PDB-5gpe: Crystal structure of the transcription regulator PbrR691 from Ral...

ID or keywords:

Entry

Database: PDB / ID: 5gpe

Title

Crystal structure of the transcription regulator PbrR691 from Ralstonia metallidurans CH34 in complex with Lead(II)

Components

Transcriptional regulator, MerR-family

Keywords

TRANSCRIPTION / PbrR691 / MerR family / Transcription activator

Function / homology

Function and homology information

DNA-binding transcription factor activity / positive regulation of DNA-templated transcription / DNA binding / metal ion binding
Similarity search - Function

Biological species

Cupriavidus metallidurans CH34 (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 2.01 Å

Authors

Huang, S.Q. / Chen, W.Z. / Wang, D. / Hu, Q.Y. / Liu, X.C. / Gan, J.H. / Chen, H.

Funding support

China, 1items

Citation

Journal: Inorg Chem / Year: 2016
Title: Structural Basis for the Selective Pb(II) Recognition of Metalloregulatory Protein PbrR691
Authors: Huang, S.Q. / Liu, X.C. / Wang, D. / Chen, W.Z. / Hu, Q.Y. / Wei, T.B. / Zhou, W.Q. / Gan, J.H. / Chen, H.

History

Deposition	Aug 1, 2016	Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0	Dec 28, 2016	Provider: repository / Type: Initial release
Revision 1.1	Aug 16, 2017	Group: Structure summary / Category: audit_author / Item: _audit_author.name
Revision 1.2	Sep 15, 2021	Group: Author supporting evidence / Database references / Category: database_2 / pdbx_audit_support Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_audit_support.funding_organization
Revision 1.3	Nov 8, 2023	Group: Data collection / Refinement description Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model / struct_ncs_dom_lim Item: _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id ..._struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

Structure viewer	Molecule: MolmilJmol/JSmol

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PDBx/mmCIF format	5gpe.cif.gz	426.5 KB	Display	PDBx/mmCIF format
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Validation report

Summary document	5gpe_validation.pdf.gz	474.4 KB	Display	wwPDB validaton report
Full document	5gpe_full_validation.pdf.gz	477.9 KB	Display
Data in XML	5gpe_validation.xml.gz	38.5 KB	Display
Data in CIF	5gpe_validation.cif.gz	54.8 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/gp/5gpe ftp://data.pdbj.org/pub/pdb/validation_reports/gp/5gpe	HTTPS FTP

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Related structure data

Related structure data	5d07 PDB Unreleased entryS S: Starting model for refinement
Similar structure data	1q06-d 1q07-d 5crl-d 1q05-d 3vuy-d 2iey-d 5d90-1 4zql-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) 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

Related structure data

5d07
PDB Unreleased entryS

S: Starting model for refinement

Similar structure data

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Links

PDB pages	PDBj / wwPDB / NCBI
Related items in Molecule of the Month	#196 - Apr 2016 Lead Poisoning similarity (1) #214 - Oct 2017 Chimeric Antigen Receptors similarity (1) #48 - Dec 2003 Catabolite Activator Protein similarity (1) #56 - Aug 2004 Caspases similarity (1) #16 - Apr 2001 Aminoacyl-tRNA Synthetases similarity (1) #255 - Mar 2021 Cisplatin and DNA similarity (1)

Deposited unit

A: Transcriptional regulator, MerR-family

B: Transcriptional regulator, MerR-family

C: Transcriptional regulator, MerR-family

D: Transcriptional regulator, MerR-family

E: Transcriptional regulator, MerR-family

F: Transcriptional regulator, MerR-family

G: Transcriptional regulator, MerR-family

H: Transcriptional regulator, MerR-family

hetero molecules

121 kDa, 8 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

A: Transcriptional regulator, MerR-family

B: Transcriptional regulator, MerR-family

hetero molecules

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

2

C: Transcriptional regulator, MerR-family

D: Transcriptional regulator, MerR-family

hetero molecules

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

3

E: Transcriptional regulator, MerR-family

F: Transcriptional regulator, MerR-family

hetero molecules

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

4

G: Transcriptional regulator, MerR-family

H: Transcriptional regulator, MerR-family

hetero molecules

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

Unit cell

Length a, b, c (Å)	62.938, 67.903, 89.723
Angle α, β, γ (deg.)	109.33, 89.82, 90.32
Int Tables number	1
Space group name H-M	P1

Noncrystallographic symmetry (NCS)

NCS domain:
NCS domain segments:

Component-ID: _ / Beg auth comp-ID: MET / Beg label comp-ID: MET / End auth comp-ID: ALA / End label comp-ID: ALA / Refine code: _ / Auth seq-ID: 1 - 129 / Label seq-ID: 1 - 129

