PDB-5vvi: Crystal Structure of the Ligand Binding Domain of LysR-type Trans...

ID or keywords:

Entry

Database: PDB / ID: 5vvi

Title

Crystal Structure of the Ligand Binding Domain of LysR-type Transcriptional Regulator, OccR from Agrobacterium tumefaciens in the Complex with Octopine

Components

Octopine catabolism/uptake operon regulatory protein OccR

Keywords

TRANSCRIPTION / alpha-beta structure / type 2 periplasmic binding fold / Structural Genomics / MCSG / PSI-Biology / Midwest Center for Structural Genomics

Function / homology

Function and homology information

DNA-binding transcription factor activity / DNA binding
Similarity search - Function

Biological species

Agrobacterium tumefaciens (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 2.28 Å

Authors

Kim, Y. / Chhor, G. / Jedrzejczak, R. / Winans, S.C. / Joachimiak, A. / Midwest Center for Structural Genomics (MCSG)

Citation

Journal: Mol. Microbiol. / Year: 2018
Title: Crystal Structure of the Ligand-Binding Domain of a LysR-type Transcriptional Regulator: Transcriptional Activation via a Rotary Switch.
Authors: Kim, Y. / Chhor, G. / Tsai, C.S. / Winans, J.B. / Jedrzejczak, R. / Joachimiak, A. / Winans, S.C.

History

Deposition	May 19, 2017	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Jun 21, 2017	Provider: repository / Type: Initial release
Revision 1.1	Nov 8, 2017	Group: Database references / Source and taxonomy / Category: citation / entity_src_gen Item: _citation.year / _entity_src_gen.pdbx_host_org_scientific_name
Revision 1.2	Sep 19, 2018	Group: Data collection / Database references / Source and taxonomy Category: citation / citation_author / entity_src_gen Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _entity_src_gen.pdbx_host_org_scientific_name
Revision 1.3	Oct 4, 2023	Group: Data collection / Database references / Refinement description Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.4	Nov 15, 2023	Group: Data collection / Category: chem_comp_atom / chem_comp_bond / Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_2

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	5vvi.cif.gz	256.5 KB	Display	PDBx/mmCIF format
PDB format	pdb5vvi.ent.gz	210.3 KB	Display	PDB format
PDBx/mmJSON format	5vvi.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	5vvi_validation.pdf.gz	485.2 KB	Display	wwPDB validaton report
Full document	5vvi_full_validation.pdf.gz	497.5 KB	Display
Data in XML	5vvi_validation.xml.gz	25.9 KB	Display
Data in CIF	5vvi_validation.cif.gz	35 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/vv/5vvi ftp://data.pdbj.org/pub/pdb/validation_reports/vv/5vvi	HTTPS FTP

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Related structure data

Related structure data	5vvhSC S: Starting model for refinement C: citing same article (ref.)
Similar structure data	6cvc-d 4u4h-2 4zzy-d 3nh2-2 3nv6-d 6s3h-2 2k2q-d 7ccf-d 4yt3-2 2yca-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	TargetTrack: MCSG-APC102401 TargetTrack: APC102401

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Links

PDB pages	PDBj / wwPDB / NCBI
Related items in Molecule of the Month	#4 - Apr 2000 Collagen similarity (1) #116 - Aug 2009 Sulfotransferases similarity (1)

Deposited unit

A: Octopine catabolism/uptake operon regulatory protein OccR

B: Octopine catabolism/uptake operon regulatory protein OccR

C: Octopine catabolism/uptake operon regulatory protein OccR

hetero molecules

70.8 kDa, 3 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

A: Octopine catabolism/uptake operon regulatory protein OccR

hetero molecules

A: Octopine catabolism/uptake operon regulatory protein OccR

hetero molecules

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

2

B: Octopine catabolism/uptake operon regulatory protein OccR

C: Octopine catabolism/uptake operon regulatory protein OccR

hetero molecules

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

Unit cell

Length a, b, c (Å)	58.417, 101.985, 112.707
Angle α, β, γ (deg.)	90.00, 98.14, 90.00
Int Tables number	5
Space group name H-M	C121

