PDB-3lv9: Crystal structure of CBS domain of a putative transporter from Cl...

ID or keywords:

Entry

Database: PDB / ID: 3lv9

Title

Crystal structure of CBS domain of a putative transporter from Clostridium difficile 630

Components

Putative transporter

Keywords

MEMBRANE PROTEIN / CBS domain / PSI / MCSG / Structural Genomics / Protein Structure Initiative / Midwest Center for Structural Genomics / Cell membrane / Membrane / Transmembrane

Function / homology

Function and homology information

flavin adenine dinucleotide binding / membrane => GO:0016020
Similarity search - Function

Biological species

Clostridium difficile 630 (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

SAD / Resolution: 2.4 Å

Authors

Nocek, B. / Tesar, C. / Cobb, G. / Joachimiak, A. / Midwest Center for Structural Genomics (MCSG)

Citation

Journal: To be Published
Title: Crystal structure of CBS domain of a putative transporter from Clostridium difficile 630
Authors: Nocek, B. / Tesar, C. / Cobb, G. / Joachimiak, A. / MCSG

History

Deposition	Feb 19, 2010	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Mar 9, 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

Structure viewer	Molecule: MolmilJmol/JSmol

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PDBx/mmCIF format	3lv9.cif.gz	37.5 KB	Display	PDBx/mmCIF format
PDB format	pdb3lv9.ent.gz	29.5 KB	Display	PDB format
PDBx/mmJSON format	3lv9.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/lv/3lv9 ftp://data.pdbj.org/pub/pdb/validation_reports/lv/3lv9	HTTPS FTP

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Related structure data

Similar structure data	5yz2-d 4qpv-2 3nqr-1 6yja-d 1vr9-d 3ddj-d 2o16-3 6xnu-d 4qlr-d 6yj7-d 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: apc62621.1

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Links

PDB pages	PDBj / wwPDB / NCBI
Related items in Molecule of the Month	#117 - Sep 2009 Xanthine Oxidoreductase similarity (2) #140 - Aug 2011 Rhomboid Protease GlpG similarity (4)

Deposited unit

A: Putative transporter

hetero molecules

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

1

A: Putative transporter

hetero molecules

A: Putative transporter

hetero molecules

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

Unit cell

Length a, b, c (Å)	43.641, 43.641, 127.763
Angle α, β, γ (deg.)	90.00, 90.00, 120.00
Int Tables number	154
Space group name H-M	P3₂21

Details

authors state that the biological assembly is likely monomer

#1: Protein	Putative transporter Mass: 17315.418 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Clostridium difficile 630 (bacteria) / Plasmid: pMCSG19 / Production host: Escherichia coli (E. coli) / Strain (production host): BL23-DE3 / References: UniProt: Q183U2
#2: Chemical	ChemComp-PO4 / PHOSPHATE ION Mass: 94.971 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: PO₄
#3: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 13 / 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: 2.03 Å³/Da / Density % sol: 39.36 %
Crystal grow	Temperature: 291 K / Method: vapor diffusion, sitting drop / pH: 6.2 Details: 0.2 M sodium Chloride 0.1M Na/K phosphate 50% PEG200, pH 6.2, VAPOR DIFFUSION, SITTING DROP, temperature 291K

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Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.9794 Å
Detector	Type: ADSC QUANTUM 315r / Detector: CCD / Date: Feb 28, 2009 / Details: mirrors
Radiation	Monochromator: double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.9794 Å / Relative weight: 1
Reflection	Resolution: 2.3→40 Å / Num. all: 6540 / Num. obs: 6532 / % possible obs: 98.7 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 6.7 % / B_iso Wilson estimate: 68.3 Å² / R_merge(I) obs: 0.086 / Net I/σ(I): 20
Reflection shell	Resolution: 2.3→2.34 Å / Redundancy: 6.4 % / R_merge(I) obs: 0.355 / Mean I/σ(I) obs: 6.3 / Num. unique all: 320 / % possible all: 99.4

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Processing

Software

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

Refinement

Method to determine structure:

SAD / Resolution: 2.4→40 Å / Cor.coef. F_o:F_c: 0.957 / Cor.coef. F_o:F_c free: 0.927 / SU B: 20.364 / SU ML: 0.214 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 2 / σ(I): 2 / ESU R: 0.44 / ESU R Free: 0.28 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.26241	271	4.6 %	RANDOM
R_work	0.20136	-	-	-
all	0.21	5912	-	-
obs	0.20423	5641	99.09 %	-

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: 28.37 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	-0.61 Å²	-0.3 Å²	0 Å²
2-	-	-0.61 Å²	0 Å²
3-	-	-	0.91 Å²

Refinement step

Cycle: LAST / Resolution: 2.4→40 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	1037	0	5	13	1055

