PDB-3lvu: Crystal structure of ABC transporter, periplasmic substrate-bindi...

ID or keywords:

Entry

Database: PDB / ID: 3lvu

Title

Crystal structure of ABC transporter, periplasmic substrate-binding protein SPO2066 from Silicibacter pomeroyi

Components

ABC transporter, periplasmic substrate-binding protein

Keywords

TRANSPORT PROTEIN / MCSG / PSI-2 / ABC transporter / periplasmic substrate-binding protein / Silicibacter pomeroyi / Structural Genomics / Protein Structure Initiative / Midwest Center for Structural Genomics

Function / homology

Function and homology information

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

Biological species

Silicibacter pomeroyi (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

SAD / Resolution: 1.79 Å

Authors

Chang, C. / Chhor, G. / Clancy, S. / Joachimiak, A. / Midwest Center for Structural Genomics (MCSG)

Citation

Journal: To be Published
Title: Crystal structure of ABC transporter, periplasmic substrate-binding protein SPO2066 from Silicibacter pomeroyi
Authors: Chang, C. / Chhor, G. / Clancy, S. / Joachimiak, A.

History

Deposition	Feb 22, 2010	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Mar 2, 2010	Provider: repository / Type: Initial release
Revision 1.1	Jul 13, 2011	Group: Advisory / Version format compliance
Revision 1.2	Nov 8, 2017	Group: Refinement description / Category: software
Revision 1.3	Oct 30, 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	3lvu.cif.gz	231.7 KB	Display	PDBx/mmCIF format
PDB format	pdb3lvu.ent.gz	189.3 KB	Display	PDB format
PDBx/mmJSON format	3lvu.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	3lvu_validation.pdf.gz	480.2 KB	Display	wwPDB validaton report
Full document	3lvu_full_validation.pdf.gz	489.8 KB	Display
Data in XML	3lvu_validation.xml.gz	53.9 KB	Display
Data in CIF	3lvu_validation.cif.gz	74 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/lv/3lvu ftp://data.pdbj.org/pub/pdb/validation_reports/lv/3lvu	HTTPS FTP

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Related structure data

Similar structure data	4jqn-d 4gu8-1 5x5v-d 2i82-3 4gu8-4 3w68-5 2pkd-3 4gu8-6 4gu8-2 2pkd-2 Search similar-shape structures by Omokage search (details) Search similar-shape structures by Omokage search (details) 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: APC63764.3

Similar structure data

Other databases

TargetDB: APC63764.3

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Links

PDB pages	PDBj / wwPDB / NCBI

Deposited unit

A: ABC transporter, periplasmic substrate-binding protein

B: ABC transporter, periplasmic substrate-binding protein

C: ABC transporter, periplasmic substrate-binding protein

D: ABC transporter, periplasmic substrate-binding protein

hetero molecules

117 kDa, 4 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

A: ABC transporter, periplasmic substrate-binding protein

hetero molecules

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

2

B: ABC transporter, periplasmic substrate-binding protein

hetero molecules

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

3

C: ABC transporter, periplasmic substrate-binding protein

hetero molecules

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

4

D: ABC transporter, periplasmic substrate-binding protein

hetero molecules

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

Unit cell

Length a, b, c (Å)	47.384, 75.517, 78.477
Angle α, β, γ (deg.)	82.63, 80.29, 77.42
Int Tables number	1
Space group name H-M	P1

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Protein , 1 types, 4 molecules ABCD

#1: Protein	ABC transporter, periplasmic substrate-binding protein Mass: 28635.301 Da / Num. of mol.: 4 / Fragment: sequence database residues 314-568 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Silicibacter pomeroyi (bacteria) / Gene: SPO2066 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)magic / References: UniProt: Q5LRQ9

#1: Protein

ABC transporter, periplasmic substrate-binding protein

Mass: 28635.301 Da / Num. of mol.: 4 / Fragment: sequence database residues 314-568
Source method: isolated from a genetically manipulated source
Source: (gene. exp.)

