PDB-4dcx: X-ray structure of NikA in complex with Fe(1R,2R)-N,N'-Bis(2-pyri...

ID or keywords:

Entry

Database: PDB / ID: 4dcx

Title

X-ray structure of NikA in complex with Fe(1R,2R)-N,N'-Bis(2-pyridylmethyl)-N,N'-dicarboxymethyl-1,2-cyclohexanediamine

Components

Nickel-binding periplasmic protein

Keywords

METAL TRANSPORT /

TRANSPORT PROTEIN / Protein-bound iron complex

Function / homology

Function and homology information

nickel cation import across plasma membrane /

metal cluster binding / peptide transport / peptide transmembrane transporter activity / negative chemotaxis / nickel cation binding / transition metal ion binding / ATP-binding cassette (ABC) transporter complex, substrate-binding subunit-containing / outer membrane-bounded periplasmic space /

periplasmic space ...
Similarity search - Function

Biological species

Escherichia coli (E. coli)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 2 Å

Authors

Cherrier, M.V. / Girgenti, E. / Amara, P. / Iannello, M. / Marchi-Delapierre, C. / Fontecilla-Camps, J.C. / Menage, S. / Cavazza, C.

Citation

Journal: J.Biol.Inorg.Chem. / Year: 2012
Title: The structure of the periplasmic nickel-binding protein NikA provides insights for artificial metalloenzyme design.
Authors: Cherrier, M.V. / Girgenti, E. / Amara, P. / Iannello, M. / Marchi-Delapierre, C. / Fontecilla-Camps, J.C. / Menage, S. / Cavazza, C.

History

Deposition	Jan 18, 2012	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	May 9, 2012	Provider: repository / Type: Initial release
Revision 1.1	Jun 13, 2012	Group: Database references
Revision 1.2	Sep 13, 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

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PDBx/mmCIF format	4dcx.cif.gz	436.9 KB	Display	PDBx/mmCIF format
PDB format	pdb4dcx.ent.gz	357.3 KB	Display	PDB format
PDBx/mmJSON format	4dcx.json.gz		Tree view	PDBx/mmJSON format
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Validation report

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

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Related structure data

Related structure data	4dcyC 1zlqS S: Starting model for refinement C: citing same article (ref.)
Similar structure data	3mvy-1 4dcy-1 3qim-1 3mvx-1 1uiv-1 4oes-d 1uiu-2 4ofl-1 4i9d-1 3mvw-1 4i8c-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

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Links

PDB pages	PDBj / wwPDB / NCBI

Deposited unit

A: Nickel-binding periplasmic protein

B: Nickel-binding periplasmic protein

hetero molecules

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

1

A: Nickel-binding periplasmic protein

hetero molecules

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

2

B: Nickel-binding periplasmic protein

hetero molecules

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

Unit cell

Length a, b, c (Å)	86.350, 95.640, 125.190
Angle α, β, γ (deg.)	90.00, 90.00, 90.00
Int Tables number	19
Space group name H-M	P2₁2₁2₁

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Protein , 1 types, 2 molecules AB

#1: Protein	Nickel-binding periplasmic protein Mass: 56360.734 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli (E. coli) / Strain: K12 / Gene: b3476, JW3441, nikA / Plasmid: pET28b / Production host: Escherichia coli (E. coli) / Strain (production host): Bl21(de3) / References: UniProt: P33590

#1: Protein

Nickel-binding periplasmic protein

Mass: 56360.734 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.)

Escherichia coli (E. coli) / Strain: K12 / Gene: b3476, JW3441, nikA / Plasmid: pET28b / Production host:

Escherichia coli (E. coli) / Strain (production host): Bl21(de3) / References: UniProt: P33590

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Non-polymers , 5 types, 908 molecules

#2: Chemical	ChemComp-SO4 / SULFATE ION / Sulfate Mass: 96.063 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: SO₄
#3: Chemical	... ChemComp-ACT / ACETATE ION / Acetate Mass: 59.044 Da / Num. of mol.: 27 / Source method: obtained synthetically / Formula: C₂H₃O₂
#4: Chemical	ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol Mass: 92.094 Da / Num. of mol.: 18 / Source method: obtained synthetically / Formula: C₃H₈O₃
#5: Chemical	ChemComp-L2D / {2,2'-[(1R,2R)-cyclohexane-1,2-diylbis{[(pyridin-2-yl-kappaN)methyl]imino-kappaN}]diacetato-kappaO(2-)}iron / Fe(1R,2R)-N,N'-Bis(2-pyridylmethyl)-N,N'-dicarboxymethyl-1,2-cyclohexanediamine Mass: 466.311 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C₂₂H₂₆FeN₄O₄
#6: Water	ChemComp-HOH / water / Water Mass: 18.015 Da / Num. of mol.: 858 / 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: 2.29 Å³/Da / Density % sol: 46.36 %
Crystal grow	Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 4.7 Details: 1.8M ammonium sulfate, 0.1M sodium acetate, pH 4.7, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: SYNCHROTRON / Site: ESRF / Beamline: BM30A / Wavelength: 0.9796 Å
Detector	Type: ADSC QUANTUM 315r / Detector: CCD / Date: Jul 18, 2010 / Details: mirrors
Radiation	Monochromator: double crystal monochromator Si (111), Si(311) Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.9796 Å / Relative weight: 1
Reflection	Resolution: 2→50 Å / Num. all: 70658 / Num. obs: 70381 / % possible obs: 99.6 % / Observed criterion σ(I): 2 / Redundancy: 7 % / B_iso Wilson estimate: 34.6 Å² / R_sym value: 0.067 / Net I/σ(I): 17.4
Reflection shell	Resolution: 2→2.1 Å / Redundancy: 7 % / Mean I/σ(I) obs: 6.4 / Num. unique all: 9346 / R_sym value: 0.303 / % possible all: 98.7

