PDB-8vdx: Crystal structure of bacterial extracellular solute-binding prote...

ID or keywords:

Entry

Database: PDB / ID: 8vdx

Title

Crystal structure of bacterial extracellular solute-binding protein from Bordetella bronchiseptica RB50

Components

bacterial extracellular solute-binding protein

Keywords

STRUCTURAL GENOMICS / CSBID / solute-binding protein / Center for Structural Biology of Infectious Diseases

Function / homology

ACETATE ION / TRIETHYLENE GLYCOL

Function and homology information

Biological species

Bordetella bronchiseptica (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 1.55 Å

Authors

Chang, C. / Tesar, C. / Endres, M. / Joachimiak, A. / Center for Structural Biology of Infectious Diseases (CSBID)

Funding support

1items

Citation

Journal: To Be Published
Title: Crystal structure of bacterial extracellular solute-binding protein from Bordetella bronchiseptica RB50
Authors: Chang, C. / Tesar, C. / Endres, M. / Joachimiak, A.

History

Deposition	Dec 18, 2023	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Dec 18, 2024	Provider: repository / Type: Initial release

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	8vdx.cif.gz	516.6 KB	Display	PDBx/mmCIF format
PDB format	pdb8vdx.ent.gz	348.8 KB	Display	PDB format
PDBx/mmJSON format	8vdx.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	8vdx_validation.pdf.gz	471.9 KB	Display	wwPDB validaton report
Full document	8vdx_full_validation.pdf.gz	477.4 KB	Display
Data in XML	8vdx_validation.xml.gz	54.2 KB	Display
Data in CIF	8vdx_validation.cif.gz	76.9 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/vd/8vdx ftp://data.pdbj.org/pub/pdb/validation_reports/vd/8vdx	HTTPS FTP

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Related structure data

Similar structure data	Similarity search - Function & homologyF&H Search Similarity search - HomologyF&H Search
Other databases	TargetTrack: IDP98033

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Links

PDB pages	PDBj / wwPDB / NCBI

Deposited unit

A: bacterial extracellular solute-binding protein

B: bacterial extracellular solute-binding protein

hetero molecules

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

1

A: bacterial extracellular solute-binding protein

hetero molecules

defined by author&software
56.8 kDa, 1 polymers
Search similar-shape structures of this assembly by Omokage search (details)

2

B: bacterial extracellular solute-binding protein

hetero molecules

defined by author&software
57 kDa, 1 polymers
Search similar-shape structures of this assembly by Omokage search (details)

Unit cell

Length a, b, c (Å)	55.677, 105.270, 199.445
Angle α, β, γ (deg.)	90.000, 90.000, 90.000
Int Tables number	19
Space group name H-M	P2₁2₁2₁
Space group name Hall	P2ac2ab

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Protein , 1 types, 2 molecules AB

#1: Protein	bacterial extracellular solute-binding protein Mass: 56128.797 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Bordetella bronchiseptica (bacteria) / Production host: Escherichia coli BL21(DE3) (bacteria)

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Non-polymers , 5 types, 1054 molecules

#2: Chemical	ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL Mass: 92.094 Da / Num. of mol.: 11 / Source method: obtained synthetically / Formula: C₃H₈O₃
#3: Chemical	ChemComp-ACT / ACETATE ION Mass: 59.044 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C₂H₃O₂
#4: Chemical	ChemComp-PGE / TRIETHYLENE GLYCOL Mass: 150.173 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C₆H₁₄O₄
#5: Chemical	ChemComp-PG4 / TETRAETHYLENE GLYCOL Mass: 194.226 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Formula: C₈H₁₈O₅ / Comment: precipitant*YM
#6: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 1038 / Source method: isolated from a natural source / Formula: H₂O

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Details

Has ligand of interest	N
Has protein modification	N

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Experiment

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

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Sample preparation

Crystal	Density Matthews: 2.6 Å³/Da / Density % sol: 52.75 %
Crystal grow	Temperature: 289 K / Method: vapor diffusion, sitting drop Details: 0.17 M Ammonium Acetate, 0.085 M Sodium Acetate pH 4.6, PEG 4000, Glycerol

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Data collection

Diffraction

Mean temperature: 100 K / Serial crystal experiment: N

Diffraction source

Source:

SYNCHROTRON / Site:

APS

/ Beamline: 19-ID / Wavelength: 0.9789 Å

Detector

Type: DECTRIS PILATUS3 X 6M / Detector: PIXEL / Date: Mar 4, 2021

Radiation

Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray

Radiation wavelength

Wavelength: 0.9789 Å / Relative weight: 1

Reflection

Resolution: 1.55→50 Å / Num. obs: 170529 / % possible obs: 99.5 % / Redundancy: 6.2 % / B_iso Wilson estimate: 13.34 Å² / CC_1/2: 0.993 / CC star: 0.998 / R_merge(I) obs: 0.12 / R_pim(I) all: 0.052 / R_rim(I) all: 0.131 / Χ²: 0.93 / Net I/σ(I): 6.9 / Num. measured all: 1064967

