PDB-3tqw: Structure of a ABC transporter, periplasmic substrate-binding pro...

ID or keywords:

Entry

Database: PDB / ID: 3tqw

Title

Structure of a ABC transporter, periplasmic substrate-binding protein from Coxiella burnetii

Components

Methionine-binding protein

Keywords

TRANSPORT PROTEIN / Transport and binding proteins

Function / homology

Lipoprotein NlpA family / NlpA lipoprotein / Periplasmic binding protein-like II / D-Maltodextrin-Binding Protein; domain 2 / 3-Layer(aba) Sandwich /

membrane / Alpha Beta /

METHIONINE /

Lipoprotein

Function and homology information

Biological species

Coxiella burnetii (bacteria)

Method

X-RAY DIFFRACTION /

MOLECULAR REPLACEMENT /

molecular replacement / Resolution: 2 Å

Authors

Cheung, J. / Franklin, M.C. / Rudolph, M. / Cassidy, M. / Gary, E. / Burshteyn, F. / Love, J.

Citation

Journal: Proteins / Year: 2015
Title: Structural genomics for drug design against the pathogen Coxiella burnetii.
Authors: Franklin, M.C. / Cheung, J. / Rudolph, M.J. / Burshteyn, F. / Cassidy, M. / Gary, E. / Hillerich, B. / Yao, Z.K. / Carlier, P.R. / Totrov, M. / Love, J.D.

History

Deposition	Sep 9, 2011	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Sep 21, 2011	Provider: repository / Type: Initial release
Revision 1.1	Jun 24, 2015	Group: Database references
Revision 1.2	Jan 27, 2016	Group: Database references
Revision 1.3	Nov 8, 2017	Group: Refinement description / Category: software

Structure viewer	Molecule: MolmilJmol/JSmol

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PDBx/mmCIF format	3tqw.cif.gz	199 KB	Display	PDBx/mmCIF format
PDB format	pdb3tqw.ent.gz	168.2 KB	Display	PDB format
PDBx/mmJSON format	3tqw.json.gz		Tree view	PDBx/mmJSON format
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Validation report

Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/tq/3tqw ftp://data.pdbj.org/pub/pdb/validation_reports/tq/3tqw	HTTPS FTP

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Related structure data

Related structure data	3tq8C 3tq9C 3tqaC 3tqbC 3tqcC 3tqdC 3tqeC 3tqfC 3tqgC 3tqhC 3tqiC 3tqjC 3tqlC 3tqmC 3tqnC 3tqoC 3tqpC 3tqqC 3tqrC 3tqsC 3tqtC 3tquC 3tqxC 3tqyC 3tqzC 3tr0C 3tr1C 3tr2C 3tr3C 3tr4C 3tr5C 3tr6C 3tr7C 3tr8C 3tr9C 3trbC 3trcC 3trdC 3treC 3trfC 3trgC 3trhC 3triC 3tthC 3ty2C 3uwcC 4f3qC 4f3rC 4nbqC 4ng4C C: citing same article (ref.)
Similar structure data	4ef2-1 3ir1-4 3gxa-6 3gxa-2 6dzx-1 4yah-d 3ir1-5 4ib2-1 6dzx-5 3up9-d 2xwp-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

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Links

PDB pages	PDBj / wwPDB / NCBI

Deposited unit

A: Methionine-binding protein

B: Methionine-binding protein

hetero molecules

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

1

A: Methionine-binding protein

hetero molecules

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

2

B: Methionine-binding protein

hetero molecules

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

Unit cell

Length a, b, c (Å)	96.787, 112.216, 100.236
Angle α, β, γ (deg.)	90.00, 90.00, 90.00
Int Tables number	20
Space group name H-M	C222₁

#1: Protein	Methionine-binding protein Mass: 26056.064 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Coxiella burnetii (bacteria) / Gene: CBU_0109 / Plasmid: pET / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q83F42
#2: Chemical	ChemComp-MET / METHIONINE / Methionine Type: L-peptide linking / Mass: 149.211 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C₅H₁₁NO₂S
#3: Chemical	ChemComp-SO4 / SULFATE ION / Sulfate Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO₄
#4: Water	ChemComp-HOH / water / Water Mass: 18.015 Da / Num. of mol.: 431 / 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: 2.61 Å³/Da / Density % sol: 52.9 %
Crystal grow	Temperature: 277 K / Method: vapor diffusion, sitting drop / pH: 6.5 Details: 0.1M sodium cacodylate, 2M ammonium sulphate, 0.2M sodium chloride, pH 6.5, vapor diffusion, sitting drop, temperature 277K

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Data collection

Diffraction

Mean temperature: 100 K

Diffraction source

Source:

ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.5418 Å

Detector

Type: RIGAKU SATURN 944 / Detector: CCD / Date: Jul 21, 2011

Radiation

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

Radiation wavelength

Wavelength: 1.5418 Å / Relative weight: 1

Reflection

Resolution: 2→30 Å / Num. all: 37145 / Num. obs: 37071 / % possible obs: 99.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 7.1 % / R_merge(I) obs: 0.083 / Net I/σ(I): 8.5

Reflection shell

Resolution (Å)	Redundancy (%)	R_merge(I) obs	Diffraction-ID	% possible all
2-2.03	5.6	0.405	1	100
2.03-2.07	6.8	0.359	1	100
2.07-2.11	7.1	0.3	1	100
2.11-2.15	7.2	0.265	1	100
2.15-2.2	7.2	0.244	1	100
2.2-2.25	7.2	0.223	1	100
2.25-2.31	7.2	0.21	1	100
2.31-2.37	7.2	0.194	1	100
2.37-2.44	7.2	0.17	1	100
2.44-2.52	7.3	0.161	1	100
2.52-2.61	7.3	0.145	1	100
2.61-2.71	7.3	0.118	1	100
2.71-2.84	7.3	0.113	1	100
2.84-2.99	7.3	0.095	1	100
2.99-3.17	7.3	0.078	1	100
3.17-3.42	7.4	0.062	1	100
3.42-3.76	7.3	0.052	1	100
3.76-4.31	7.3	0.045	1	100
4.31-5.42	7.3	0.043	1	100
5.42-30	6.9	0.038	1	97.2

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Phasing

Phasing	Method: molecular replacement

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Processing

Software

Name	Version	Classification
DENZO		data reduction
SCALEPACK		data scaling
PHASER		phasing
PHENIX	1.7_650	refinement
PDB_EXTRACT	3.1	data extraction
HKL-2000		data collection
HKL-2000		data reduction
HKL-2000		data scaling

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT / Resolution: 2→17.588 Å / Occupancy max: 1 / Occupancy min: 0.29 / SU ML: 0.22 / σ(F): 0 / Phase error: 18 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection
R_free	0.1952	1852	5 %
R_work	0.1697	-	-
obs	0.171	37038	99.81 %
all	-	38964	-

Solvent computation

Shrinkage radii: 0.95 Å / VDW probe radii: 1.2 Å / Solvent model: FLAT BULK SOLVENT MODEL / B_sol: 39.813 Å² / k_sol: 0.366 e/Å³

Displacement parameters

	B_aniso -1	B_aniso -2	B_aniso -3
1-	-0.3113 Å²	-0 Å²	-0 Å²
2-	-	1.7198 Å²	-0 Å²
3-	-	-	-1.4085 Å²

Refinement step

Cycle: LAST / Resolution: 2→17.588 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	3536	0	23	431	3990

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.005	3811
X-RAY DIFFRACTION	f_angle_d	0.92	5197
X-RAY DIFFRACTION	f_dihedral_angle_d	10.901	1462
X-RAY DIFFRACTION	f_chiral_restr	0.064	613
X-RAY DIFFRACTION	f_plane_restr	0.004	681

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 (%)
2-2.054	0.2606	134	0.2042	2620	X-RAY DIFFRACTION	98
2.054-2.1144	0.217	138	0.1651	2696	X-RAY DIFFRACTION	100
2.1144-2.1825	0.1723	143	0.1555	2682	X-RAY DIFFRACTION	100
2.1825-2.2604	0.2006	141	0.1582	2661	X-RAY DIFFRACTION	100
2.2604-2.3507	0.2104	146	0.1695	2693	X-RAY DIFFRACTION	100
2.3507-2.4574	0.2133	131	0.1691	2697	X-RAY DIFFRACTION	100
2.4574-2.5866	0.2389	150	0.1776	2686	X-RAY DIFFRACTION	100
2.5866-2.7481	0.1858	151	0.1672	2688	X-RAY DIFFRACTION	100
2.7481-2.9593	0.2108	141	0.1848	2718	X-RAY DIFFRACTION	100
2.9593-3.2554	0.1858	127	0.173	2732	X-RAY DIFFRACTION	100
3.2554-3.7226	0.1849	135	0.1704	2742	X-RAY DIFFRACTION	100
3.7226-4.6754	0.17	155	0.146	2729	X-RAY DIFFRACTION	100
4.6754-17.5882	0.1912	160	0.1839	2842	X-RAY DIFFRACTION	100

