PDB-3quf: The structure of a family 1 extracellular solute-binding protein ...

ID or keywords:

Entry

Database: PDB / ID: 3quf

Title

The structure of a family 1 extracellular solute-binding protein from Bifidobacterium longum subsp. infantis

Components

Extracellular solute-binding protein, family 1

Keywords

TRANSPORT PROTEIN / Structural Genomics / PSI-Biology / Midwest Center for Structural Genomics / MCSG

Function / homology

Function and homology information

transmembrane transport
Similarity search - Function

Biological species

Bifidobacterium longum subsp. infantis ATCC 15697 (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MAD / Resolution: 1.7 Å

Authors

Cuff, M.E. / Xu, X. / Cui, H. / Chin, S. / Savchenko, A. / Edwards, A. / Joachimiak, A. / Midwest Center for Structural Genomics (MCSG)

Citation

Journal: TO BE PUBLISHED
Title: The structure of a family 1 extracellular solute-binding protein from Bifidobacterium longum subsp. infantis
Authors: Cuff, M.E. / Xu, X. / Cui, H. / Chin, S. / Savchenko, A. / Edwards, A. / Joachimiak, A.

History

Deposition	Feb 23, 2011	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	May 4, 2011	Provider: repository / Type: Initial release
Revision 1.1	Jul 13, 2011	Group: Version format compliance
Revision 1.2	Nov 20, 2024	Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / struct_conn / struct_ref_seq_dif / struct_site Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	3quf.cif.gz	347.8 KB	Display	PDBx/mmCIF format
PDB format	pdb3quf.ent.gz	281.6 KB	Display	PDB format
PDBx/mmJSON format	3quf.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	3quf_validation.pdf.gz	460 KB	Display	wwPDB validaton report
Full document	3quf_full_validation.pdf.gz	463.9 KB	Display
Data in XML	3quf_validation.xml.gz	42.9 KB	Display
Data in CIF	3quf_validation.cif.gz	61.9 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/qu/3quf ftp://data.pdbj.org/pub/pdb/validation_reports/qu/3quf	HTTPS FTP

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Related structure data

Similar structure data	3ds6-2 4f9w-d 3kee-2 2puu-d 1yw2-d 3kee-1 5aq9-3 4lop-1 3iw6-d 3obj-d Search similar-shape structures by Omokage search (details) 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	TargetDB: APC102125

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Links

PDB pages	PDBj / wwPDB / NCBI
Related items in Molecule of the Month	#205 - Jan 2017 Nuclear Pore Complex similarity (4) #221 - May 2018 Human Papillomavirus and Vaccines similarity (4) #243 - Mar 2020 Voltage-gated Sodium Channels similarity (4) #4 - Apr 2000 Collagen similarity (1) #116 - Aug 2009 Sulfotransferases similarity (1)

Deposited unit

A: Extracellular solute-binding protein, family 1

B: Extracellular solute-binding protein, family 1

hetero molecules

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

1

A: Extracellular solute-binding protein, family 1

hetero molecules

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

2

B: Extracellular solute-binding protein, family 1

hetero molecules

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

Unit cell

Length a, b, c (Å)	96.532, 105.095, 145.375
Angle α, β, γ (deg.)	90.000, 90.000, 90.000
Int Tables number	20
Space group name H-M	C222₁

Details

THE AUTHOR STATES THAT THE BIOLOGICAL UNIT OF THIS PROTEIN IS UNKNOWN.

#1: Protein	Extracellular solute-binding protein, family 1 Mass: 45734.715 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Bifidobacterium longum subsp. infantis ATCC 15697 (bacteria) Strain: ATCC 15697 / Gene: Blon_0375 / Plasmid: modified p11 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: B7GMZ0
#2: Chemical	ChemComp-SO4 / SULFATE ION Mass: 96.063 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: SO₄
#3: Chemical	ChemComp-ACY / ACETIC ACID Mass: 60.052 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C₂H₄O₂
#4: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 825 / 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: 2.02 Å³/Da / Density % sol: 38.97 %
Crystal grow	Temperature: 294 K / Method: vapor diffusion, hanging drop / pH: 4.6 Details: 0.1M sodium acetate pH 4.6, 2.5M ammonium sulfate, 1/10 papain, VAPOR DIFFUSION, HANGING DROP, temperature 294K

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Data collection

Diffraction

Mean temperature: 100 K

Diffraction source

Source:

SYNCHROTRON / Site:

APS

/ Beamline: 19-ID / Wavelength: 0.97935, 0.97921

Detector

Type: ADSC QUANTUM 315r / Detector: CCD / Date: Jul 11, 2010

Radiation

Monochromator: SAGITALLY FOCUSED Si(111) / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray

