PDB-4oer: Crystal structure of NikA from Brucella suis, unliganded form

ID or keywords:

Entry

Database: PDB / ID: 4oer

Title

Crystal structure of NikA from Brucella suis, unliganded form

Components

NikA protein

Keywords

TRANSPORT PROTEIN / Extracytoplasmic / Nickel import / Metal transport / ABC-type importer / extracytoplasmic nickel-binding protein

Function / homology

Function and homology information

nickel cation transport / nickel cation binding / ATP-binding cassette (ABC) transporter complex / transmembrane transport / outer membrane-bounded periplasmic space /

heme binding
Similarity search - Function

Biological species

Brucella suis (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 1.85 Å

Authors

Lebrette, H. / Cavazza, C.

Citation

Journal: Structure / Year: 2014
Title: Promiscuous nickel import in human pathogens: structure, thermodynamics, and evolution of extracytoplasmic nickel-binding proteins.
Authors: Lebrette, H. / Brochier-Armanet, C. / Zambelli, B. / de Reuse, H. / Borezee-Durant, E. / Ciurli, S. / Cavazza, C.

History

Deposition	Jan 13, 2014	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Oct 1, 2014	Provider: repository / Type: Initial release
Revision 1.1	Nov 19, 2014	Group: Database references
Revision 1.2	Sep 20, 2023	Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_site Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

Structure viewer	Molecule: MolmilJmol/JSmol

-
Download

PDBx/mmCIF format	4oer.cif.gz	421.1 KB	Display	PDBx/mmCIF format
PDB format	pdb4oer.ent.gz	345.3 KB	Display	PDB format
PDBx/mmJSON format	4oer.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

-
Validation report

Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/oe/4oer ftp://data.pdbj.org/pub/pdb/validation_reports/oe/4oer	HTTPS FTP

-
Related structure data

Related structure data	4oesC 4oetC 4oeuC 4oevC 4oflC 4ofoC 1zlqS C: citing same article (ref.) S: Starting model for refinement
Similar structure data	3fto-d 1uiu-1 6oyt-1 1vfg-1 2shp-2 3o2w-d 3t66-d 3drk-d 4ohl-2 5ibs-1 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

-
Links

PDB pages	PDBj / wwPDB / NCBI

Deposited unit

A: NikA protein

B: NikA protein

hetero molecules

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

1

A: NikA protein

hetero molecules

defined by author&software
56.5 kDa, 1 polymers
Search similar-shape structures of this assembly by Omokage search (details)

2

B: NikA protein

hetero molecules

defined by author&software
56.2 kDa, 1 polymers
Search similar-shape structures of this assembly by Omokage search (details)

Unit cell

Length a, b, c (Å)	176.020, 62.231, 114.483
Angle α, β, γ (deg.)	90.00, 105.30, 90.00
Int Tables number	5
Space group name H-M	C121

#1: Protein	NikA protein Mass: 55540.676 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Brucella suis (bacteria) / Gene: nikA / Production host: Escherichia coli (E. coli) / References: UniProt: Q9AL82
#2: Chemical	ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol Mass: 92.094 Da / Num. of mol.: 13 / Source method: obtained synthetically / Formula: C₃H₈O₃
#3: Chemical	ChemComp-SO4 / SULFATE ION / Sulfate Mass: 96.063 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: SO₄
#4: Water	ChemComp-HOH / water / Water Mass: 18.015 Da / Num. of mol.: 752 / Source method: isolated from a natural source / Formula: H₂O

-
Experiment

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

-
Sample preparation

Crystal	Density Matthews: 2.72 Å³/Da / Density % sol: 54.82 %
Crystal grow	Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8.5 Details: 1.7 M ammonium sulfate, 0.1 M Tris pH 8.5, 25 mM MgSO4, VAPOR DIFFUSION, HANGING DROP, temperature 293K

-
Data collection

Diffraction source	Source: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 0.97627 Å
Detector	Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Feb 27, 2012
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.97627 Å / Relative weight: 1
Reflection	Resolution: 1.85→43.67 Å / Num. all: 102353 / Num. obs: 99676 / % possible obs: 97.4 % / Observed criterion σ(I): -3 / Redundancy: 3.4 % / R_sym value: 0.043 / Net I/σ(I): 15.87
Reflection shell	Resolution: 1.85→1.95 Å / Redundancy: 3.2 % / Mean I/σ(I) obs: 3.29 / Num. unique all: 14894 / R_sym value: 0.452 / % possible all: 93.1

-
Processing

Software

Name	Version	Classification
PHASER		phasing
PHENIX	(phenix.refine: 1.8.2_1309)	refinement
XDS		data reduction
XSCALE		data scaling

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1ZLQ

1zlq

Resolution: 1.85→43.666 Å / SU ML: 0.2 / σ(F): 1.99 / Phase error: 26.91 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.2217	4969	5 %	Random
R_work	0.1849	-	-	-
obs	0.1867	99449	97.23 %	-

Solvent computation

Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL

Refinement step

Cycle: LAST / Resolution: 1.85→43.666 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	7808	0	98	752	8658