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.019	0.022	1073
X-RAY DIFFRACTION	r_bond_other_d	0.001	0.02	732
X-RAY DIFFRACTION	r_angle_refined_deg	1.638	1.994	1451
X-RAY DIFFRACTION	r_angle_other_deg	0.958	3	1795
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	6.243	5	133
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	31.053	24.808	52
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	17.721	15	211
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	24.169	15	9
X-RAY DIFFRACTION	r_chiral_restr	0.091	0.2	172
X-RAY DIFFRACTION	r_gen_planes_refined	0.006	0.02	1174
X-RAY DIFFRACTION	r_gen_planes_other	0.001	0.02	203
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	0.76	1.5	654
X-RAY DIFFRACTION	r_mcbond_other	0.158	1.5	266
X-RAY DIFFRACTION	r_mcangle_it	1.521	2	1067
X-RAY DIFFRACTION	r_scbond_it	2.456	3	419
X-RAY DIFFRACTION	r_scangle_it	4.099	4.5	383
X-RAY DIFFRACTION	r_rigid_bond_restr
X-RAY DIFFRACTION	r_sphericity_free
X-RAY DIFFRACTION	r_sphericity_bonded

LS refinement shell

Resolution: 2.401→2.463 Å / Total num. of bins used: 20

	R_factor	Num. reflection	% reflection
R_free	0.163	19	-
R_work	0.174	404	-
obs	-	-	98.83 %

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	15.0256	3.7797	8.6241	-0.2825	-3.4302	23.9723	-0.1438	0.151	1.6426	0.6917	-0.1572	0.2916	-0.6003	0.1059	0.301	0.9796	-0.0951	-0.0797	0.0411	-0.0925	0.3731	17.4083	25.528	17.5677
2	2.4412	1.036	-0.5482	2.4174	0.2222	1.1211	0.012	-0.0025	0.0772	0.021	-0.0023	-0.0209	-0.0517	0.1687	-0.0097	0.2672	0.0021	-0.0042	0.1797	0.0156	0.199	22.4143	11.4414	7.9966
3	2.9029	1.877	-0.7884	4.9273	0.3372	5.2309	-0.0201	0.0819	-0.0473	-0.06	0.0182	-0.059	0.1221	0.1069	0.0019	0.1997	-0.0217	0.0263	0.1842	-0.0071	0.1788	18.8967	-9.161	4.6204
4	10.611	-7.6873	1.7184	11.8643	1.386	6.7402	-0.1924	-0.4169	0.7633	0.7242	0.4652	-0.8327	0.0109	0.5577	-0.2728	0.2768	-0.0909	-0.0285	0.1957	-0.0208	0.1882	20.0929	-4.5939	14.965
5	0.0202	0.5819	0.3228	4.6307	-1.1624	3.5001	0.0012	0.0257	0.0248	0.0728	0.0255	0.2017	-0.0918	-0.0366	-0.0267	0.1726	-0.0008	0.0166	0.2071	-0.0249	0.2255	14.0661	-0.5807	3.4532
6	4.1633	-1.4969	3.4132	8.7668	4.6343	9.0727	0.0047	0.2966	0.1521	0.7023	0.066	0.061	0.0673	-0.3196	-0.0708	0.284	0.0018	0.0468	0.2535	0.0266	0.1293	10.292	-12.6972	14.6789
7	1.6806	-0.4416	0.9306	13.1266	-2.1878	0.6883	0.2217	0.0099	0.0687	-0.3397	-0.0089	0.6159	0.1429	0.0232	-0.2128	0.2408	-0.0077	0.0525	0.1647	-0.0127	0.3075	7.1727	-9.9825	7.1188
8	3.4053	-1.353	-0.4578	2.105	2.2245	4.0548	-0.0095	-0.0223	0.1795	0.0997	0.1218	-0.0129	-0.2584	-0.1259	-0.1122	0.2476	0.0481	0.027	0.1298	0.0062	0.2412	11.5879	16.9223	9.7222
9	4.3137	5.6523	1.1056	9.7807	2.8104	-4.2703	-0.5724	0.6517	0.2855	0.1245	0.4504	0.6072	0.3164	-0.004	0.122	0.4211	0.0213	0.0781	0.364	0.0659	0.2183	5.204	11.7304	12.9697
10	1.9404	-0.5337	-2.7601	1.29	0.2686	9.1371	0.1831	-0.0166	0.1008	0.0736	0.0394	0.1496	-0.2492	0.0228	-0.2225	0.1817	0.0018	-0.0139	0.1883	-0.0103	0.2206	16.0006	11.374	5.9267
11	4.0972	-4.6602	-1.0387	5.8401	3.5093	6.0729	-0.279	-0.2354	0.182	0.1099	0.426	-0.4531	-0.084	0.6267	-0.1469	0.3227	0.0208	0.0613	0.2329	0.0082	0.2461	16.9125	16.0916	22.5002

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Auth asym-ID	Auth seq-ID
1	X-RAY DIFFRACTION	1	A	15 - 21
2	X-RAY DIFFRACTION	2	A	22 - 32
3	X-RAY DIFFRACTION	3	A	33 - 46
4	X-RAY DIFFRACTION	4	A	47 - 55
5	X-RAY DIFFRACTION	5	A	56 - 72
6	X-RAY DIFFRACTION	6	A	73 - 81
7	X-RAY DIFFRACTION	7	A	82 - 93
8	X-RAY DIFFRACTION	8	A	94 - 108
9	X-RAY DIFFRACTION	9	A	109 - 116
10	X-RAY DIFFRACTION	10	A	117 - 134
11	X-RAY DIFFRACTION	11	A	135 - 144

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