PDB-3qsi: Nickel binding domain of NikR from Helicobacter pylori disclosing...

ID or keywords:

Entry

Database: PDB / ID: 3qsi

Title

Nickel binding domain of NikR from Helicobacter pylori disclosing partial metal occupancy

Components

NikR nickel-responsive regulator

Keywords

METAL BINDING PROTEIN / NIKR / nickel / Helicobacter pylori / DNA-binding / transcription regulator

Function / homology

Function and homology information

response to nickel cation / DNA-binding transcription repressor activity / nickel cation binding / protein-DNA complex / sequence-specific DNA binding / transcription cis-regulatory region binding / negative regulation of DNA-templated transcription / regulation of DNA-templated transcription / DNA binding / identical protein binding
Similarity search - Function

Biological species

Helicobacter pylori (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT /

molecular replacement / Resolution: 3.08 Å

Authors

Gonzalez, J.M. / Pozharski, E.

Citation

Journal: Proc.Natl.Acad.Sci.USA / Year: 2012
Title: Ni(II) coordination to mixed sites modulates DNA binding of HpNikR via a long-range effect.
Authors: West, A.L. / Evans, S.E. / Gonzalez, J.M. / Carter, L.G. / Tsuruta, H. / Pozharski, E. / Michel, S.L.

History

Deposition	Feb 21, 2011	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Apr 4, 2012	Provider: repository / Type: Initial release
Revision 1.1	Jun 13, 2012	Group: Database references
Revision 1.2	Nov 8, 2017	Group: Refinement description / Category: software Item: _software.classification / _software.contact_author ..._software.classification / _software.contact_author / _software.contact_author_email / _software.date / _software.language / _software.location / _software.name / _software.type / _software.version
Revision 1.3	Feb 21, 2024	Group: Data collection / Database references / Derived calculations Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_conn_angle / struct_conn / struct_site Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

Structure viewer	Molecule: MolmilJmol/JSmol

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PDBx/mmCIF format	3qsi.cif.gz	313.3 KB	Display	PDBx/mmCIF format
PDB format	pdb3qsi.ent.gz	259.7 KB	Display	PDB format
PDBx/mmJSON format	3qsi.json.gz		Tree view	PDBx/mmJSON format
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Validation report

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

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Related structure data

Related structure data	3phtC C: citing same article (ref.)
Similar structure data	5dxy-d 2hs8-1 4m24-d 2hs8-2 2ich-1 4mhu-1 2hs6-1 4f8z-d 4d4b-2 3amd-4 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

3phtC

C: citing same article (ref.)

Similar structure data

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Links

PDB pages	PDBj / wwPDB / NCBI
Related items in Molecule of the Month	#263 - Nov 2021 Acetohydroxyacid Synthase similarity (1)

Deposited unit

B: NikR nickel-responsive regulator

C: NikR nickel-responsive regulator

D: NikR nickel-responsive regulator

A: NikR nickel-responsive regulator

F: NikR nickel-responsive regulator

G: NikR nickel-responsive regulator

H: NikR nickel-responsive regulator

E: NikR nickel-responsive regulator

J: NikR nickel-responsive regulator

I: NikR nickel-responsive regulator

hetero molecules

102 kDa, 10 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

B: NikR nickel-responsive regulator

C: NikR nickel-responsive regulator

D: NikR nickel-responsive regulator

A: NikR nickel-responsive regulator

hetero molecules

defined by author&software
40.9 kDa, 4 polymers
Search similar-shape structures of this assembly by Omokage search (details)

2

F: NikR nickel-responsive regulator

G: NikR nickel-responsive regulator

H: NikR nickel-responsive regulator

E: NikR nickel-responsive regulator

hetero molecules

defined by author&software
41 kDa, 4 polymers
Search similar-shape structures of this assembly by Omokage search (details)

