PDB-5u4o: A 2.05A X-Ray Structureof A Bacterial Extracellular Solute-bindin...

ID or keywords:

Entry

Database: PDB / ID: 5u4o

Title

A 2.05A X-Ray Structureof A Bacterial Extracellular Solute-binding Protein, family 5 for Bacillus anthracis str. Ames

Components

ABC transporter substrate-binding protein

Keywords

STRUCTURAL GENOMICS / UNKNOWN FUNCTION / Alpha/Beta protein / Center for Structural Genomics of Infectious Diseases / CSGID

Function / homology

Function and homology information

peptide transport / peptide transmembrane transporter activity / ATP-binding cassette (ABC) transporter complex / outer membrane-bounded periplasmic space
Similarity search - Function

Biological species

Bacillus anthracis (anthrax bacterium)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

SAD / Resolution: 2.05 Å

Authors

Brunzelle, J.S. / Wawrzak, Z. / Sandoval, J. / Savchenko, A. / Anderson, W.F. / Center for Structural Genomics of Infectious Diseases (CSGID)

Citation

Journal: To Be Published
Title: A 2.05A X-Ray Structureof A Bacterial Extracellular Solute-binding Protein, family 5 for Bacillus anthracis str. Ames
Authors: Brunzelle, J.S. / Wawrzak, Z. / Sandoval, J. / Savchenko, A. / Anderson, W.F. / Center for Structural Genomics of Infectious Diseases (CSGID)

History

Deposition	Dec 5, 2016	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Mar 8, 2017	Provider: repository / Type: Initial release
Revision 1.1	Nov 20, 2024	Group: 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

Structure viewer	Molecule: MolmilJmol/JSmol

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PDBx/mmCIF format	5u4o.cif.gz	212.1 KB	Display	PDBx/mmCIF format
PDB format	pdb5u4o.ent.gz	170.4 KB	Display	PDB format
PDBx/mmJSON format	5u4o.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	5u4o_validation.pdf.gz	420.4 KB	Display	wwPDB validaton report
Full document	5u4o_full_validation.pdf.gz	423.3 KB	Display
Data in XML	5u4o_validation.xml.gz	20.9 KB	Display
Data in CIF	5u4o_validation.cif.gz	31.1 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/u4/5u4o ftp://data.pdbj.org/pub/pdb/validation_reports/u4/5u4o	HTTPS FTP

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Related structure data

Similar structure data	4n0l-d 4ofl-d 6wqx-d 3ggw-d 6iu6-d 6zdx-d 5a2p-d 4xcz-1 Search similar-shape structures by Omokage search (details) Search similar-shape structures by Omokage search (details) Similarity search - Function & homologyF&H Search Similarity search - FunctionF&H Search Similarity search - HomologyF&H Search
Other databases	TargetTrack: CSGID-IDP05181

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Links

PDB pages	PDBj / wwPDB / NCBI
Related items in Molecule of the Month	#261 - Sep 2021 DNA-Sequencing Nanopores similarity (1) #22 - Oct 2001 Photosystem I similarity (1) #262 - Oct 2021 Fifty Years of Open Access to PDB Structures similarity (1) #29 - May 2002 Penicillin-binding Proteins similarity (1) #95 - Nov 2007 Multidrug Resistance Transporters similarity (1)

Deposited unit

A: ABC transporter substrate-binding protein

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

1

A: ABC transporter substrate-binding protein

defined by software
117 kDa, 2 polymers
Search similar-shape structures of this assembly by Omokage search (details)

Unit cell

Length a, b, c (Å)	101.700, 101.700, 220.420
Angle α, β, γ (deg.)	90.00, 90.00, 120.00
Int Tables number	180
Space group name H-M	P6₂22

Components on special symmetry positions

ID	Model	Components
1	1	A-655- HOH
2	1	A-729- HOH

#1: Protein	ABC transporter substrate-binding protein / Bacterial extracellular solute-binding protein / family 5 / Glutathione-binding protein gsiB Mass: 58710.059 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Bacillus anthracis (anthrax bacterium) / Gene: gsiB, GBAA_4729, A8C77_22970, BASH2_01234 / Plasmid: pMCSG53 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)-Magic / References: UniProt: Q81L97, UniProt: A0A6H3AI29*PLUS
#2: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 295 / Source method: isolated from a natural source / Formula: H₂O
Has protein modification	Y

