PDB-5f7p: Rok Repressor Lmo0178 from Listeria monocytogenes

ID or keywords:

Entry

Database: PDB / ID: 5f7p

Title

Rok Repressor Lmo0178 from Listeria monocytogenes

Components

Lmo0178 protein

Keywords

TRANSCRIPTION / Repressor / Open reading frame / Kinase / Structural Genomics / Center for Structural Genomics of Infectious Diseases / CSGID

Function / homology

Function and homology information

D-xylose metabolic process / metal ion binding
Similarity search - Function

Biological species

Listeria monocytogenes serovar 1/2a (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 2.84 Å

Authors

Light, S.H. / Anderson, W.F. / Center for Structural Genomics of Infectious Diseases (CSGID)

Citation

Journal: Nat Microbiol / Year: 2016
Title: Structure to function of an alpha-glucan metabolic pathway that promotes Listeria monocytogenes pathogenesis.
Authors: Light, S.H. / Cahoon, L.A. / Halavaty, A.S. / Freitag, N.E. / Anderson, W.F.

History

Deposition	Dec 8, 2015	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Sep 7, 2016	Provider: repository / Type: Initial release
Revision 1.1	Nov 23, 2016	Group: Database references
Revision 1.2	Sep 27, 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

Structure viewer	Molecule: MolmilJmol/JSmol

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PDBx/mmCIF format	5f7p.cif.gz	275 KB	Display	PDBx/mmCIF format
PDB format	pdb5f7p.ent.gz	223.2 KB	Display	PDB format
PDBx/mmJSON format	5f7p.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/f7/5f7p ftp://data.pdbj.org/pub/pdb/validation_reports/f7/5f7p	HTTPS FTP

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Related structure data

Related structure data	4kmqC 5do8C 5f7qC 5f7rSC 5f7sC 5f7uC 5f7vC C: citing same article (ref.) S: Starting model for refinement
Similar structure data	1ruo-d 3lpo-1 3noy-2 1o3t-d 1eud-d 1cgp-d 1pxd-1 4x6r-d 3mq6-3 6aqr-d 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: IDP95184

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Links

PDB pages	PDBj / wwPDB / NCBI

Deposited unit

E: Lmo0178 protein

A: Lmo0178 protein

hetero molecules

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

1

Idetical with deposited unit
defined by author&software

Unit cell

Length a, b, c (Å)	68.970, 81.785, 141.089
Angle α, β, γ (deg.)	90.00, 90.00, 90.00
Int Tables number	19
Space group name H-M	P2₁2₁2₁

#1: Protein	Lmo0178 protein / Rok repressor Mass: 45366.551 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Listeria monocytogenes serovar 1/2a (strain ATCC BAA-679 / EGD-e) (bacteria) Strain: ATCC BAA-679 / EGD-e / Gene: lmo0178 / Production host: Escherichia coli BL21 (bacteria) / References: UniProt: Q8YAF1
#2: Chemical	ChemComp-ZN / ZINC ION Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#3: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 3 / Source method: isolated from a natural source / Formula: H₂O

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Experiment

Experiment	Method: X-RAY DIFFRACTION

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Sample preparation

Crystal	Density Matthews: 2.19 Å³/Da / Density % sol: 43.91 %
Crystal grow	Temperature: 300 K / Method: vapor diffusion, sitting drop Details: 10 mg/mL proten in 10 mM Tris, pH 8.3, 100 mM sodium chloride against JCSG+ (Qiagen) A10 (0.2 M potassium formate, 20% PEG3350)

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Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: SYNCHROTRON / Site: APS / Beamline: 21-ID-F / Wavelength: 0.97872 Å
Detector	Type: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Apr 20, 2015
Radiation	Monochromator: diamond(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.97872 Å / Relative weight: 1
Reflection	Resolution: 2.838→70.757 Å / Num. obs: 19017 / % possible obs: 97.7 % / Redundancy: 4.8 % / R_merge(I) obs: 0.033 / Net I/σ(I): 27.1
Reflection shell	Resolution: 2.838→2.9 Å / Redundancy: 5 % / R_merge(I) obs: 0.628 / Mean I/σ(I) obs: 2.3 / % possible all: 98.7