3

J: NikR nickel-responsive regulator

I: NikR nickel-responsive regulator

hetero molecules

J: NikR nickel-responsive regulator

I: NikR nickel-responsive regulator

hetero molecules

defined by author&software
40.6 kDa, 4 polymers
Search similar-shape structures of this assembly by Omokage search (details)

Unit cell

Length a, b, c (Å)	147.379, 79.400, 122.423
Angle α, β, γ (deg.)	90.00, 122.28, 90.00
Int Tables number	5
Space group name H-M	C121

Noncrystallographic symmetry (NCS)

NCS domain:

ID	Ens-ID	Details
1	1	A
2	1	C
3	1	E
1	2	B
2	2	D
3	2	H
4	2	F
1	3	A
2	3	I
3	3	G
1	4	B
2	4	J

NCS domain segments:

Dom-ID	Component-ID	Ens-ID	Refine code	Auth asym-ID	Auth seq-ID
1	1	1	1	A	62 - 142
2	1	1	1	C	62 - 142
3	1	1	1	E	62 - 142
1	1	2	1	B	64 - 144
2	1	2	1	D	64 - 144
3	1	2	1	H	64 - 144
4	1	2	1	F	64 - 144
1	1	3	1	A	62 - 142
2	1	3	1	I	62 - 142
3	1	3	1	G	62 - 142
1	1	4	1	B	64 - 142
2	1	4	1	J	64 - 142

NCS ensembles :

ID
1
2
3
4

#1: Protein	NikR nickel-responsive regulator Mass: 10128.504 Da / Num. of mol.: 10 / Fragment: Nickel binding domain (UNP residues 61-148) Source method: isolated from a genetically manipulated source Source: (gene. exp.) Helicobacter pylori (bacteria) / Gene: HP_1338 / Plasmid: pET15b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: O25896
#2: Chemical	ChemComp-NI / NICKEL (II) ION Mass: 58.693 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: Ni
#3: Chemical	ChemComp-SO4 / SULFATE ION Mass: 96.063 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: SO₄

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Experiment

Experiment	Method: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

Crystal	Density Matthews: 2.99 Å³/Da / Density % sol: 58.86 %
Crystal grow	Temperature: 293 K / Method: vapor diffusion / pH: 7.5 Details: 0.1 M HEPES sodium salt pH 7.5, 2 %(v/v) PEG 400, 2.0 M Ammonium sulfate, vapor diffusion, temperature 293K

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Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: SYNCHROTRON / Site: SSRL / Beamline: BL7-1 / Wavelength: 1 Å
Detector	Type: ADSC QUANTUM 315 / Detector: CCD / Date: Feb 27, 2010
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 1 Å / Relative weight: 1
Reflection	Resolution: 3.08→103.5 Å / Num. obs: 21352

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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
REFMAC		refinement
PDB_EXTRACT	3.1	data extraction

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT / Resolution: 3.08→103.5 Å / Cor.coef. F_o:F_c: 0.895 / Cor.coef. F_o:F_c free: 0.84 / Occupancy max: 1 / Occupancy min: 0.5 / SU B: 57.211 / SU ML: 0.467 / Cross valid method: THROUGHOUT / ESU R Free: 0.556 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.30361	2165	10.1 %	RANDOM
R_work	0.25726	-	-	-
obs	0.26195	19187	95.53 %	-

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: 48.803 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	-5.88 Å²	0 Å²	-0.44 Å²
2-	-	4.74 Å²	0 Å²
3-	-	-	0.67 Å²

Refinement step

Cycle: LAST / Resolution: 3.08→103.5 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	6104	0	34	0	6138