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Protein , 1 types, 3 molecules ABC

#1: Protein	Octopine catabolism/uptake operon regulatory protein OccR Mass: 23295.623 Da / Num. of mol.: 3 / Fragment: UNP residues 92-298 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Agrobacterium tumefaciens (strain Ach5) (bacteria) Strain: Ach5 / Gene: occR / Plasmid: pMCSG68 / Production host: Escherichia coli BL21(DE3) / Strain (production host): BL21(DE3) gold / References: UniProt: P0A4T4

#1: Protein

Octopine catabolism/uptake operon regulatory protein OccR

Mass: 23295.623 Da / Num. of mol.: 3 / Fragment: UNP residues 92-298
Source method: isolated from a genetically manipulated source
Source: (gene. exp.)

Agrobacterium tumefaciens (strain Ach5) (bacteria)
Strain: Ach5 / Gene: occR / Plasmid: pMCSG68 / Production host: Escherichia coli BL21(DE3) / Strain (production host): BL21(DE3) gold / References: UniProt: P0A4T4

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Non-polymers , 5 types, 105 molecules

#2: Chemical	ChemComp-6DB / octopine Mass: 246.264 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C₉H₁₈N₄O₄
#3: Chemical	ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL Mass: 62.068 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C₂H₆O₂
#4: Chemical	ChemComp-CL / CHLORIDE ION Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#5: Chemical	ChemComp-ACY / ACETIC ACID Mass: 60.052 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C₂H₄O₂
#6: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 98 / 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: 2.42 Å³/Da / Density % sol: 49.1 %
Crystal grow	Temperature: 298 K / Method: vapor diffusion, sitting drop / pH: 5.5 Details: 0.1 ammonium acetate, 0.1 M Bis-Tris pH 5.5, 17 5(w/v) PEG 10000

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Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.97895 Å
Detector	Type: ADSC QUANTUM 315r / Detector: CCD / Date: Nov 7, 2014
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.97895 Å / Relative weight: 1
Reflection	Resolution: 2.27→31.84 Å / Num. obs: 29566 / % possible obs: 99.1 % / Redundancy: 3.5 % / R_sym value: 0.064 / Net I/σ(I): 15
Reflection shell	Resolution: 2.27→2.31 Å / Redundancy: 2.8 % / R_sym value: 0.645 / % possible all: 98.4

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Processing

Software

Name	Version	Classification
PHENIX	DEV_1839	refinement
HKL-3000		data reduction
HKL-3000		data scaling
MOLREP		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: 5VVH

5vvh

Resolution: 2.28→31.84 Å / SU ML: 0.32 / Cross valid method: THROUGHOUT / σ(F): 1.37 / Phase error: 25.89

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.249	1413	5.3 %	random
R_work	0.192	-	-	-
obs	0.195	26654	89 %	-

Solvent computation

Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å

Displacement parameters

B_iso mean: 41.8 Å²

Refinement step

Cycle: LAST / Resolution: 2.28→31.84 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	4699	0	64	98	4861

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.01	4919
X-RAY DIFFRACTION	f_angle_d	1.297	6657
X-RAY DIFFRACTION	f_dihedral_angle_d	16.106	1852
X-RAY DIFFRACTION	f_chiral_restr	0.048	761
X-RAY DIFFRACTION	f_plane_restr	0.006	882