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.007	8194
X-RAY DIFFRACTION	f_angle_d	1.106	11153
X-RAY DIFFRACTION	f_dihedral_angle_d	13.082	3037
X-RAY DIFFRACTION	f_chiral_restr	0.047	1213
X-RAY DIFFRACTION	f_plane_restr	0.006	1460

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 (%)
1.8501-1.8712	0.3637	134	0.3146	2567	X-RAY DIFFRACTION	79
1.8712-1.8932	0.3254	165	0.2787	3136	X-RAY DIFFRACTION	97
1.8932-1.9163	0.3172	163	0.262	3122	X-RAY DIFFRACTION	97
1.9163-1.9405	0.3081	166	0.2558	3163	X-RAY DIFFRACTION	98
1.9405-1.966	0.263	161	0.2384	3086	X-RAY DIFFRACTION	97
1.966-1.993	0.2716	167	0.2316	3155	X-RAY DIFFRACTION	97
1.993-2.0214	0.253	164	0.2305	3111	X-RAY DIFFRACTION	98
2.0214-2.0516	0.2786	166	0.2314	3143	X-RAY DIFFRACTION	98
2.0516-2.0837	0.28	167	0.2263	3169	X-RAY DIFFRACTION	98
2.0837-2.1178	0.2714	166	0.2152	3145	X-RAY DIFFRACTION	98
2.1178-2.1544	0.2794	166	0.2114	3147	X-RAY DIFFRACTION	98
2.1544-2.1935	0.2794	167	0.2052	3164	X-RAY DIFFRACTION	98
2.1935-2.2357	0.2484	166	0.2072	3166	X-RAY DIFFRACTION	98
2.2357-2.2814	0.2589	167	0.2068	3165	X-RAY DIFFRACTION	98
2.2814-2.331	0.2276	167	0.1944	3176	X-RAY DIFFRACTION	98
2.331-2.3852	0.2587	167	0.1919	3148	X-RAY DIFFRACTION	98
2.3852-2.4448	0.2602	166	0.1977	3166	X-RAY DIFFRACTION	98
2.4448-2.5109	0.2579	169	0.1987	3191	X-RAY DIFFRACTION	98
2.5109-2.5848	0.2467	166	0.1914	3155	X-RAY DIFFRACTION	98
2.5848-2.6682	0.2315	169	0.1912	3204	X-RAY DIFFRACTION	98
2.6682-2.7636	0.222	164	0.1898	3125	X-RAY DIFFRACTION	98
2.7636-2.8742	0.2135	168	0.1836	3190	X-RAY DIFFRACTION	98
2.8742-3.005	0.2031	169	0.1832	3189	X-RAY DIFFRACTION	98
3.005-3.1634	0.2102	168	0.1825	3201	X-RAY DIFFRACTION	99
3.1634-3.3615	0.2201	168	0.1753	3194	X-RAY DIFFRACTION	98
3.3615-3.6209	0.2318	169	0.1642	3203	X-RAY DIFFRACTION	98
3.6209-3.9851	0.1704	169	0.1523	3212	X-RAY DIFFRACTION	98
3.9851-4.5612	0.1875	168	0.1375	3187	X-RAY DIFFRACTION	98
4.5612-5.7446	0.171	169	0.1576	3258	X-RAY DIFFRACTION	99
5.7446-43.678	0.1828	168	0.1832	3242	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	2.2937	-0.7269	-0.9027	1.2392	-0.0004	1.7575	-0.037	-0.3007	0.0694	0.097	0.0207	-0.1431	-0.0432	0.166	0.0287	0.1825	0.0036	-0.0263	0.0641	0.0057	0.1814	33.727	-12.5781	49.4487
2	2.6109	0.3059	0.4497	1.8923	-0.0968	1.7141	0.2096	0.7764	0.3935	-0.3897	-0.3264	-0.1749	-0.0031	0.0424	0.0768	0.2609	0.0905	0.054	0.2452	0.0872	0.2122	32.5443	-10.4262	26.6504
3	0.5763	-0.773	-1.0739	1.0909	1.6691	5.9294	0.3553	0.846	0.0458	-0.3447	-0.313	0.0066	-0.097	-0.2109	-0.0391	0.27	0.0441	-0.0262	0.5878	-0.0028	0.2383	12.6695	-9.4697	26.8113
4	2.189	-0.3366	0.7282	0.9143	0.389	2.6836	-0.0021	-0.1686	0.1572	0.0011	-0.0589	0.0631	-0.1443	-0.3972	0.0147	0.1192	-0.0187	0.0034	0.2237	-0.0134	0.1518	-0.3575	-1.7751	44.5074
5	2.4529	-0.5872	-0.5218	0.6237	-0.0424	2.2386	0.0989	0.16	-0.1712	-0.0795	-0.0553	0.0262	0.2349	-0.1949	0.0253	0.1857	-0.0492	-0.0377	0.1054	-0.0011	0.16	13.7089	-15.2511	40.3645
6	3.3487	-0.8502	-0.328	1.3512	-0.0215	1.8359	-0.1388	-1.269	0.2388	0.1221	0.2042	-0.1774	-0.1562	0.1371	-0.0387	0.2301	0.009	-0.0548	0.6038	-0.0739	0.1973	48.7769	-13.8667	-5.6061
7	3.7686	-0.1498	0.8425	2.4865	-1.0901	1.9398	0.1118	0.1224	0.3907	-0.1934	-0.1314	-0.08	-0.1812	0.0401	0.0537	0.2762	-0.0023	0.0422	0.1421	-0.0005	0.1958	47.984	-10.0743	-28.1803
8	5.9261	-2.1079	-4.4988	1.3583	1.1763	3.9668	0.2295	0.1544	0.3124	-0.2613	-0.0345	0.019	-0.0812	-0.1828	-0.1666	0.2536	-0.0674	-0.0504	0.269	-0.0079	0.2213	28.0511	-9.244	-28.3639
9	3.6251	-0.2413	-0.104	0.6279	-0.1524	2.2329	0.0334	-0.3981	-0.0593	0.0251	-0.0037	0.034	0.0534	-0.1477	-0.0278	0.1569	-0.0381	-0.0414	0.3209	0.0098	0.1682	14.4248	-9.04	-14.5296
10	3.6606	-0.4571	-1.6539	3.6694	0.68	3.9987	0.3556	-0.6011	0.5904	-0.0952	-0.1131	0.1876	-0.6087	-0.5935	-0.2393	0.2834	0.0325	0.0154	0.5972	-0.1335	0.3139	1.9852	3.0711	-14.4121
11	2.4793	-1.2266	-0.4001	0.7782	0.6984	1.941	-0.1415	-1.0973	0.7481	0.0262	0.3143	-0.352	-0.257	0.2796	0.1251	0.2164	-0.0617	-0.0329	0.6439	-0.1916	0.2707	20.1917	-0.728	-6.7939
12	1.9771	-0.637	0.1346	0.5125	-0.0549	0.7382	-0.0302	-0.5619	-0.1962	-0.0521	0.0826	0.0983	0.1322	-0.0174	0.0537	0.2106	-0.0334	-0.0225	0.2908	0.044	0.1784	28.9962	-15.5841	-15.4076