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Processing

Software

Name	Version	Classification
REFMAC	5.8.0135	refinement
HKL-3000		data reduction
HKL-3000		data scaling
PHASER		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: PDB entry 5F7R

5f7r

Resolution: 2.84→70.757 Å / Cor.coef. F_o:F_c: 0.933 / Cor.coef. F_o:F_c free: 0.899 / SU B: 42.326 / SU ML: 0.384 / Cross valid method: THROUGHOUT / ESU R Free: 0.455 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.29257	955	5 %	RANDOM
R_work	0.22254	-	-	-
obs	0.22622	18018	97.13 %	-

Solvent computation

Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK

Displacement parameters

B_iso mean: 103.604 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	1.32 Å²	-0 Å²	-0 Å²
2-	-	-5.85 Å²	0 Å²
3-	-	-	4.53 Å²

Refinement step

Cycle: LAST / Resolution: 2.84→70.757 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	5117	0	2	3	5122

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.013	0.019	5210
X-RAY DIFFRACTION	r_bond_other_d	0.001	0.02	4996
X-RAY DIFFRACTION	r_angle_refined_deg	1.694	1.956	7026
X-RAY DIFFRACTION	r_angle_other_deg	0.924	3	11488
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	3.806	5	651
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	33.161	24.937	239
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	14.433	15	912
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	14.03	15	21
X-RAY DIFFRACTION	r_chiral_restr	0.106	0.2	783
X-RAY DIFFRACTION	r_gen_planes_refined	0.025	0.02	5922
X-RAY DIFFRACTION	r_gen_planes_other	0.019	0.02	1193
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	6.063	5.755	2625
X-RAY DIFFRACTION	r_mcbond_other	6.063	5.757	2624
X-RAY DIFFRACTION	r_mcangle_it	9.209	8.606	3269
X-RAY DIFFRACTION	r_mcangle_other	9.208	8.605	3270
X-RAY DIFFRACTION	r_scbond_it	6.337	6.431	2585
X-RAY DIFFRACTION	r_scbond_other	6.335	6.43	2586
X-RAY DIFFRACTION	r_scangle_it
X-RAY DIFFRACTION	r_scangle_other	9.78	9.415	3758
X-RAY DIFFRACTION	r_long_range_B_refined	13.693	25.793	5894
X-RAY DIFFRACTION	r_long_range_B_other	13.692	25.791	5895
X-RAY DIFFRACTION	r_rigid_bond_restr
X-RAY DIFFRACTION	r_sphericity_free
X-RAY DIFFRACTION	r_sphericity_bonded

LS refinement shell

Resolution: 2.838→2.912 Å / Total num. of bins used: 20

	R_factor	Num. reflection	% reflection
R_free	0.336	73	-
R_work	0.286	1255	-
obs	-	-	92.67 %