Radiation wavelength

ID	Wavelength (Å)	Relative weight
1	0.97935	1
2	0.97921	1

Reflection

Redundancy: 4.6 % / Av σ(I) over netI: 27.81 / Number: 434178 / R_merge(I) obs: 0.081 / Χ²: 2.14 / D res high: 1.6 Å / D res low: 50 Å / Num. obs: 95082 / % possible obs: 98.1

Diffraction reflection shell

Highest resolution (Å)	Lowest resolution (Å)	% possible obs (%)	ID	R_merge(I) obs	Chi squared	Redundancy
4.34	50	98.8	1	0.06	6.723	4.4
3.45	4.34	99.4	1	0.055	4.646	4.4
3.01	3.45	99.4	1	0.067	4.533	4.5
2.74	3.01	99.3	1	0.077	3.913	4.6
2.54	2.74	99.1	1	0.084	3.274	4.6
2.39	2.54	98.9	1	0.086	2.676	4.6
2.27	2.39	98.8	1	0.089	2.307	4.6
2.17	2.27	98.6	1	0.095	1.988	4.6
2.09	2.17	98.3	1	0.105	1.789	4.6
2.02	2.09	98.3	1	0.115	1.552	4.6
1.95	2.02	98	1	0.141	1.381	4.7
1.9	1.95	97.9	1	0.162	1.227	4.6
1.85	1.9	97.8	1	0.196	1.074	4.7
1.8	1.85	97.6	1	0.241	0.991	4.7
1.76	1.8	97.4	1	0.273	0.869	4.7
1.72	1.76	97.4	1	0.333	0.822	4.7
1.69	1.72	97.3	1	0.411	0.78	4.6
1.66	1.69	96.9	1	0.482	0.763	4.6
1.63	1.66	96.8	1	0.527	0.735	4.5
1.6	1.63	95	1	0.582	0.684	4.2

Reflection

Resolution: 1.6→50 Å / Num. all: 95082 / Num. obs: 95082 / % possible obs: 98.1 % / Observed criterion σ(I): -3 / Redundancy: 4.6 % / B_iso Wilson estimate: 20.1 Å² / R_merge(I) obs: 0.081 / Χ²: 2.144 / Net I/σ(I): 9

Reflection shell

Resolution (Å)	Redundancy (%)	R_merge(I) obs	Num. unique all	Χ²	% possible all
1.6-1.63	4.2	0.582	4569	0.684	95
1.63-1.66	4.5	0.527	4642	0.735	96.8
1.66-1.69	4.6	0.482	4648	0.763	96.9
1.69-1.72	4.6	0.411	4690	0.78	97.3
1.72-1.76	4.7	0.333	4637	0.822	97.4
1.76-1.8	4.7	0.273	4680	0.869	97.4
1.8-1.85	4.7	0.241	4711	0.991	97.6
1.85-1.9	4.7	0.196	4704	1.074	97.8
1.9-1.95	4.6	0.162	4701	1.227	97.9
1.95-2.02	4.7	0.141	4767	1.381	98
2.02-2.09	4.6	0.115	4727	1.552	98.3
2.09-2.17	4.6	0.105	4752	1.789	98.3
2.17-2.27	4.6	0.095	4765	1.988	98.6
2.27-2.39	4.6	0.089	4801	2.307	98.8
2.39-2.54	4.6	0.086	4795	2.676	98.9
2.54-2.74	4.6	0.084	4821	3.274	99.1
2.74-3.01	4.6	0.077	4843	3.913	99.3
3.01-3.45	4.5	0.067	4868	4.533	99.4
3.45-4.34	4.4	0.055	4899	4.646	99.4
4.34-50	4.4	0.06	5062	6.723	98.8

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Phasing

Phasing

Method:

MAD

Phasing MAD

D res high: 1.7 Å / D res low: 50 Å / FOM : 0.415 / FOM acentric: 0.428 / FOM centric: 0.222 / Reflection: 79496 / Reflection acentric: 74507 / Reflection centric: 4989

Phasing MAD set

Highest resolution: 1.7 Å / Lowest resolution: 50 Å

ID	R cullis acentric	R cullis centric	Loc acentric	Loc centric	Power acentric	Power centric	Reflection acentric	Reflection centric
1	1.77	1	0.4	0.3	0	0	74507	4989
2	0.95	0.91	30.6	42.1	0.53	0.44	57767	4228