Silicibacter pomeroyi (bacteria) / Gene: SPO2066 / Production host:

Escherichia coli (E. coli) / Strain (production host): BL21(DE3)magic / References: UniProt: Q5LRQ9

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Non-polymers , 5 types, 750 molecules

#2: Chemical	ChemComp-IOD / IODIDE ION Mass: 126.904 Da / Num. of mol.: 14 / Source method: obtained synthetically / Formula: I
#3: Chemical	ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL Mass: 92.094 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C₃H₈O₃
#4: Chemical	ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL Mass: 62.068 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C₂H₆O₂
#5: Chemical	ChemComp-PG5 / 1-METHOXY-2-[2-(2-METHOXY-ETHOXY]-ETHANE Mass: 178.226 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C₈H₁₈O₄
#6: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 726 / Source method: isolated from a natural source / Formula: H₂O

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Details

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: 2.35 Å³/Da / Density % sol: 47.61 %
Crystal grow	Temperature: 297 K / Method: vapor diffusion, sitting drop / pH: 6.5 Details: 0.2M Sodium iodide, 20% PEG3350, pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 297K

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Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.97901 Å
Detector	Type: ADSC QUANTUM 315r / Detector: CCD / Date: Dec 17, 2009
Radiation	Monochromator: Si(111) double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.97901 Å / Relative weight: 1
Reflection	Resolution: 1.8→50 Å / Num. all: 97131 / Num. obs: 94748 / % possible obs: 97.5 % / Observed criterion σ(I): -3 / Redundancy: 4.5 % / B_iso Wilson estimate: 19.7 Å² / R_merge(I) obs: 0.116 / Net I/σ(I): 23
Reflection shell	Resolution: 1.8→1.82 Å / Redundancy: 4.1 % / R_merge(I) obs: 0.802 / Mean I/σ(I) obs: 2.37 / Num. unique all: 2293 / % possible all: 96.3

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Processing

Software

Name	Version	Classification
SBC-Collect		data collection
HKL-3000		phasing
SHELXD		phasing
SHELXE		model building
MLPHARE		phasing
DM		model building
RESOLVE		model building
Coot		model building
ARP/wARP		model building
REFMAC	5.5.0102	refinement
HKL-3000		data reduction
HKL-3000		data scaling
DM		phasing
RESOLVE		phasing

Refinement

Method to determine structure:

SAD / Resolution: 1.79→50 Å / Cor.coef. F_o:F_c: 0.961 / Cor.coef. F_o:F_c free: 0.944 / SU B: 5.401 / SU ML: 0.079 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.13 / ESU R Free: 0.121
Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.20476	4666	5 %	RANDOM
R_work	0.16905	-	-	-
all	0.17084	93537	-	-
obs	0.17084	93537	95.8 %	-

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 mean: 14.701 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	0.82 Å²	-0.36 Å²	0.88 Å²
2-	-	-0.08 Å²	0.03 Å²
3-	-	-	-0.89 Å²

Refinement step

Cycle: LAST / Resolution: 1.79→50 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	7977	0	76	726	8779