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	1.9937	-3.731	0.7846	11.2024	0.7561	3.2233	0.1156	-0.5127	0.1618	0.3367	-0.0637	-0.0162	0.644	-0.2381	-0.0519	0.3839	0.03	0.0515	0.5983	-0.0817	0.3312	-13.3308	18.4263	-19.6995
2	6.7823	-7.1441	-0.448	8.3608	0.7278	0.1215	0.2694	0.4851	0.0545	-0.3342	-0.257	-0.0827	0.047	0.0127	-0.0125	0.6522	0.0535	-0.0063	0.5593	-0.024	0.2127	-4.2367	7.264	-30.136
3	7.5873	-2.5197	1.6377	6.9452	-5.06	4.0471	0.0178	0.0104	-0.6679	0.5634	-0.2588	-0.6951	-0.7046	0.3979	0.2409	0.5969	0.0567	0.0283	0.5909	-0.1251	0.5286	18.5503	-9.1161	-30.7379
4	3.9172	-0.7172	0.1072	2.8759	-0.5341	5.086	0.2983	0.366	0.1511	-0.5758	-0.2825	-0.4764	-0.2353	0.3976	-0.0159	0.7815	-0.0407	0.1025	0.7744	0.0133	0.3124	11.0559	0.0976	-25.3082
5	1.7631	-0.516	0.5942	5.6169	-3.9137	2.8356	0.1679	0.146	0.0216	0.1185	-0.1988	0.0318	-0.2715	0.0543	0.0309	0.7329	0.0294	-0.1132	0.7699	-0.0118	0.4211	-1.6645	-2.7726	-10.6303
6	5.2057	2.3311	1.6157	4.5056	2.1286	3.4638	-0.1551	0.4532	-0.6248	-0.2494	0.3146	-0.4196	0.1291	0.3737	-0.1595	0.3631	0.0032	0.0631	0.6527	-0.0653	0.3216	5.6422	-24.9545	-7.7318
7	4.3401	-0.0047	0.1711	5.8265	3.0509	3.8051	-0.018	0.4507	0.3103	-0.9766	-0.0756	0.3669	-0.3825	-0.4985	0.0935	0.563	0.0406	-0.0959	0.7405	-0.0002	0.339	-4.8297	-14.3004	-11.5667
8	2.5042	0.409	-2.407	2.8477	-2.9998	5.3429	0.2524	-0.0767	0.0493	-0.4472	-0.0984	0.6947	-0.0515	-0.0366	-0.154	0.6015	-0.0875	-0.2256	0.8459	-0.1184	0.7508	-5.5001	-9.1225	-10.76
9	5.6852	0.7212	0.2088	1.5247	-0.6711	0.4469	0.3497	-0.6289	-0.0902	0.1198	0.0293	0.3912	-0.1464	-0.0293	-0.379	0.1917	-0.1644	0.2504	0.4779	-0.1989	0.4612	-7.3725	5.4378	24.712
10	1.6547	0.5804	-0.5108	0.3441	-0.0737	0.2549	0.2495	-0.1202	0.3854	0.0822	-0.1222	0.17	-0.0546	0.0393	-0.1273	0.1121	0.0118	0.0649	0.3901	-0.2252	0.4747	3.5036	5.5072	10.139
11	1.2551	0.5736	1.2552	1.0445	0.98	1.4757	0.0785	-0.3488	0.1148	0.2281	-0.1389	0.0145	0.1888	-0.2884	0.0604	0.1579	-0.0233	0.0044	0.615	-0.0775	0.0876	12.4765	-13.9275	15.94
12	1.1513	1.2882	-0.1527	1.8249	-0.4421	0.2138	0.1511	0.0244	0.371	0.4131	-0.2247	0.1939	-0.1782	0.1882	0.0736	0.1607	-0.0916	-0.1015	0.5215	-0.0936	0.3954	11.0677	4.9817	12.1121
13	40.0886	28.2708	33.8958	19.9421	23.915	28.7251	0.6147	-2.2272	0.822	0.408	-1.5599	0.6094	0.4924	-1.9373	0.9452	0.2231	0.0143	0.1149	0.3787	-0.1745	1.1301	-3.8001	18.5103	12.0622

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Auth asym-ID	Auth seq-ID
1	X-RAY DIFFRACTION	1	A	14 - 43
2	X-RAY DIFFRACTION	2	A	44 - 112
3	X-RAY DIFFRACTION	3	A	113 - 124
4	X-RAY DIFFRACTION	4	A	125 - 201
5	X-RAY DIFFRACTION	5	A	202 - 236
6	X-RAY DIFFRACTION	6	A	237 - 327
7	X-RAY DIFFRACTION	7	A	328 - 346
8	X-RAY DIFFRACTION	8	A	347 - 390
9	X-RAY DIFFRACTION	9	E	83 - 184
10	X-RAY DIFFRACTION	10	E	185 - 239
11	X-RAY DIFFRACTION	11	E	240 - 358
12	X-RAY DIFFRACTION	12	E	359 - 387
13	X-RAY DIFFRACTION	13	E	388 - 391

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