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	chain 'A' and (resid 1 through 162 )
2	X-RAY DIFFRACTION	2	chain 'A' and (resid 163 through 223 )
3	X-RAY DIFFRACTION	3	chain 'A' and (resid 224 through 251 )
4	X-RAY DIFFRACTION	4	chain 'A' and (resid 252 through 441 )
5	X-RAY DIFFRACTION	5	chain 'A' and (resid 442 through 498 )
6	X-RAY DIFFRACTION	6	chain 'B' and (resid 1 through 162 )
7	X-RAY DIFFRACTION	7	chain 'B' and (resid 163 through 223 )
8	X-RAY DIFFRACTION	8	chain 'B' and (resid 224 through 251 )
9	X-RAY DIFFRACTION	9	chain 'B' and (resid 252 through 309 )
10	X-RAY DIFFRACTION	10	chain 'B' and (resid 310 through 348 )
11	X-RAY DIFFRACTION	11	chain 'B' and (resid 349 through 441 )
12	X-RAY DIFFRACTION	12	chain 'B' and (resid 442 through 498 )

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

Version 3 of the EMDB header file is now the official format.
The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

+
Jul 12, 2017. Major update of PDB

-
Yorodumi

Thousand views of thousand structures

Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

-
Movie

-
Structure viewers

+
Viewer log

-
This page

-
This web site

-
Options

+
Open data

-
Basic information

-
Structure visualization

-
Downloads & links

-
Download

-
Validation report

-
Related structure data

-
Links

-
Assembly

-
Components

-
Experimental details

-
Experiment

-
Sample preparation

-
Data collection

-
Processing

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

-
Aug 12, 2020. Covid-19 info

+
Mar 5, 2020. Novel coronavirus structure data

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

+
Jul 12, 2017. Major update of PDB

-
Yorodumi

-Movie

-Structure viewers

+Viewer log

-This page

-This web site

-Options

+Open data

-Basic information

-Structure visualization

-Downloads & links

-Download

-Validation report

-Related structure data

-Links

-Assembly

-Components

-Experimental details

-Experiment

-Sample preparation

-Data collection

-Processing

+About Yorodumi

-News

-Feb 9, 2022. New format data for meta-information of EMDB entries

-Aug 12, 2020. Covid-19 info

+Mar 5, 2020. Novel coronavirus structure data

+Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

+Jul 12, 2017. Major update of PDB

-Yorodumi

-
Movie

-
Structure viewers

+
Viewer log

-
This page

-
This web site

-
Options

+
Open data

-
Basic information

-
Structure visualization

-
Downloads & links

-
Download

-
Validation report

-
Related structure data

-
Links

-
Assembly

-
Components

-
Experimental details

-
Experiment

-
Sample preparation

-
Data collection

-
Processing

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

-
Aug 12, 2020. Covid-19 info

+
Mar 5, 2020. Novel coronavirus structure data

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

+
Jul 12, 2017. Major update of PDB

-
Yorodumi