Reflection shell

Diffraction-ID: 1

Resolution (Å)	Redundancy (%)	R_merge(I) obs	Num. unique obs	CC_1/2	CC star	R_pim(I) all	R_rim(I) all	Χ²	% possible all
1.55-1.58	4.9	1.002	8234	0.504	0.819	0.487	1.12	0.926	98.2
1.58-1.61	5	1.038	8382	0.461	0.794	0.506	1.16	0.928	98.6
1.61-1.64	4.9	1.068	8363	0.449	0.787	0.528	1.198	0.919	98.2
1.64-1.67	6	1.052	8394	0.579	0.857	0.472	1.156	0.93	99.5
1.67-1.71	6.3	0.99	8489	0.647	0.886	0.43	1.081	0.945	99.7
1.71-1.75	6.5	0.89	8488	0.779	0.936	0.376	0.967	0.934	99.9
1.75-1.79	6.5	0.723	8487	0.841	0.956	0.305	0.786	0.953	99.9
1.79-1.84	6.5	0.611	8498	0.873	0.966	0.258	0.664	0.953	99.9
1.84-1.89	6.5	0.469	8483	0.916	0.978	0.199	0.51	0.955	99.9
1.89-1.95	6.5	0.36	8487	0.944	0.985	0.154	0.392	0.965	99.6
1.95-2.02	5.9	0.266	8505	0.95	0.987	0.119	0.292	0.99	99.4
2.02-2.1	6.2	0.208	8476	0.97	0.992	0.091	0.228	0.985	99.4
2.1-2.2	6.9	0.163	8530	0.986	0.997	0.066	0.176	0.964	99.8
2.2-2.32	6.9	0.134	8552	0.989	0.997	0.055	0.145	0.944	99.9
2.32-2.46	6.8	0.108	8570	0.991	0.998	0.045	0.117	0.933	100
2.46-2.65	6.7	0.086	8650	0.994	0.998	0.036	0.093	0.913	100
2.65-2.92	5.9	0.066	8523	0.994	0.999	0.029	0.072	0.933	98.9
2.92-3.34	6.8	0.051	8654	0.996	0.999	0.021	0.055	0.915	99.8
3.34-4.21	6.8	0.038	8762	0.997	0.999	0.016	0.041	0.848	99.9
4.21-50	6.3	0.033	9002	0.997	0.999	0.014	0.036	0.78	98.7

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Processing

Software

Name	Version	Classification
PHENIX	1.20.1_4487	refinement
SCALEPACK		data scaling
PDB_EXTRACT	3.27	data extraction
HKL-3000		data reduction
HKL-3000		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT / Resolution: 1.55→46.55 Å / SU ML: 0.1326 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 17.75
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2

	R_factor	Num. reflection	% reflection
R_free	0.185	7844	4.96 %
R_work	0.1668	150392	-
obs	0.1677	158236	92.29 %

Solvent computation

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

Displacement parameters

B_iso mean: 19.34 Å²

Refinement step

Cycle: LAST / Resolution: 1.55→46.55 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	7870	0	101	1038	9009

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.0025	8485
X-RAY DIFFRACTION	f_angle_d	0.5887	11547
X-RAY DIFFRACTION	f_chiral_restr	0.0446	1230
X-RAY DIFFRACTION	f_plane_restr	0.0054	1525
X-RAY DIFFRACTION	f_dihedral_angle_d	11.8491	3146