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.017	0.021	6236
X-RAY DIFFRACTION	r_bond_other_d	0.009	0.02	3954
X-RAY DIFFRACTION	r_angle_refined_deg	1.669	1.935	8389
X-RAY DIFFRACTION	r_angle_other_deg	1.269	3.001	9718
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	7.311	5	785
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	40.43	24.416	274
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	19.697	15	1102
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	21.375	15	31
X-RAY DIFFRACTION	r_chiral_restr	0.167	0.2	1024
X-RAY DIFFRACTION	r_gen_planes_refined	0.005	0.02	6841
X-RAY DIFFRACTION	r_gen_planes_other	0.003	0.02	1188
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	0.991	1.5	3915
X-RAY DIFFRACTION	r_mcbond_other	0.123	1.5	1630
X-RAY DIFFRACTION	r_mcangle_it	1.842	2	6273
X-RAY DIFFRACTION	r_scbond_it	1.834	3	2321
X-RAY DIFFRACTION	r_scangle_it	2.73	4.5	2116
X-RAY DIFFRACTION	r_rigid_bond_restr
X-RAY DIFFRACTION	r_sphericity_free
X-RAY DIFFRACTION	r_sphericity_bonded

Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION

Ens-ID	Dom-ID	Auth asym-ID	Number	Type	Rms dev position (Å)	Weight position
1	1	A	952	tight positional	0.06	0.05
1	2	C	952	tight positional	0.07	0.05
1	3	E	952	tight positional	0.06	0.05
2	1	B	895	tight positional	0.09	0.05
2	2	D	895	tight positional	0.06	0.05
2	3	H	895	tight positional	0.07	0.05
2	4	F	895	tight positional	0.07	0.05
3	1	A	891	tight positional	0.08	0.05
3	2	I	891	tight positional	0.06	0.05
3	3	G	891	tight positional	0.08	0.05
4	1	B	927	tight positional	0.08	0.05
1	1	A	952	tight thermal	0.1	0.5
1	2	C	952	tight thermal	0.09	0.5
1	3	E	952	tight thermal	0.09	0.5
2	1	B	895	tight thermal	0.08	0.5
2	2	D	895	tight thermal	0.08	0.5
2	3	H	895	tight thermal	0.08	0.5
2	4	F	895	tight thermal	0.08	0.5
3	1	A	891	tight thermal	0.1	0.5
3	2	I	891	tight thermal	0.1	0.5
3	3	G	891	tight thermal	0.11	0.5
4	1	B	927	tight thermal	0.09	0.5

LS refinement shell

Resolution: 3.079→3.159 Å / Total num. of bins used: 20

	R_factor	Num. reflection	% reflection
R_free	0.438	126	-
R_work	0.371	1325	-
obs	-	-	89.73 %

