 2017
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.97264 Å / Relative weight: 1
Reflection	Resolution: 1.9→44.19 Å / Num. obs: 19572 / % possible obs: 99.63 % / Redundancy: 2 % / R_merge(I) obs: 0.03281 / Net I/σ(I): 19.41
Reflection shell	Resolution: 1.9→1.968 Å / R_merge(I) obs: 0.3075

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Processing

Software

Name	Version	Classification
PHENIX	(1.13_2998: ???)	refinement
xia2		data reduction
xia2		data scaling
PHASER		phasing

Refinement

Method 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

	R_factor	Num. reflection	% reflection
R_free	0.2065	922	4.73 %
R_work	0.1934	-	-
obs	0.1941	19504	99.63 %

Solvent computation

Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL

Refinement step

Cycle: LAST / Resolution: 1.9→44.195 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	1848	0	0	83	1931

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.008	1893
X-RAY DIFFRACTION	f_angle_d	0.872	2560
X-RAY DIFFRACTION	f_dihedral_angle_d	15.323	1151
X-RAY DIFFRACTION	f_chiral_restr	0.041	259
X-RAY DIFFRACTION	f_plane_restr	0.007	342

LS refinement shell

Resolution (Å)	R_factor R_free	Num. reflection R_free	R_factor R_work	Num. reflection R_work	Refine-ID	% reflection obs (%)
1.9-2.0002	0.2965	139	0.2521	2600	X-RAY DIFFRACTION	100
2.0002-2.1255	0.2619	112	0.222	2621	X-RAY DIFFRACTION	100
2.1255-2.2896	0.2452	127	0.2049	2612	X-RAY DIFFRACTION	100
2.2896-2.52	0.2353	133	0.199	2644	X-RAY DIFFRACTION	100
2.52-2.8846	0.2146	120	0.201	2650	X-RAY DIFFRACTION	100
2.8846-3.634	0.2069	115	0.1995	2689	X-RAY DIFFRACTION	99
3.634-44.2068	0.1835	176	0.1756	2766	X-RAY DIFFRACTION	99

Refinement TLS params.

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

ID	L11 (°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)
1	2.5048	-2.0757	-2.385	1.6947	2.0707	3.988	0.228	0.6216	0.6342	-0.3799	-0.0522	-0.2613	-0.2667	-0.3929	-0.1134	0.5672	-0.0313	0.0514	0.373	0.1062	0.451	101.7939	85.7321	101.21
2	4.3661	3.6622	-2.4521	3.3091	-1.3125	7.3319	0.3159	0.3165	0.1057	0.1451	-0.2036	0.2795	-0.7359	-0.4633	0.0925	0.3533	0.1205	-0.0218	0.458	0.0648	0.4455	89.53	74.7262	91.9054
3	1.3137	1.5946	0.9745	4.944	0.4517	3.2037	0.0887	0.2386	0.1659	0.1424	0.0282	0.4376	0.0614	-0.1912	-0.0527	0.2672	0.0055	0.0044	0.3787	0.0309	0.3436	93.1312	65.2315	93.348
4	3.0234	-0.8503	-1.345	2.3543	1.3398	3.722	0.1193	0.0601	0.3528	0.0271	-0.0549	0.1218	-0.4039	-0.2533	0.0384	0.378	0.0212	0.0149	0.3144	0.0382	0.3335	96.9723	77.3147	104.7675
5	5.6927	-3.1617	-1.4777	3.6959	2.293	3.9219	-0.0758	-0.3257	-0.2438	0.1932	0.1816	0.3867	0.2356	-0.1382	0.0932	0.309	-0.0348	0.0025	0.3531	0.0558	0.3045	94.8744	59.4644	98.6446
6	3.282	0.1383	0.2367	3.6316	2.9118	4.6611	0.2643	-0.3649	-0.5646	0.4096	-0.1309	0.2544	0.9971	-0.5635	-0.095	0.4232	-0.0102	-0.0024	0.3608	0.0754	0.4767	100.1562	45.6995	102.67
7	4.0507	1.4919	-0.0976	3.7164	-0.9089	2.7521	-0.0513	-0.2524	0.3318	0.2331	0.0074	0.0131	-0.2158	-0.1335	0.1651	0.2882	0.0432	-0.0138	0.3548	0.0006	0.3317	113.8333	62.116	107.741
8	3.3601	-1.1447	0.5197	5.4898	-4.5504	4.16	0.1968	0.1317	-0.253	-0.0003	-0.0858	-0.2296	0.1103	0.6546	-0.0102	0.4393	0.1193	-0.0171	0.4569	-0.028	0.4135	111.1845	47.3779	98.4939
9	1.7193	3.0827	0.952	7.6282	4.0018	3.8445	0.0144	-0.3721	-0.0541	0.3936	0.2092	-0.6861	0.3711	1.0265	-0.1391	0.2616	0.0236	-0.0381	0.4337	0.0399	0.3318	107.8246	61.8386	95.0281
10	5.2253	-2.3157	1.1978	6.8551	-0.8179	6.1112	0.3118	0.6568	0.1282	-0.7875	-0.4095	-0.3632	0.0064	-0.1079	-0.0858	0.3065	0.0353	0.003	0.4801	0.0251	0.3328	120.5521	61.524	99.8301
11	1.0324	-1.4644	-1.4837	4.0125	3.782	3.6946	-0.0273	0.4211	-0.0603	0.1139	-0.0298	0.54	0.0666	-0.5853	-0.117	0.4132	0.0285	-0.0464	0.4733	0.0368	0.4644	125.8529	48.4889	103.1819

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	chain 'A' and (resid -1 through 22 )
2	X-RAY DIFFRACTION	2	chain 'A' and (resid 23 through 41 )
3	X-RAY DIFFRACTION	3	chain 'A' and (resid 42 through 65 )
4	X-RAY DIFFRACTION	4	chain 'A' and (resid 66 through 93 )
5	X-RAY DIFFRACTION	5	chain 'A' and (resid 94 through 114 )
6	X-RAY DIFFRACTION	6	chain 'A' and (resid 115 through 127 )
7	X-RAY DIFFRACTION	7	chain 'A' and (resid 128 through 172 )
8	X-RAY DIFFRACTION	8	chain 'A' and (resid 173 through 188 )
9	X-RAY DIFFRACTION	9	chain 'A' and (resid 189 through 199 )
10	X-RAY DIFFRACTION	10	chain 'A' and (resid 200 through 211 )
11	X-RAY DIFFRACTION	11	chain 'A' and (resid 212 through 223 )

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