NCS ensembles :

#1: Protein	Transcriptional regulator, MerR-family Mass: 14958.383 Da / Num. of mol.: 8 / Fragment: UNP residues 1-129 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Cupriavidus metallidurans CH34 (bacteria) Strain: CH34 / Gene: pbrR2, Rmet_2302 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21DE3 / References: UniProt: Q1LKZ5
#2: Chemical	ChemComp-PB / LEAD (II) ION Mass: 207.200 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: Pb
#3: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 465 / 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: 3.12 Å³/Da / Density % sol: 60.56 %
Crystal grow	Temperature: 289 K / Method: vapor diffusion, sitting drop / pH: 7.5 / Details: Tacsimate, HEPES, PEG3350

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Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 1 Å
Detector	Type: ADSC QUANTUM 315r / Detector: CCD / Date: Dec 1, 2014
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 1 Å / Relative weight: 1
Reflection	Resolution: 2→30 Å / Num. obs: 88839 / % possible obs: 95.9 % / Redundancy: 3.2 % / R_sym value: 0.11 / Net I/σ(I): 23.5
Reflection shell	Resolution: 2→2.07 Å / Redundancy: 3 % / R_merge(I) obs: 0.42 / Mean I/σ(I) obs: 5.3 / % possible all: 94.2

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Processing

Software

Name	Version	Classification
REFMAC	5.8.0131	refinement
HKL-2000		data reduction
HKL-2000		data scaling
PHASER		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: 5D07

5d07
PDB Unreleased entry

Resolution: 2.01→30 Å / Cor.coef. F_o:F_c: 0.944 / Cor.coef. F_o:F_c free: 0.923 / SU B: 7.923 / SU ML: 0.097 / Cross valid method: THROUGHOUT / ESU R: 0.419 / ESU R Free: 0.142 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.21356	4470	5 %	RANDOM
R_work	0.17661	-	-	-
obs	0.17847	84363	94.87 %	-

Solvent computation

Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å

Displacement parameters

B_iso mean: 28.445 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	-1.3 Å²	-0.47 Å²	-0.31 Å²
2-	-	-2.29 Å²	0.48 Å²
3-	-	-	2.61 Å²

Refinement step

Cycle: 1 / Resolution: 2.01→30 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	8159	0	8	465	8632

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.01	0.019	8228
X-RAY DIFFRACTION	r_bond_other_d	0.007	0.02	8318
X-RAY DIFFRACTION	r_angle_refined_deg	1.361	2.002	10995
X-RAY DIFFRACTION	r_angle_other_deg	1.581	3	19005
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	4.421	5	995
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	32.762	21.986	423
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	15.213	15	1680
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	15.879	15	142
X-RAY DIFFRACTION	r_chiral_restr	0.063	0.2	1238
X-RAY DIFFRACTION	r_gen_planes_refined	0.006	0.02	9137
X-RAY DIFFRACTION	r_gen_planes_other	0.005	0.02	1905
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	2.093	1.903	4022
X-RAY DIFFRACTION	r_mcbond_other	2.094	1.902	4021
X-RAY DIFFRACTION	r_mcangle_it	2.716	2.831	5000
X-RAY DIFFRACTION	r_mcangle_other	2.715	2.832	5001
X-RAY DIFFRACTION	r_scbond_it	2.889	2.444	4206
X-RAY DIFFRACTION	r_scbond_other	2.881	2.444	4206
X-RAY DIFFRACTION	r_scangle_it
X-RAY DIFFRACTION	r_scangle_other	3.494	3.49	5994
X-RAY DIFFRACTION	r_long_range_B_refined	4.015	15.29	9468
X-RAY DIFFRACTION	r_long_range_B_other	3.846	15.006	9259
X-RAY DIFFRACTION	r_rigid_bond_restr	4.482	3	16546
X-RAY DIFFRACTION	r_sphericity_free	27.899	5	142
X-RAY DIFFRACTION	r_sphericity_bonded	9.731	5	16813

Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Weight position: 0.05

Ens-ID	Dom-ID	Auth asym-ID	Number	Rms dev position (Å)
1	1	A	13928	0.11
1	2	B	13928	0.11
2	1	A	14120	0.1
2	2	C	14120	0.1
3	1	A	14308	0.07
3	2	D	14308	0.07
4	1	A	14430	0.06
4	2	E	14430	0.06
5	1	A	13884	0.11
5	2	F	13884	0.11
6	1	A	14414	0.07
6	2	G	14414	0.07
7	1	A	13940	0.11
7	2	H	13940	0.11
8	1	B	14462	0.1
8	2	C	14462	0.1
9	1	B	14428	0.1
9	2	D	14428	0.1
10	1	B	13766	0.11
10	2	E	13766	0.11
11	1	B	14692	0.09
11	2	F	14692	0.09
12	1	B	14218	0.11
12	2	G	14218	0.11
13	1	B	14724	0.08
13	2	H	14724	0.08
14	1	C	14514	0.11
14	2	D	14514	0.11
15	1	C	14054	0.1
15	2	E	14054	0.1
16	1	C	14798	0.08
16	2	F	14798	0.08
17	1	C	14764	0.1
17	2	G	14764	0.1
18	1	C	14880	0.09
18	2	H	14880	0.09
19	1	D	14320	0.07
19	2	E	14320	0.07
20	1	D	14622	0.09
20	2	F	14622	0.09
21	1	D	15064	0.06
21	2	G	15064	0.06
22	1	D	14832	0.09
22	2	H	14832	0.09
23	1	E	13904	0.1
23	2	F	13904	0.1
24	1	E	14422	0.07
24	2	G	14422	0.07
25	1	E	13950	0.1
25	2	H	13950	0.1
26	1	F	14482	0.1
26	2	G	14482	0.1
27	1	F	15042	0.06
27	2	H	15042	0.06
28	1	G	14514	0.11
28	2	H	14514	0.11

LS refinement shell

Resolution: 2.008→2.06 Å / Total num. of bins used: 20

	R_factor	Num. reflection	% reflection
R_free	0.259	282	-
R_work	0.216	5239	-
obs	-	-	79.83 %

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	0.1033	-0.1087	0.0531	0.1973	-0.15	0.2219	-0.0121	-0.0261	0.0004	0.0049	0.0008	-0.0005	0.0181	0.0004	0.0113	0.0874	0.0051	0.0064	0.1053	0.0003	0.0017	51.9494	12.8563	64.3366
2	0.0202	0.0081	-0.0404	0.0681	-0.0371	0.0891	-0.0059	-0.0019	-0.001	-0.0059	0.0075	0.0087	0.003	-0.008	-0.0016	0.0863	0.0011	-0.0006	0.1078	0.0033	0.0086	46.859	18.9385	45.6329
3	0.0603	0.0467	-0.0696	0.262	0.0589	0.146	-0.0063	-0.0053	-0.0136	0.0156	-0.0009	-0.0265	-0.0046	0.0256	0.0072	0.0777	-0.0001	0.0037	0.1086	-0.0024	0.0089	25.0833	-15.2081	47.2246
4	0.1166	0.0756	0.033	0.1401	0.1269	0.2419	-0.0171	0.0253	-0.0051	-0.0037	-0.0001	0.0077	0.0207	0.0074	0.0172	0.0872	-0.0006	0.0071	0.1086	0.0014	0.0022	20.0609	-21.8144	27.3577
5	0.0802	0.0684	-0.0324	0.1158	-0.1113	0.1807	-0.0122	0.0206	-0.002	-0.0055	-0.001	-0.0027	-0.0095	-0.0036	0.0133	0.0899	-0.0046	0.0021	0.1094	0.0008	0.0033	20.7937	-12.7204	28.2821
6	0.0226	-0.0163	0.0425	0.0723	-0.0594	0.0948	-0.008	0.0007	0.0018	0.006	0.0067	0.0079	-0.0081	-0.0085	0.0013	0.0843	-0.0011	0.01	0.1054	0.0033	0.0088	15.3428	-18.5526	47.0057
7	0.1131	-0.0861	0.0011	0.1199	0.0769	0.1467	-0.0232	-0.0298	0.0072	0.0045	0.0003	0.0076	-0.0203	-0.0017	0.0229	0.0853	0.0034	0.0025	0.1103	-0.0014	0.0049	51.3412	22.0942	65.0788
8	0.0139	0.0015	0.0272	0.1039	0.0366	0.0688	-0.0077	-0.0017	0.0032	-0.0088	0.0044	-0.0152	0.0024	0.0026	0.0033	0.0824	0.0019	0.0092	0.1073	-0.0028	0.008	56.3809	15.4836	45.2133

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Auth asym-ID	Auth seq-ID
1	X-RAY DIFFRACTION	1	A	1 - 129
2	X-RAY DIFFRACTION	2	B	1 - 129
3	X-RAY DIFFRACTION	3	C	1 - 129
4	X-RAY DIFFRACTION	4	D	1 - 129
5	X-RAY DIFFRACTION	5	E	1 - 129
6	X-RAY DIFFRACTION	6	F	1 - 129
7	X-RAY DIFFRACTION	7	G	1 - 129
8	X-RAY DIFFRACTION	8	H	1 - 129

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