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 (%)
2.2777-2.3591	0.3754	29	0.2874	746	X-RAY DIFFRACTION	26
2.3591-2.4535	0.2986	139	0.2543	2081	X-RAY DIFFRACTION	74
2.4535-2.5651	0.2924	189	0.2433	2717	X-RAY DIFFRACTION	98
2.5651-2.7003	0.3042	177	0.2367	2787	X-RAY DIFFRACTION	100
2.7003-2.8693	0.3002	143	0.232	2849	X-RAY DIFFRACTION	100
2.8693-3.0907	0.2708	135	0.2269	2886	X-RAY DIFFRACTION	100
3.0907-3.4014	0.2775	145	0.216	2802	X-RAY DIFFRACTION	100
3.4014-3.8929	0.2409	163	0.1748	2836	X-RAY DIFFRACTION	99
3.8929-4.9017	0.1869	157	0.1456	2772	X-RAY DIFFRACTION	97
4.9017-31.8415	0.2072	136	0.1534	2765	X-RAY DIFFRACTION	95

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	4.6611	1.2992	-0.0677	6.1984	-1.7126	4.2842	-0.2874	-0.3623	-0.1068	0.2927	0.1316	-0.4856	0.376	0.3193	0.0741	0.1366	0.0438	-0.0155	0.1923	-0.0468	0.1956	-0.7392	1.0671	66.8412
2	2.4572	0.4672	-0.2229	3.9703	1.6365	5.1707	-0.0352	-0.154	0.3556	0.2988	0.0312	-0.5973	-0.3594	0.629	0.0806	0.2165	-0.0926	-0.0026	0.2387	-0.101	0.3466	2.5758	9.2011	63.9395
3	3.1132	1.5971	-0.2483	3.2105	-0.8709	1.8486	0.0313	0.1893	-0.0258	-0.6719	0.0194	-0.4764	0.1053	0.3275	0.0394	0.2842	-0.0349	0.1191	0.1542	0.0069	0.1924	3.6197	-3.9894	39.0091
4	6.1087	-1.7928	-0.1183	4.8716	0.9124	1.1921	-0.1596	0.4558	-0.0396	-0.3825	0.0393	-0.0871	0.2992	0.0473	0.1482	0.1807	-0.0237	0.0378	0.1297	0.0182	0.1669	-0.5768	-4.4517	44.0764
5	1.8938	0.8806	0.8934	3.9488	0.3242	4.5321	-0.3846	-0.3974	0.1525	0.3191	0.477	-0.8897	0.3016	0.8689	-0.3599	0.2537	0.0869	-0.1297	0.4511	-0.0954	0.3311	9.7847	0.9187	64.2189
6	2.65	-0.0995	0.1031	3.7613	-1.5414	1.9373	-0.0237	0.5981	-0.0467	-0.4764	-0.0769	-0.1847	0.5712	0.4412	0.2308	0.3538	-0.0238	-0.018	0.505	-0.0142	0.1909	18.3868	23.0769	12.6978
7	5.1402	0.8745	-1.6753	2.2123	-0.8506	3.6339	0.3949	0.2027	0.5824	-0.401	-0.309	0.1188	0.0903	0.6337	0.0565	0.5896	0.0041	-0.0518	0.7143	-0.055	0.2676	19.025	25.2165	6.4251
8	1.2427	0.8811	-0.0919	1.521	1.2396	2.6447	-0.2308	0.587	-0.712	-0.327	0.2097	0.2671	0.8115	-0.2035	-0.0997	0.8668	-0.1744	-0.134	0.4944	-0.1294	0.5421	12.6557	11.1236	16.1473
9	3.8259	0.8673	1.3061	5.4752	0.152	4.1039	0.1999	-0.4476	-0.3591	0.3313	-0.1281	-0.1982	0.214	-0.2842	-0.0114	0.2162	-0.0462	0.0356	0.1366	0.0439	0.2437	16.1814	23.699	41.1358
10	1.1892	-0.1201	0.1542	1.0842	-1.5122	2.2749	-0.0706	0.0035	-0.425	0.4403	-0.339	0.0005	0.0788	-0.3239	-0.2563	0.2103	-0.1523	0.097	-0.0029	0.1178	0.4588	10.0558	22.1882	34.3188
11	5.0388	-0.7622	1.4138	2.7084	1.9953	4.46	0.0197	0.3383	0.1451	-0.4051	0.0094	-0.2571	-0.1657	0.2523	-0.0568	0.1902	-0.0472	0.0088	0.1627	0.0539	0.2589	19.4513	25.1196	34.057
12	4.1605	0.9114	-1.9862	2.8633	0.7393	4.1044	0.0798	0.0531	-0.424	-0.6155	-0.321	-0.1409	0.9185	0.787	0.023	0.6147	0.1956	0.0058	0.4743	-0.0545	0.3757	24.5345	15.159	16.7
13	4.2373	-1.0521	-0.3142	4.7163	-0.5465	3.6007	-0.2968	-0.0842	-0.2464	0.184	0.4336	0.8714	-0.0227	-0.9117	0.0359	0.1754	0.0343	0.0906	0.4999	0.1349	0.3576	-2.3326	30.3216	27.4654
14	4.5314	-0.7747	0.0226	3.7697	-1.0873	4.4801	-0.0286	0.7809	0.3683	-0.4961	-0.1286	-0.1415	-0.6882	0.212	0.1384	0.4127	-0.024	-0.103	0.5475	0.1286	0.3055	8.9891	40.8817	7.9487
15	3.0315	1.7802	-2.486	5.7896	-1.5097	3.5785	0.0167	0.8017	0.4505	-1.1959	0.4714	-0.9102	-0.3545	0.2688	-0.2494	0.4137	-0.038	0.0991	0.7749	0.0609	0.4489	13.5292	31.1107	4.1868
16	4.8694	-0.2424	-0.3627	2.5992	-1.6256	4.2631	-0.044	0.0716	0.2523	0.1544	-0.075	0.179	-0.4473	-0.1667	0.1298	0.3192	0.0068	-0.0835	0.3372	0.0201	0.2355	6.9128	38.4136	17.0391
17	5.7685	-0.3012	-2.5697	2.6104	0.7073	9.2372	0.0808	-0.1129	0.6626	1.0714	0.6493	0.182	-2.2211	-0.582	-0.278	0.6394	0.2998	-0.0542	0.4453	0.0418	0.4167	-0.7031	43.9698	28.022