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.014	0.022	8531
X-RAY DIFFRACTION	r_bond_other_d
X-RAY DIFFRACTION	r_angle_refined_deg	1.468	1.971	11600
X-RAY DIFFRACTION	r_angle_other_deg
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	5.301	5	1095
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	25.927	22.388	423
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	13.772	15	1354
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	16.48	15	115
X-RAY DIFFRACTION	r_chiral_restr	0.097	0.2	1259
X-RAY DIFFRACTION	r_gen_planes_refined	0.007	0.021	6759
X-RAY DIFFRACTION	r_gen_planes_other
X-RAY DIFFRACTION	r_nbd_refined
X-RAY DIFFRACTION	r_nbd_other
X-RAY DIFFRACTION	r_nbtor_refined
X-RAY DIFFRACTION	r_nbtor_other
X-RAY DIFFRACTION	r_xyhbond_nbd_refined
X-RAY DIFFRACTION	r_xyhbond_nbd_other
X-RAY DIFFRACTION	r_metal_ion_refined
X-RAY DIFFRACTION	r_metal_ion_other
X-RAY DIFFRACTION	r_symmetry_vdw_refined
X-RAY DIFFRACTION	r_symmetry_vdw_other
X-RAY DIFFRACTION	r_symmetry_hbond_refined
X-RAY DIFFRACTION	r_symmetry_hbond_other
X-RAY DIFFRACTION	r_symmetry_metal_ion_refined
X-RAY DIFFRACTION	r_symmetry_metal_ion_other
X-RAY DIFFRACTION	r_mcbond_it	0.842	1.5	5327
X-RAY DIFFRACTION	r_mcbond_other
X-RAY DIFFRACTION	r_mcangle_it	1.512	2	8531
X-RAY DIFFRACTION	r_scbond_it	2.548	3	3204
X-RAY DIFFRACTION	r_scangle_it	4.021	4.5	3069
X-RAY DIFFRACTION	r_rigid_bond_restr
X-RAY DIFFRACTION	r_sphericity_free
X-RAY DIFFRACTION	r_sphericity_bonded

LS refinement shell

Resolution: 1.794→1.84 Å / Total num. of bins used: 20

	R_factor	Num. reflection	% reflection
R_free	0.314	295	-
R_work	0.271	5863	-
obs	-	6158	84.93 %