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	2.4052	-0.9207	-0.0389	1.767	-2.2576	3.6574	0.1437	-0.0689	0.2309	0.0191	-0.1574	-0.0716	-0.1229	0.2993	0.0137	0.1238	0.0071	-0.0024	0.1009	-0.0691	0.2439	54.7281	21.8077	45.3365
2	0.9942	0.7415	1.1994	0.9625	0.841	1.6804	-0.0593	-0.0779	0.1195	0.1559	-0.0734	-0.1009	-0.1029	-0.1446	0.1327	0.1212	-0.003	-0.0518	0.1936	-0.0508	0.1961	34.6098	17.5812	40.1913
3	2.695	1.5442	3.323	0.9537	2.3819	7.4808	-0.085	-0.5439	0.0823	-0.0727	-0.3656	0.1102	-0.2666	-0.8045	0.4505	0.1129	0.081	-0.0897	0.1768	-0.1313	0.2342	22.5198	-9.5604	-1.4815
4	1.4419	-0.004	2.0006	1.0846	-0.8474	3.4409	-0.1722	-0.0236	0.0334	0.2695	0.0128	-0.1037	-0.4703	-0.09	0.1594	0.211	0.1199	-0.1174	0.1702	-0.1396	0.1225	22.546	-14.2617	-20.7218
5	0.3307	0.4811	0.0669	2.4025	-0.7358	0.4265	-0.0728	-0.0602	0.1623	0.0397	-0.0784	0.0324	-0.1023	0.0235	0.1512	0.1231	-0.0902	-0.0275	0.2849	-0.0049	0.1431	0.8325	-14.5238	38.8681
6	4.4433	-0.1307	-1.7339	0.8124	-0.4319	0.9683	-0.222	-0.0275	-0.0484	-0.227	0.1194	-0.1528	0.2282	-0.0394	0.1025	0.168	-0.1124	-0.0497	0.2206	0.0073	0.1599	7.8359	-17.5972	21.0582
7	2.9373	0.9104	-0.6268	1.4597	-0.7518	0.3979	0.0051	-0.2026	0.1154	-0.1192	0.0845	0.1605	0.0552	-0.0372	-0.0896	0.1154	-0.0588	-0.026	0.3174	-0.1039	0.0718	23.6106	-4.0398	23.7536
8	1.0421	0.9024	-0.1276	4.0886	0.4615	0.1182	-0.0338	-0.2884	-0.0556	0.0098	0.0002	0.1907	0.0216	0.0885	0.0336	0.0764	-0.0615	-0.0274	0.4297	0.0185	0.056	20.8631	-8.8337	42.3097
9	0.1022	0.3296	-0.035	1.1973	0.0127	0.8805	-0.0723	-0.0547	-0.0073	-0.0834	-0.0907	-0.0023	-0.0678	0.237	0.163	0.1942	0.0546	0.0191	0.1655	-0.0148	0.1366	35.7355	-30.7386	-16.8925
10	2.7217	-1.8233	-0.3637	2.779	0.4057	0.0797	-0.1757	-0.0256	0.0883	0.4096	0.1175	0.2265	0.1053	0.0262	0.0582	0.3004	0.0281	0.066	0.085	0.0583	0.1229	27.4533	-30.1997	0.4864

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Auth asym-ID	Auth seq-ID
1	X-RAY DIFFRACTION	1	I	64 - 80
2	X-RAY DIFFRACTION	1	I	81 - 124
3	X-RAY DIFFRACTION	1	I	125 - 142
4	X-RAY DIFFRACTION	2	J	64 - 77
5	X-RAY DIFFRACTION	2	J	78 - 107
6	X-RAY DIFFRACTION	2	J	108 - 142
7	X-RAY DIFFRACTION	3	G	64 - 85
8	X-RAY DIFFRACTION	3	G	86 - 117
9	X-RAY DIFFRACTION	3	G	118 - 142
10	X-RAY DIFFRACTION	3	G	1
11	X-RAY DIFFRACTION	4	H	64 - 82
12	X-RAY DIFFRACTION	4	H	83 - 107
13	X-RAY DIFFRACTION	4	H	108 - 142
14	X-RAY DIFFRACTION	5	A	62 - 85
15	X-RAY DIFFRACTION	5	A	86 - 124
16	X-RAY DIFFRACTION	5	A	125 - 141
17	X-RAY DIFFRACTION	6	B	64 - 82
18	X-RAY DIFFRACTION	6	B	83 - 107
19	X-RAY DIFFRACTION	6	B	108 - 144
20	X-RAY DIFFRACTION	7	C	63 - 85
21	X-RAY DIFFRACTION	7	C	86 - 124
22	X-RAY DIFFRACTION	7	C	125 - 142
23	X-RAY DIFFRACTION	8	D	64 - 83
24	X-RAY DIFFRACTION	8	D	84 - 107
25	X-RAY DIFFRACTION	8	D	108 - 142
26	X-RAY DIFFRACTION	9	E	63 - 85
27	X-RAY DIFFRACTION	9	E	86 - 127
28	X-RAY DIFFRACTION	9	E	128 - 142
29	X-RAY DIFFRACTION	10	F	64 - 83
30	X-RAY DIFFRACTION	10	F	84 - 107
31	X-RAY DIFFRACTION	10	F	108 - 141

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