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	CHAIN 'A' AND (RESID 91 THROUGH 114 )
2	X-RAY DIFFRACTION	2	CHAIN 'A' AND (RESID 115 THROUGH 163 )
3	X-RAY DIFFRACTION	3	CHAIN 'A' AND (RESID 164 THROUGH 206 )
4	X-RAY DIFFRACTION	4	CHAIN 'A' AND (RESID 207 THROUGH 258 )
5	X-RAY DIFFRACTION	5	CHAIN 'A' AND (RESID 259 THROUGH 298 )
6	X-RAY DIFFRACTION	6	CHAIN 'B' AND (RESID 91 THROUGH 113 )
7	X-RAY DIFFRACTION	7	CHAIN 'B' AND (RESID 114 THROUGH 128 )
8	X-RAY DIFFRACTION	8	CHAIN 'B' AND (RESID 129 THROUGH 163 )
9	X-RAY DIFFRACTION	9	CHAIN 'B' AND (RESID 164 THROUGH 198 )
10	X-RAY DIFFRACTION	10	CHAIN 'B' AND (RESID 199 THROUGH 227 )
11	X-RAY DIFFRACTION	11	CHAIN 'B' AND (RESID 230 THROUGH 258 )
12	X-RAY DIFFRACTION	12	CHAIN 'B' AND (RESID 259 THROUGH 298 )
13	X-RAY DIFFRACTION	13	CHAIN 'C' AND (RESID 91 THROUGH 154 )
14	X-RAY DIFFRACTION	14	CHAIN 'C' AND (RESID 155 THROUGH 207 )
15	X-RAY DIFFRACTION	15	CHAIN 'C' AND (RESID 208 THROUGH 220 )
16	X-RAY DIFFRACTION	16	CHAIN 'C' AND (RESID 221 THROUGH 273 )
17	X-RAY DIFFRACTION	17	CHAIN 'C' AND (RESID 274 THROUGH 297 )

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