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	1.7321	-0.0213	-0.0389	0.9533	-0.3877	2.1944	-0.0736	0.111	0.0685	-0.0986	0.0413	-0.008	-0.0259	-0.12	0.0324	0.0669	-0.0331	0.0139	0.037	-0.0061	0.0298	48.6373	61.6794	30.3775
2	1.3376	1.03	0.5978	1.4644	0.2068	2.3491	-0.0404	0.0314	-0.0196	-0.0735	-0.0075	-0.1163	-0.3333	0.0451	0.0479	0.0852	-0.0124	0.0168	0.0078	0.0048	0.0448	54.6022	75.6158	38.8108
3	0.8685	0.0767	-0.402	0.594	-0.8008	1.6956	-0.0891	0.0784	-0.0611	-0.1441	0.0574	-0.034	0.1953	-0.0574	0.0316	0.1029	-0.0409	0.0203	0.0321	-0.0241	0.0204	49.5908	53.6576	26.5097
4	1.1384	0.4273	0.2588	1.3656	0.1168	0.8999	0.0001	-0.0783	0.0299	0.0181	-0.0238	-0.05	-0.0952	-0.0664	0.0237	0.0475	-0.0013	0.0047	0.0484	-0.0019	0.0395	50.6132	67.8724	46.7408
5	1.2458	-0.5054	-0.4969	1.2828	0.0852	0.5321	0.0051	-0.0616	0.0342	-0.0888	0.0398	-0.0956	0.0018	0.1053	-0.0449	0.0127	-0.0045	0.0142	0.0929	-0.0005	0.0728	68.0719	76.9075	-6.3962
6	2.9889	0.4938	0.0119	0.9693	0.424	2.0865	-0.1182	0.0024	-0.0962	-0.0688	-0.0494	0.036	0.0859	0.0344	0.1676	0.0371	0.0232	0.015	0.0174	0.003	0.0581	54.8681	64.8065	-6.2308
7	0.8054	-0.428	-0.4636	1.5165	0.5453	1.6756	0.0142	-0.0378	0.1305	-0.1135	0.114	-0.2318	-0.1108	0.2566	-0.1282	0.0145	-0.025	0.0199	0.0968	0.0089	0.0999	72.3814	83.658	-9.7595
8	0.4637	0.295	0.0404	1.9459	0.1759	0.9944	0.029	0.0028	-0.0282	0.042	-0.0647	0.1949	-0.0457	-0.0249	0.0357	0.0103	0.0157	-0.0067	0.065	-0.0109	0.0677	51.3569	75.1362	-0.6082
9	1.2184	0.0384	-0.6306	1.5066	0.3629	0.8265	0.0113	0.0466	-0.03	0.056	-0.0434	0.0971	0.0199	-0.0562	0.0321	0.032	0.0158	0.0003	0.0555	0.0047	0.0623	60.8871	39.5459	-15.4989
10	1.4887	-0.9921	-0.3997	1.9012	0.8735	1.4836	-0.11	0.0156	-0.1139	0.2188	0.0266	0.1549	0.0383	-0.0314	0.0834	0.0492	-0.0077	0.0135	0.0195	0.0191	0.0504	68.4553	23.8143	-15.8326
11	1.7644	0.6651	-0.7378	1.0172	-0.3201	1.2508	0.1284	0.0003	0.1415	0.1346	-0.0045	0.1218	-0.0832	-0.0427	-0.1239	0.0455	0.0231	0.0173	0.0215	0.0009	0.0383	59.6645	47.3515	-11.5705
12	0.5787	-0.283	0.094	1.6686	0.101	0.8848	-0.0235	0.0337	-0.0509	-0.029	0.0764	-0.1146	0.0105	-0.0111	-0.0529	0.0325	0.0018	-0.0039	0.0667	0.0142	0.0563	75.1732	31.1399	-21.8185
13	0.9491	-0.5453	-0.2997	1.6505	0.6224	2.5413	-0.0944	-0.0916	0.033	0.23	0.0707	-0.0228	0.0921	0.1909	0.0236	0.1055	0.0045	-0.0065	0.0446	0.0008	0.0156	36.852	25.5416	24.3456
14	1.2382	-0.6256	0.0522	2.614	-0.6263	2.2878	0.1205	-0.0382	0.0623	0.031	-0.0391	0.0001	-0.2663	0.075	-0.0814	0.0694	-0.0236	0.0105	0.012	-0.0091	0.0205	37.3451	40.8729	15.7146
15	0.9313	-0.0769	-0.0616	1.2981	1.41	1.8684	-0.0726	-0.0371	-0.0781	0.3352	-0.0149	0.0999	0.2946	-0.0085	0.0875	0.1659	-0.0177	0.0286	0.0376	0.0272	0.0336	32.8449	18.6722	27.9994
16	0.8356	-0.1931	-0.3679	1.7704	0.1217	0.6702	0.0477	0.0416	0.0398	-0.1192	-0.0302	-0.0422	-0.0978	0.0233	-0.0175	0.0766	-0.0016	-0.0064	0.0484	-0.0085	0.0274	37.8564	32.0284	7.9179

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Auth asym-ID	Auth seq-ID
1	X-RAY DIFFRACTION	1	A	311 - 354
2	X-RAY DIFFRACTION	2	A	355 - 398
3	X-RAY DIFFRACTION	3	A	399 - 493
4	X-RAY DIFFRACTION	4	A	494 - 568
5	X-RAY DIFFRACTION	5	B	311 - 354
6	X-RAY DIFFRACTION	6	B	355 - 398
7	X-RAY DIFFRACTION	7	B	399 - 493
8	X-RAY DIFFRACTION	8	B	494 - 568
9	X-RAY DIFFRACTION	9	C	311 - 354
10	X-RAY DIFFRACTION	10	C	355 - 398
11	X-RAY DIFFRACTION	11	C	399 - 493
12	X-RAY DIFFRACTION	12	C	494 - 568
13	X-RAY DIFFRACTION	13	D	311 - 354
14	X-RAY DIFFRACTION	14	D	355 - 398
15	X-RAY DIFFRACTION	15	D	399 - 493
16	X-RAY DIFFRACTION	16	D	494 - 568

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