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Processing

Software

Name	Version	Classification
PHASER		phasing
PHENIX	(phenix.refine: 1.7_650)	refinement
XDS		data reduction
XSCALE		data scaling

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1ZLQ

1zlq

Resolution: 2→47.82 Å / SU ML: 0.24 / σ(F): 1.99 / Phase error: 20.54 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.2032	3518	5 %	RANDOM
R_work	0.1549	-	-	-
obs	0.1574	70379	99.62 %	-
all	-	70381	-	-

Solvent computation

Shrinkage radii: 0.95 Å / VDW probe radii: 1.2 Å / Solvent model: FLAT BULK SOLVENT MODEL / B_sol: 49.58 Å² / k_sol: 0.364 e/Å³

Displacement parameters

	B_aniso -1	B_aniso -2	B_aniso -3
1-	3.7995 Å²	-0 Å²	0 Å²
2-	-	-5.2032 Å²	-0 Å²
3-	-	-	1.4037 Å²

Refinement step

Cycle: LAST / Resolution: 2→47.82 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	7892	0	293	858	9043

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.007	8526
X-RAY DIFFRACTION	f_angle_d	1.086	11594
X-RAY DIFFRACTION	f_dihedral_angle_d	13.297	3200
X-RAY DIFFRACTION	f_chiral_restr	0.07	1250
X-RAY DIFFRACTION	f_plane_restr	0.006	1519

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 (%)
2-2.0274	0.3015	131	0.209	2507	X-RAY DIFFRACTION	96
2.0274-2.0564	0.2612	140	0.1907	2658	X-RAY DIFFRACTION	100
2.0564-2.0871	0.2301	140	0.1856	2653	X-RAY DIFFRACTION	100
2.0871-2.1197	0.2618	140	0.1778	2660	X-RAY DIFFRACTION	100
2.1197-2.1544	0.2397	139	0.1754	2646	X-RAY DIFFRACTION	100
2.1544-2.1916	0.2098	139	0.1784	2645	X-RAY DIFFRACTION	100
2.1916-2.2314	0.2403	140	0.1744	2650	X-RAY DIFFRACTION	100
2.2314-2.2744	0.2621	141	0.1792	2678	X-RAY DIFFRACTION	100
2.2744-2.3208	0.2386	139	0.1767	2644	X-RAY DIFFRACTION	100
2.3208-2.3712	0.2441	139	0.1664	2647	X-RAY DIFFRACTION	100
2.3712-2.4264	0.2487	140	0.1686	2663	X-RAY DIFFRACTION	100
2.4264-2.4871	0.2353	141	0.1752	2672	X-RAY DIFFRACTION	100
2.4871-2.5543	0.2615	140	0.1765	2665	X-RAY DIFFRACTION	100
2.5543-2.6295	0.2328	142	0.1746	2683	X-RAY DIFFRACTION	100
2.6295-2.7143	0.2035	140	0.1662	2659	X-RAY DIFFRACTION	100
2.7143-2.8113	0.2223	141	0.1692	2693	X-RAY DIFFRACTION	100
2.8113-2.9239	0.2474	141	0.1753	2669	X-RAY DIFFRACTION	100
2.9239-3.0569	0.2449	141	0.1649	2685	X-RAY DIFFRACTION	100
3.0569-3.2181	0.2172	142	0.1685	2705	X-RAY DIFFRACTION	100
3.2181-3.4196	0.2079	142	0.1554	2680	X-RAY DIFFRACTION	100
3.4196-3.6836	0.1697	142	0.1378	2715	X-RAY DIFFRACTION	100
3.6836-4.0541	0.1615	143	0.1206	2705	X-RAY DIFFRACTION	100
4.0541-4.6403	0.1538	144	0.115	2733	X-RAY DIFFRACTION	100
4.6403-5.8447	0.1568	146	0.1291	2772	X-RAY DIFFRACTION	100
5.8447-47.8337	0.1762	145	0.1634	2774	X-RAY DIFFRACTION	96