Phasing MAD set shell

ID	Resolution (Å)	R cullis acentric	R cullis centric	Loc acentric	Loc centric	Power acentric	Power centric	Reflection acentric	Reflection centric
1	10.99-50	1.47	1	0.8	0.4	0	0	228	109
1	6.17-10.99	1.55	1	0.8	0.5	0	0	1219	267
1	4.29-6.17	1.31	1	0.7	0.5	0	0	3040	427
1	3.29-4.29	1.17	1	0.6	0.5	0	0	5672	569
1	2.67-3.29	1.67	1	0.5	0.3	0	0	9143	714
1	2.24-2.67	1.9	1	0.4	0.2	0	0	13353	851
1	1.93-2.24	1.97	1	0.3	0.2	0	0	18411	975
1	1.7-1.93	2.53	1	0.3	0.1	0	0	23441	1077
2	10.99-50	0.99	0.98	66.5	70.6	0.7	0.67	227	107
2	6.17-10.99	0.89	0.84	46.9	51.2	0.91	0.69	1219	262
2	4.29-6.17	0.92	0.84	47.5	52.6	0.73	0.64	3040	424
2	3.29-4.29	0.94	0.89	47.3	56.7	0.56	0.44	5670	567
2	2.67-3.29	0.94	0.9	34.8	44.6	0.58	0.4	9139	714
2	2.24-2.67	0.94	0.91	25.3	32.7	0.57	0.41	13345	851
2	1.93-2.24	0.97	0.97	24.6	32.6	0.41	0.28	18401	975
2	1.7-1.93	0.99	1	26.3	34.6	0.3	0.2	6726	328

Phasing MAD set site

Atom type symbol: Se

ID	B iso	Fract x	Fract y	Fract z	Occupancy	Occupancy iso
1	30.9057	-0.214	-0.551	-0.052	4.662	0
2	27.7396	-0.444	-0.731	-0.102	4.917	0
3	36.8143	-0.103	-0.786	-0.107	4.338	0
4	26.0222	-0.213	-0.515	-0.16	3.658	0
5	31.6195	-0.307	-0.656	-0.09	3.826	0
6	27.2276	-0.398	-0.614	-0.074	3.237	0
7	67.0881	0.164	-0.605	-0.078	3.479	0
8	33.2924	-0.089	-0.64	-0.209	2.966	0
9	34.6682	0.09	-0.508	-0.119	2.929	0
10	29.1757	-0.165	-0.513	-0.225	2.345	0
11	36.8907	-0.069	-0.819	-0.019	2.079	0
12	33.256	-0.273	-0.412	-0.201	1.092	0
13	29.2621	-0.214	-0.551	-0.053	2.783	-0.164
14	25.534	-0.444	-0.73	-0.102	2.731	-0.164
15	37.0216	-0.104	-0.786	-0.107	2.367	-0.14
16	23.985	-0.212	-0.515	-0.16	2.218	-0.122
17	40.3171	-0.308	-0.656	-0.09	1.726	-0.116
18	26.1019	-0.398	-0.613	-0.074	1.767	-0.082
19	91.8271	0.165	-0.605	-0.077	2.344	-0.166
20	32.2277	-0.089	-0.64	-0.209	1.698	-0.083
21	32.4048	0.09	-0.507	-0.119	1.516	-0.089
22	20.5854	-0.166	-0.513	-0.224	1.171	-0.086
23	57.1746	-0.069	-0.821	-0.019	1.536	-0.133
24	23.3614	-0.273	-0.412	-0.201	0.708	-0.035

Phasing MAD shell

Resolution (Å)	FOM	FOM acentric	FOM centric	Reflection	Reflection acentric	Reflection centric
10.99-50	0.383	0.454	0.234	337	228	109
6.17-10.99	0.613	0.667	0.37	1486	1219	267
4.29-6.17	0.644	0.679	0.39	3467	3040	427
3.29-4.29	0.579	0.606	0.317	6241	5672	569
2.67-3.29	0.572	0.593	0.308	9857	9143	714
2.24-2.67	0.53	0.546	0.268	14204	13353	851
1.93-2.24	0.394	0.406	0.163	19386	18411	975
1.7-1.93	0.217	0.226	0.028	24518	23441	1077

Phasing dm

Method: Solvent flattening and Histogram matching / Reflection: 79496

Phasing dm shell

Resolution (Å)	Delta phi final	FOM	Reflection
9.21-100	56.2	0.479	559
6.52-9.21	47.6	0.906	986
5.32-6.52	44	0.923	1273
4.61-5.32	43.5	0.939	1462
4.12-4.61	43.9	0.952	1667
3.76-4.12	46.4	0.946	1801
3.48-3.76	49.3	0.936	1996
3.26-3.48	51.4	0.928	2098
3.07-3.26	48.8	0.924	2257
2.91-3.07	48.1	0.918	2358
2.78-2.91	48.9	0.915	2467
2.66-2.78	50.8	0.919	2591
2.56-2.66	47.4	0.912	2671
2.46-2.56	48.4	0.911	2780
2.38-2.46	50.4	0.915	2892
2.3-2.38	50.4	0.916	2952
2.23-2.3	52.9	0.908	3090
2.17-2.23	53.4	0.912	3154
2.11-2.17	56.9	0.916	3233
2.06-2.11	59	0.909	3318
2.01-2.06	59.8	0.913	3391
1.96-2.01	61.8	0.908	3459
1.92-1.96	62.9	0.904	3520
1.88-1.92	62	0.905	3600
1.84-1.88	68.9	0.902	3703
1.81-1.84	70.5	0.901	3769
1.77-1.81	72.4	0.901	3787
1.74-1.77	74.4	0.89	3832
1.7-1.74	76.6	0.855	4830