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Experiment

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

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Sample preparation

Crystal	Density Matthews: 2.82 Å³/Da / Density % sol: 56.46 %
Crystal grow	Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7 Details: 2M NH4 Citrate pH 7.0, 0.1M B-T-Propane pH 7, 1mM MgSulphate

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Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: SYNCHROTRON / Site: APS / Beamline: 21-ID-G / Wavelength: 0.97857 Å
Detector	Type: RAYONIX MX-300 / Detector: CCD / Date: Apr 14, 2016 / Details: Be Lens
Radiation	Monochromator: Single Diamond / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.97857 Å / Relative weight: 1
Reflection	Resolution: 2.05→88.07 Å / Num. obs: 43090 / % possible obs: 99.9 % / Observed criterion σ(I): -3 / Redundancy: 8.4 % / B_iso Wilson estimate: 35.95 Å² / CC_1/2: 0.999 / R_merge(I) obs: 0.118 / Net I/σ(I): 14.4
Reflection shell	Resolution: 2.05→2.09 Å / Redundancy: 8.3 % / R_merge(I) obs: 1.523 / Mean I/σ(I) obs: 1.9 / CC_1/2: 0.676 / % possible all: 99.2

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Processing

Software

Name	Version	Classification
BUSTER	2.10.3	refinement
XDS		data reduction
Aimless		data scaling
PHENIX		phasing

Refinement

Method to determine structure:

SAD / Resolution: 2.05→88.07 Å / Cor.coef. F_o:F_c: 0.945 / Cor.coef. F_o:F_c free: 0.941 / R_factor R_free error: 0 / SU R Cruickshank DPI: 0.141 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.148 / SU R_free Blow DPI: 0.128 / SU R_free Cruickshank DPI: 0.125

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.198	2191	5.09 %	RANDOM
R_work	0.175	-	-	-
obs	0.177	43038	99.8 %	-

Displacement parameters

B_iso mean: 47.64 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	-4.5059 Å²	0 Å²	0 Å²
2-	-	-4.5059 Å²	0 Å²
3-	-	-	9.0118 Å²

Refine analyze

Luzzati coordinate error obs: 0.23 Å

Refinement step

Cycle: 1 / Resolution: 2.05→88.07 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	3762	0	0	295	4057

Refine LS restraints

Refine-ID	Type	Dev ideal	Number	Restraint function	Weight
X-RAY DIFFRACTION	t_bond_d	0.01	3891	HARMONIC	2
X-RAY DIFFRACTION	t_angle_deg	1.04	5270	HARMONIC	2
X-RAY DIFFRACTION	t_dihedral_angle_d		1816	SINUSOIDAL	2
X-RAY DIFFRACTION	t_incorr_chiral_ct
X-RAY DIFFRACTION	t_pseud_angle
X-RAY DIFFRACTION	t_trig_c_planes		114	HARMONIC	2
X-RAY DIFFRACTION	t_gen_planes		551	HARMONIC	5
X-RAY DIFFRACTION	t_it		3891	HARMONIC	20
X-RAY DIFFRACTION	t_nbd
X-RAY DIFFRACTION	t_omega_torsion	3.42
X-RAY DIFFRACTION	t_other_torsion	2.97
X-RAY DIFFRACTION	t_improper_torsion
X-RAY DIFFRACTION	t_chiral_improper_torsion		500	SEMIHARMONIC	5
X-RAY DIFFRACTION	t_sum_occupancies
X-RAY DIFFRACTION	t_utility_distance
X-RAY DIFFRACTION	t_utility_angle
X-RAY DIFFRACTION	t_utility_torsion
X-RAY DIFFRACTION	t_ideal_dist_contact		4635	SEMIHARMONIC	4

LS refinement shell

Resolution: 2.05→2.1 Å / R_factor R_free error: 0 / Total num. of bins used: 20

	R_factor	Num. reflection	% reflection
R_free	0.215	159	5.12 %
R_work	0.212	2945	-
all	0.213	3104	-
obs	-	-	99.17 %

