PDB-4dcy: X-ray structure of NikA in complex with Fe(1S,2S)-N,N-kappa-Bis(2...

ID or keywords:

Entry

Database: PDB / ID: 4dcy

Title

X-ray structure of NikA in complex with Fe(1S,2S)-N,N-kappa-Bis(2-pyridylmethyl)-N-carboxymethyl-N-kappa-methyl-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	4dcy.cif.gz	439.2 KB	Display	PDBx/mmCIF format
PDB format	pdb4dcy.ent.gz	358.8 KB	Display	PDB format
PDBx/mmJSON format	4dcy.json.gz		Tree view	PDBx/mmJSON format
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Validation report

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

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Related structure data

Related structure data	4dcxC 1zlqS S: Starting model for refinement C: citing same article (ref.)
Similar structure data	4dcx-2 4dcx-1 4i8c-1 3qim-1 3mvw-1 5on9-1 4i9d-1 4qfk-6 4qfk-7 3mvy-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
59 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
57.6 kDa, 1 polymers
Search similar-shape structures of this assembly by Omokage search (details)

Unit cell

Length a, b, c (Å)	86.880, 95.190, 125.150
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 , 6 types, 1017 molecules

#2: Chemical	ChemComp-ACT / ACETATE ION / Acetate Mass: 59.044 Da / Num. of mol.: 20 / Source method: obtained synthetically / Formula: C₂H₃O₂
#3: 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
#4: Chemical	ChemComp-L2M / {(R)-N-[(1S,2S)-2-{methyl[(pyridin-2-yl-kappaN)methyl]amino-kappaN}cyclohexyl]-N-[(pyridin-2-yl-kappaN)methyl]glycinato-kappa~2~N,O}iron(2+) Mass: 423.310 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C₂₁H₂₇FeN₄O₂
#5: Chemical	ChemComp-UNX / UNKNOWN ATOM OR ION Num. of mol.: 2 / Source method: obtained synthetically
#6: Chemical	ChemComp-SO4 / SULFATE ION / Sulfate Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO₄
#7: Water	ChemComp-HOH / water / Water Mass: 18.015 Da / Num. of mol.: 973 / 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: 2.3 Å³/Da / Density % sol: 46.42 %
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: ID23-1 / Wavelength: 1.2798 Å
Detector	Type: ADSC QUANTUM 315r / Detector: CCD / Date: May 2, 2010 / Details: mirrors
Radiation	Monochromator: Single crystal Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 1.2798 Å / Relative weight: 1
Reflection	Resolution: 2→50 Å / Num. all: 70762 / Num. obs: 70698 / % possible obs: 99.9 % / Observed criterion σ(I): 2 / Redundancy: 7.2 % / B_iso Wilson estimate: 31.1 Å² / R_sym value: 0.07 / Net I/σ(I): 19.3
Reflection shell	Resolution: 2→2.1 Å / Redundancy: 7.2 % / Mean I/σ(I) obs: 6.23 / Num. unique all: 9513 / R_sym value: 0.321 / % possible all: 100

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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→41.742 Å / SU ML: 0.24 / σ(F): 1.99 / Phase error: 18.35 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.1958	3535	5 %	RANDOM
R_work	0.1461	-	-	-
obs	0.1486	70693	99.92 %	-
all	-	70762	-	-

Solvent computation

Shrinkage radii: 0.95 Å / VDW probe radii: 1.2 Å / Solvent model: FLAT BULK SOLVENT MODEL / B_sol: 47.655 Å² / k_sol: 0.372 e/Å³

Displacement parameters

	B_aniso -1	B_aniso -2	B_aniso -3
1-	-0.6245 Å²	-0 Å²	0 Å²
2-	-	-1.9857 Å²	-0 Å²
3-	-	-	2.6101 Å²

Refinement step

Cycle: LAST / Resolution: 2→41.742 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	7906	0	256	973	9135

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.007	8600
X-RAY DIFFRACTION	f_angle_d	1.055	11705
X-RAY DIFFRACTION	f_dihedral_angle_d	13.265	3232
X-RAY DIFFRACTION	f_chiral_restr	0.07	1265
X-RAY DIFFRACTION	f_plane_restr	0.005	1532