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Processing

Software

Name	Version	Classification
SCALEPACK		data scaling
MLPHARE		phasing
DM	6.1	phasing
REFMAC	5.5.0109	refinement
PDB_EXTRACT	3.1	data extraction
SBC-Collect		data collection
HKL-3000		data reduction
HKL-3000		data scaling
HKL-3000		phasing
SHELXD		phasing
SHELXE		model building
SOLVE		phasing
RESOLVE		phasing
ARP/wARP		model building
CCP4		phasing
O		model building
Coot		model building

Refinement

Method to determine structure:

MAD / Resolution: 1.7→48.27 Å / Cor.coef. F_o:F_c: 0.97 / Cor.coef. F_o:F_c free: 0.959 / Occupancy max: 1 / Occupancy min: 0.5 / SU B: 3.742 / SU ML: 0.057 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.101 / ESU R Free: 0.096
Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : RESIDUAL ONLY

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.1804	3974	5 %	RANDOM
R_work	0.1509	-	-	-
all	0.1523	79400	-	-
obs	0.1523	79400	98.15 %	-

Solvent computation

Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK

Displacement parameters

B_iso max: 95.3 Å² / B_iso mean: 24.077 Å² / B_iso min: 4.95 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	1.42 Å²	0 Å²	0 Å²
2-	-	-0.55 Å²	0 Å²
3-	-	-	-0.87 Å²

Refinement step

Cycle: LAST / Resolution: 1.7→48.27 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	5996	0	33	825	6854

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.015	0.022	6318
X-RAY DIFFRACTION	r_bond_other_d	0.001	0.02	4294
X-RAY DIFFRACTION	r_angle_refined_deg	1.417	1.952	8577
X-RAY DIFFRACTION	r_angle_other_deg	0.895	3	10553
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	5.244	5	818
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	35.17	25.986	289
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	13.703	15	1075
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	19.918	15	10
X-RAY DIFFRACTION	r_chiral_restr	0.092	0.2	891
X-RAY DIFFRACTION	r_gen_planes_refined	0.008	0.021	7156
X-RAY DIFFRACTION	r_gen_planes_other	0.001	0.02	1254
X-RAY DIFFRACTION	r_mcbond_it	0.945	1.5	3908
X-RAY DIFFRACTION	r_mcbond_other	0.267	1.5	1611
X-RAY DIFFRACTION	r_mcangle_it	1.743	2	6256
X-RAY DIFFRACTION	r_scbond_it	2.879	3	2410
X-RAY DIFFRACTION	r_scangle_it	4.748	4.5	2298

LS refinement shell

Resolution: 1.702→1.747 Å / Total num. of bins used: 20

	R_factor	Num. reflection	% reflection
R_free	0.228	258	-
R_work	0.203	5198	-
all	-	5456	-
obs	-	-	92.3 %

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	0.2343	0.1575	-0.0772	0.919	0.1695	1.17	0.0202	-0.0316	-0.0114	0.1107	0.0078	-0.0555	-0.0047	0.0641	-0.028	0.0165	0.0065	-0.0086	0.0324	0.0079	0.0359	31.7157	1.3849	39.1053
2	0.5168	-0.0394	-0.1449	0.3158	-0.0191	0.5939	-0.0071	-0.0335	0.031	-0.0338	0.0008	0.0311	-0.091	-0.0061	0.0063	0.032	0.0135	-0.0126	0.0119	-0.0054	0.0261	22.3676	21.8896	11.8394

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Auth asym-ID	Auth seq-ID
1	X-RAY DIFFRACTION	1	A	36 - 420
2	X-RAY DIFFRACTION	2	B	32 - 421

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-Yorodumi

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Movie

-
Structure viewers

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Viewer log

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This page

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This web site

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Options

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Open data

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Basic information

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Structure visualization

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Downloads & links

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Download

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Validation report

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Related structure data

-
Links

-
Assembly

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Components

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Experimental details

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Experiment

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Sample preparation

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Data collection

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Phasing

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Processing

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About Yorodumi

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News

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Feb 9, 2022. New format data for meta-information of EMDB entries

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Aug 12, 2020. Covid-19 info

+
Mar 5, 2020. Novel coronavirus structure data

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Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

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Jul 12, 2017. Major update of PDB

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Yorodumi