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	2.3062	0.4683	1.0414	0.8127	0.3617	2.5341	-0.1313	0.6122	-0.1083	-0.0987	0.0785	-0.0634	0.1009	0.1895	0.0527	-0.1701	-0.0253	0.018	0.1708	-0.0412	-0.0977	17.2023	24.8687	99.0524
2	1.0231	0.5123	1.0538	2.2272	1.8447	5.3874	-0.0905	0.5155	0.04	-0.302	0.0392	0.0034	-0.3625	-0.4509	0.0514	-0.1641	-0.0173	0.0072	0.2605	-0.001	-0.1148	5.8313	29.6789	92.0797
3	1.9849	0.0417	-0.3976	1.2009	0.0815	3.5347	-0.0911	0.5355	0.0103	-0.2919	0.2635	-0.0558	-0.2017	0.3094	-0.1724	-0.2	-0.0888	0.0186	0.2678	-0.0268	-0.1589	13.6083	29.5305	90.7866
4	4.9121	0.8133	0.7844	1.926	-0.1654	1.8774	-0.0395	-0.084	0.2979	0.1065	-0.0851	0.1261	-0.0993	-0.2307	0.1246	-0.0831	-0.0092	0.0134	0.0667	-0.0246	-0.0456	14.0614	31.0308	113.511
5	0.406	-0.0335	-1.1337	0.2545	-0.1597	1.9148	-0.0073	0.1506	-0.1309	-0.0025	-0.0371	0.0075	0.0486	-0.1826	0.0444	-0.1001	0.0092	-0.0423	0.1848	-0.0451	-0.0677	42.2776	25.1585	103.557
6	1.9615	0.1683	3.0781	0.2393	0.5945	3.4672	-0.0391	0.1308	-0.231	0.0804	-0.0165	0.0617	0.2078	-0.2601	0.0556	-0.1508	-0.0479	0.0284	0.3122	-0.0442	-0.0238	41.5512	17.7956	95.0395
7	2.6794	-0.1894	-1.8239	3.4547	-0.4057	5.6352	0.1094	0.0919	0.0005	-0.1096	-0.1119	0.0833	0.3481	0.1279	0.0026	-0.0793	0.0903	-0.043	0.1339	-0.0938	-0.112	60.3872	21.013	83.1752
8	1.2426	-1.5304	0.6586	3.4245	0.1095	0.9239	0.0669	-0.2573	-0.0999	0.1945	-0.0946	0.1685	-0.1371	-0.1486	0.0278	-0.0813	0.0238	-0.0272	0.1288	-0.0569	-0.0792	52.3692	35.2596	94.5052
9	2.9501	1.004	0.5578	1.0405	0.8478	2.2319	-0.0547	-0.2643	0.0018	-0.0081	-0.2134	0.1352	0.0506	-0.6668	0.268	-0.1727	0.061	-0.0075	0.2786	-0.1373	-0.1452	35.5938	26.1467	82.6019
10	10.0047	-0.626	2.6358	-0.2194	-0.6051	2.7941	0.1595	0.1462	-0.352	0.0674	-0.1258	-0.1973	0.3746	0.166	-0.0337	-0.0676	-0.0041	0.0034	0.0003	-0.0414	-0.0339	26.409	19.1311	111.741

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	{A\|42 - A\|107}
2	X-RAY DIFFRACTION	2	{A\|108 - A\|160}
3	X-RAY DIFFRACTION	3	{A\|161 - A\|188}
4	X-RAY DIFFRACTION	4	{A\|189 - A\|239}
5	X-RAY DIFFRACTION	5	{A\|240 - A\|310}
6	X-RAY DIFFRACTION	6	{A\|311 - A\|341}
7	X-RAY DIFFRACTION	7	{A\|342 - A\|360}
8	X-RAY DIFFRACTION	8	{A\|361 - A\|408}
9	X-RAY DIFFRACTION	9	{A\|409 - A\|492}
10	X-RAY DIFFRACTION	10	{A\|493 - A\|521}

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