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	0.2214	139	0.1711	2648	X-RAY DIFFRACTION	100
2.0274-2.0563	0.2534	140	0.1749	2659	X-RAY DIFFRACTION	100
2.0563-2.087	0.2606	141	0.166	2682	X-RAY DIFFRACTION	100
2.087-2.1197	0.2028	140	0.152	2653	X-RAY DIFFRACTION	100
2.1197-2.1544	0.2143	139	0.1502	2638	X-RAY DIFFRACTION	100
2.1544-2.1915	0.2472	139	0.1538	2645	X-RAY DIFFRACTION	100
2.1915-2.2314	0.2379	140	0.1729	2661	X-RAY DIFFRACTION	100
2.2314-2.2743	0.2711	141	0.1763	2679	X-RAY DIFFRACTION	100
2.2743-2.3207	0.2703	139	0.1743	2651	X-RAY DIFFRACTION	100
2.3207-2.3712	0.2053	139	0.1539	2636	X-RAY DIFFRACTION	100
2.3712-2.4263	0.204	142	0.1448	2688	X-RAY DIFFRACTION	100
2.4263-2.487	0.2258	140	0.1584	2662	X-RAY DIFFRACTION	100
2.487-2.5542	0.2167	140	0.1534	2662	X-RAY DIFFRACTION	100
2.5542-2.6294	0.2333	141	0.1542	2690	X-RAY DIFFRACTION	100
2.6294-2.7143	0.2149	142	0.1585	2684	X-RAY DIFFRACTION	100
2.7143-2.8112	0.2473	141	0.1596	2677	X-RAY DIFFRACTION	100
2.8112-2.9238	0.231	139	0.1629	2655	X-RAY DIFFRACTION	100
2.9238-3.0568	0.2023	142	0.1488	2698	X-RAY DIFFRACTION	100
3.0568-3.2179	0.1875	143	0.1474	2703	X-RAY DIFFRACTION	100
3.2179-3.4194	0.1796	141	0.1421	2685	X-RAY DIFFRACTION	100
3.4194-3.6833	0.1834	143	0.1329	2714	X-RAY DIFFRACTION	100
3.6833-4.0537	0.1484	142	0.1213	2707	X-RAY DIFFRACTION	100
4.0537-4.6396	0.13	144	0.1047	2739	X-RAY DIFFRACTION	100
4.6396-5.8429	0.1711	147	0.128	2779	X-RAY DIFFRACTION	100
5.8429-41.7509	0.1823	151	0.1691	2863	X-RAY DIFFRACTION	99

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	0.3542	0.3369	0.0251	0.7315	0.0388	0.3786	-0.0182	-0.0485	0.0429	-0.1828	-0.0412	0.1357	0.0532	-0.0454	0.0189	0.1294	0.0076	-0.0136	0.1081	-0.033	0.1468	-14.4757	-11.4597	-41.2891
2	0.2849	0.2405	0.2848	1.3334	0.4962	0.3405	-0.0308	0.0629	-0.0191	-0.3578	0.1094	0.0441	-0.1266	0.0099	-0.0138	0.2358	-0.0438	-0.0123	0.1567	-0.013	0.1518	-9.0486	9.2068	-50.9541
3	0.1229	-0.0299	-0.0526	0.1464	0.0246	0.0243	0.001	-0.0355	0.0187	0.0473	0.0047	-0.0081	-0.0829	0.037	-0.0081	0.1224	-0.0205	0.0128	0.0951	-0.013	0.0809	-1.5286	12.293	-23.9954
4	0.4412	0.1057	0.5322	0.1299	0.1664	0.8934	-0.0187	-0.0228	0.0231	0.0162	0.0483	-0.0779	-0.0414	0.2186	-0.0346	0.1457	-0.0112	-0.0387	0.2292	-0.0199	0.1203	18.5834	9.1915	-8.3851
5	0.5177	0.1394	-0.119	0.0956	-0.0874	0.3673	-0.0304	0.0119	-0.1598	-0.0175	0.0199	-0.0774	0.0483	0.051	0.0135	0.1399	-0.0023	0.0142	0.0995	-0.0261	0.1165	2.6229	-1.1196	-21.3526
6	0.1425	0.1253	0.0041	0.7859	0.0293	0.1132	0.0412	0.0432	-0.0587	-0.0201	0.0225	0.0176	0.034	-0.0047	-0.0389	0.1735	0.019	-0.0481	0.1592	-0.0351	0.202	-15.6933	12.0515	-41.0701
7	0.7052	0.144	0.128	0.3197	0.0083	0.3048	-0.1095	0.3356	-0.1721	-0.172	0.2047	0.2292	0.1112	-0.2622	-0.0281	0.0591	-0.2052	-0.1318	0.4486	0.0754	0.3225	-43.4699	10.5905	-29.5335
8	0.1251	-0.0292	-0.0451	0.1795	-0.0861	0.2702	0.0262	-0.0406	-0.0094	0.0952	-0.0154	0.0645	-0.0053	-0.0227	-0.0013	0.1854	-0.01	0.0433	0.1351	0.0231	0.1242	-24.0531	15.042	-10.9338
9	0.2244	0.1766	-0.0401	0.3499	-0.009	1.9366	0.0427	-0.1177	-0.0969	0.0194	-0.0701	-0.0824	-0.1522	0.0668	0.0255	0.1038	-0.0104	0.0074	0.1373	0.0094	0.1139	-13.522	22.5814	-17.1181
10	0.7193	0.2427	-0.5598	0.4291	-0.4035	0.7959	0.1372	-0.1509	0.0772	0.1452	0.0089	0.0307	-0.1841	0.0289	-0.0518	0.2341	-0.0709	0.0629	0.1843	-0.0119	0.1386	-19.9549	38.0205	-6.6612
11	0.4551	-0.267	-0.2041	0.5074	0.0864	0.2071	0.0933	0.137	0.0199	-0.1311	-0.023	0.0699	-0.1374	-0.1849	-0.0134	0.1493	0.0425	0.0257	0.1738	0.0281	0.1227	-26.4609	31.0117	-27.5722
12	0.1883	-0.4759	0.2576	1.3728	-0.8466	0.5819	-0.0065	-0.047	-0.1224	0.0334	0.0454	0.2866	0.0476	-0.0716	-0.063	0.1681	-0.0307	0.0138	0.1356	0.0148	0.2047	-27.2575	1.404	-17.3076

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 472:500)
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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