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 (%)
1.55-1.56	0.2486	184	0.2184	3330	X-RAY DIFFRACTION	62.85
1.56-1.58	0.2051	183	0.2018	3797	X-RAY DIFFRACTION	70.64
1.58-1.6	0.2201	190	0.2066	3990	X-RAY DIFFRACTION	73.73
1.6-1.62	0.2434	202	0.2048	4064	X-RAY DIFFRACTION	75.54
1.62-1.64	0.227	229	0.1948	4299	X-RAY DIFFRACTION	79.73
1.64-1.67	0.2176	223	0.1917	4531	X-RAY DIFFRACTION	84.49
1.67-1.69	0.2036	246	0.1895	4662	X-RAY DIFFRACTION	86.01
1.69-1.72	0.2107	251	0.1891	4686	X-RAY DIFFRACTION	87.97
1.72-1.74	0.2077	255	0.1862	4850	X-RAY DIFFRACTION	89.53
1.74-1.77	0.2128	252	0.1825	4930	X-RAY DIFFRACTION	91.49
1.77-1.8	0.205	278	0.1871	5042	X-RAY DIFFRACTION	93.28
1.8-1.83	0.203	257	0.1913	5058	X-RAY DIFFRACTION	94.32
1.83-1.87	0.2058	285	0.1913	5167	X-RAY DIFFRACTION	96.09
1.87-1.91	0.2136	285	0.1849	5220	X-RAY DIFFRACTION	97.04
1.91-1.95	0.2259	255	0.1729	5278	X-RAY DIFFRACTION	97.26
1.95-1.99	0.1924	296	0.1748	5264	X-RAY DIFFRACTION	97.44
1.99-2.04	0.1995	254	0.1718	5204	X-RAY DIFFRACTION	96.5
2.04-2.1	0.1889	275	0.174	5385	X-RAY DIFFRACTION	98.95
2.1-2.16	0.1806	277	0.1641	5375	X-RAY DIFFRACTION	99.51
2.16-2.23	0.2069	279	0.1694	5429	X-RAY DIFFRACTION	99.63
2.23-2.31	0.1926	271	0.1649	5396	X-RAY DIFFRACTION	99.61
2.31-2.4	0.2045	279	0.1682	5440	X-RAY DIFFRACTION	99.7
2.4-2.51	0.212	294	0.1703	5426	X-RAY DIFFRACTION	99.74
2.51-2.65	0.2019	258	0.1676	5474	X-RAY DIFFRACTION	99.83
2.65-2.81	0.1968	287	0.1658	5398	X-RAY DIFFRACTION	99.08
2.81-3.03	0.185	301	0.1703	5384	X-RAY DIFFRACTION	98.82
3.03-3.33	0.1948	293	0.1688	5506	X-RAY DIFFRACTION	99.88
3.33-3.81	0.1453	297	0.1471	5522	X-RAY DIFFRACTION	99.81
3.81-4.8	0.1395	300	0.1304	5584	X-RAY DIFFRACTION	99.98
4.81-46.55	0.1478	308	0.1554	5701	X-RAY DIFFRACTION	97.96

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	0.213206965437	0.0626310434751	0.240416840365	0.887576882502	0.57757183197	1.00687312512	-0.116913249277	-0.201469622061	-0.0563362686383	0.128162093994	0.203788760125	0.0793617438766	0.158346022112	0.480294939752	0.0118747836084	0.134987306333	0.122185372765	0.0107500516754	0.112961940374	0.0063135737288	0.0632777518794	-9.69274198392	20.3690381416	157.27291538
2	0.25861816063	0.0831856459109	-0.0386457006436	0.204390154207	0.31664953924	1.27290904742	-0.0371997939452	0.0348411101606	0.0078753523902	-0.0118995389072	-0.0755156668593	0.0485651389223	-0.0738655937692	-0.172154836219	-0.140801212684	0.0715382644081	0.011128415649	-0.00412657727758	0.102044355969	-0.0442544885694	0.0858954833492	-27.4792617477	27.5060841473	135.600341514
3	0.336558604182	0.110563741061	-0.0688655254246	0.422947485603	-0.042994272025	0.312537291494	0.0151147413423	0.0122912299838	0.0356936879603	-0.0365909226138	-0.0441867571811	-0.00574053041098	-0.0310218223712	-0.00236445036554	-0.0248033440404	0.067966620723	0.00624306482016	-0.00573357405692	0.0549887154014	0.00800282004901	0.067852790424	8.69267462338	11.6840142256	197.065390147
4	0.339111758982	0.178867071031	-0.0792674627195	0.291822047669	-0.161952440594	0.288428833426	0.00860970798814	-0.0111834405962	-0.0547520831846	-0.0211594401902	-0.00017010898199	-0.00640619564254	0.0155400433197	-0.020432639544	0.0356685026469	0.0596072389379	-0.00133492224619	-0.0052932748606	0.0437483396998	0.00770316639994	0.0717491658901	-9.10971591471	-10.3172840211	203.112087828

Refinement TLS group

Refine-ID: X-RAY DIFFRACTION

ID	Refine TLS-ID	Selection details	Auth asym-ID	Label asym-ID	Auth seq-ID	Label seq-ID
1	1	chain 'A' and (resid 28 through 262 )	A	A	28 - 262	1 - 235
2	2	chain 'A' and (resid 263 through 530 )	A	A	263 - 530	236 - 503
3	3	chain 'B' and (resid 29 through 262 )	B	H	29 - 262	1 - 234
4	4	chain 'B' and (resid 263 through 530 )	B	H	263 - 530	235 - 502

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