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	0.2468	-0.0961	0.0301	0.4588	-0.0108	0.1388	-0.0117	-0.0936	-0.0202	0.0961	-0.0167	-0.0675	0.0471	0.0647	0.0011	0.0865	0.0058	0.0082	0.1011	-0.0029	0.0804	34.3649	17.6886	26.5714
2	0.2528	-0.1667	-0.2075	0.1152	0.1016	0.3127	-0.032	0.0358	-0.1184	0.0273	-0.0242	0.0676	-0.0133	-0.0742	0.0152	0.1149	-0.0054	0.0252	0.1103	0.0076	0.1303	17.928	18.4458	37.6941
3	0.2323	0.1851	-0.1626	0.1707	-0.1348	0.1153	-0.0773	0.0266	-0.0437	0.0404	0.0913	0.1318	0.0612	-0.1059	0.0009	0.1257	-0.013	0.0772	0.1475	0.0726	0.231	7.8734	15.6279	50.1776
4	0.373	-0.1086	-0.0712	0.1399	0.1271	0.4678	-0.0399	0.0494	-0.1635	-0.0207	-0.0221	0.0677	0.0323	0.0827	0.0355	0.1295	0.0149	0.0276	0.1072	0.0148	0.13	21.2798	13.8447	39.9018
5	0.6006	0.0727	-0.0733	0.7086	0.5251	0.4211	0.0011	0.0758	-0.065	-0.0584	-0.0495	0.0115	-0.0172	-0.0329	0.024	0.1824	0.0216	0.0073	0.1526	-0.0147	0.1365	28.9492	13.1599	20.3394
6	0.0469	-0.0288	-0.0116	0.0693	0.0455	0.0533	-0.0082	-0.0075	-0.037	-0.0596	-0.0307	0.0492	0.1276	0.0541	0.0075	0.1677	0.0311	0.0025	0.096	0.0088	0.2191	31.3074	5.9791	35.093
7	0.2067	0.088	-0.0477	0.1142	0.0173	0.0501	0.0238	-0.1702	0.0374	0.0498	-0.0776	0.0018	0.0105	-0.0028	0.022	0.1155	-0.0016	-0.0059	0.1429	-0.0107	0.1038	1.5585	38.1836	60.7695
8	0.2007	0.0864	0.049	0.1542	0.0235	0.3145	-0.0053	-0.0245	-0.1445	0.0335	-0.039	-0.0051	0.1454	-0.0666	0.0082	0.1252	0.0002	0.0033	0.1125	-0.0023	0.1105	2.4694	30.6822	51.7936
9	0.2887	-0.1405	-0.168	0.1067	0.1044	0.2341	0.03	0.1127	0.0591	-0.0573	0.0106	-0.0498	-0.103	-0.0636	0.0014	0.0912	0.0164	-0.003	0.0897	-0.0046	0.0868	10.5851	39.5504	43.8202
10	0.4408	-0.0576	-0.0734	0.1982	0.0314	0.1013	-0.0205	-0.0454	-0.039	-0.146	0.1188	-0.152	-0.0592	0.064	0.0345	0.0992	-0.0532	0.0786	0.0919	-0.0076	0.1145	25.8161	40.8726	38.7661
11	0.7276	-0.0268	0.0875	0.1424	0.0655	0.3496	0.065	-0.0467	0.1503	-0.055	-0.0378	0.0091	-0.1561	-0.0863	0.0295	0.1168	0.0148	-0.0045	0.0943	-0.0225	0.0948	10.0909	44.3345	47.9732
12	0.1914	-0.0783	0.1381	0.1725	0.0752	0.4268	-0.0048	-0.0689	0.0509	0.0241	-0.0403	0.0232	-0.1288	-0.0988	0.0332	0.1512	0.0066	-0.015	0.13	-0.0063	0.1361	4.0193	47.4391	57.4881

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	CHAIN A AND (RESSEQ 1:26)
2	X-RAY DIFFRACTION	2	CHAIN A AND (RESSEQ 27:120)
3	X-RAY DIFFRACTION	3	CHAIN A AND (RESSEQ 121:158)
4	X-RAY DIFFRACTION	4	CHAIN A AND (RESSEQ 159:207)
5	X-RAY DIFFRACTION	5	CHAIN A AND (RESSEQ 208:219)
6	X-RAY DIFFRACTION	6	CHAIN A AND (RESSEQ 220:237)
7	X-RAY DIFFRACTION	7	CHAIN B AND (RESSEQ 1:26)
8	X-RAY DIFFRACTION	8	CHAIN B AND (RESSEQ 27:52)
9	X-RAY DIFFRACTION	9	CHAIN B AND (RESSEQ 53:92)
10	X-RAY DIFFRACTION	10	CHAIN B AND (RESSEQ 93:175)
11	X-RAY DIFFRACTION	11	CHAIN B AND (RESSEQ 176:207)
12	X-RAY DIFFRACTION	12	CHAIN B AND (RESSEQ 208:237)

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