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	0.7219	1.0874	0.0161	2.191	0.0394	0.9561	-0.0149	-0.1231	0.0392	-0.505	-0.1782	0.2936	0.1746	-0.0937	-0.0055	0.0702	0.0767	0.0064	0.0778	-0.0666	0.1399	-13.9312	-11.2212	-41.2823
2	0.3584	0.3231	0.2026	1.8853	0.2517	0.4691	-0.0124	0.1774	-0.0164	-0.5802	0.1004	0.1773	-0.0766	0.0428	-0.0308	0.3156	0.018	-0.0367	0.2022	-0.035	0.2408	-9.2969	9.4804	-51.1173
3	0.1909	0.0078	0.0821	0.2844	-0.062	0.3862	0.0018	-0.0036	-0	0.0809	0.0141	-0.0022	-0.1879	0.0583	-0.011	0.1914	-0.0142	0.0302	0.129	-0.028	0.1157	-1.5624	12.3896	-24.0229
4	0.2572	0.0024	0.3776	0.412	0.0612	0.8039	-0.0844	-0.0333	0.0776	0.0165	0.0773	-0.1947	-0.1387	0.2899	-0.0174	0.2216	-0.031	-0.049	0.2773	-0.0135	0.183	18.1208	9.8645	-8.0657
5	0.5524	-0.0424	0.2394	0.6492	-0.0849	0.2496	0.0407	0.0831	-0.1276	-0.0362	-0.0014	-0.0149	0.013	0.0584	-0.0054	0.1746	0.0071	0.0355	0.1474	-0.0352	0.1331	2.6357	-0.8039	-21.4076
6	0.5995	-0.7354	0.1879	2.2942	-0.5407	1.1382	0.1156	0.1643	-0.2095	0.0233	0.0647	0.3652	-0.0573	-0.0474	-0.1043	0.1778	0.0136	-0.0073	0.1898	-0.0439	0.2344	-15.2565	12.0848	-40.9693
7	1.6713	0.4143	-0.0418	0.7222	-0.0634	0.9665	-0.1604	0.4653	-0.2652	-0.0844	0.278	0.36	0.226	-0.5658	0.0086	0.0749	-0.0642	-0.0677	0.434	0.0103	0.3276	-43.4409	10.7895	-29.579
8	0.4616	-0.102	-0.0644	0.1954	-0.0953	1.0247	0.0921	-0.0925	-0.0029	0.2021	-0.0179	0.1005	-0.0556	0.0498	-0.02	0.2101	0.0255	0.0814	0.1464	0.0032	0.1603	-24.1101	15.1298	-11.0225
9	0.3729	0.1959	-0.1344	0.5068	0.0381	1.6786	0.1543	-0.1322	-0.1873	0.0592	0.005	-0.1317	-0.1817	0.2973	-0.0587	0.1856	-0.0147	0.024	0.2333	-0.0248	0.1723	-13.8503	23.1715	-19.493
10	0.5961	-0.2869	-0.1641	0.3417	-0.2707	1.0282	0.2252	-0.1369	0.0968	0.1417	0.0471	0.133	-0.437	0.1477	-0.0579	0.3563	-0.0821	0.1505	0.2397	-0.058	0.2681	-19.6934	37.9903	-6.656
11	0.3172	-0.1219	-0.0945	0.2483	0.1513	0.713	0.0882	0.0916	0.0705	-0.0787	0.0366	0.1303	-0.396	-0.2717	-0.0386	0.2677	0.0819	0.0583	0.2287	0.0327	0.1995	-26.4806	31.0869	-27.7352
12	0.9821	-0.0397	0.1744	0.0396	-0.2564	1.7408	-0.0896	-0.0703	-0.2839	-0.0147	0.0329	0.4031	0.3368	-0.1275	0.0087	0.2233	-0.0025	0.0116	0.1483	0.0209	0.306	-27.2875	1.4844	-17.3414

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	(chain A and resid 3:170)
2	X-RAY DIFFRACTION	2	(chain A and resid 171:215)
3	X-RAY DIFFRACTION	3	(chain A and resid 216:308)
4	X-RAY DIFFRACTION	4	(chain A and resid 309:343)
5	X-RAY DIFFRACTION	5	(chain A and resid 344:471)
6	X-RAY DIFFRACTION	6	(chain A and resid 472:499)
7	X-RAY DIFFRACTION	7	(chain B and resid 4:186)
8	X-RAY DIFFRACTION	8	(chain B and resid 187:275)
9	X-RAY DIFFRACTION	9	(chain B and resid 276:309)
10	X-RAY DIFFRACTION	10	(chain B and resid 310:385)
11	X-RAY DIFFRACTION	11	(chain B and resid 386:471)
12	X-RAY DIFFRACTION	12	(chain B and resid 472:500)

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