PDB-3lay: Alpha-Helical barrel formed by the decamer of the zinc resistance...

ID or keywords:

Entry

Database: PDB / ID: 3lay

Title

Alpha-Helical barrel formed by the decamer of the zinc resistance-associated protein (STM4172) from Salmonella enterica subsp. enterica serovar Typhimurium str. LT2

Components

Zinc resistance-associated protein

Keywords

METAL BINDING PROTEIN / Zinc resistance-associated protein / Salmonella typhimurium LT2 / zraP / Structural Genomics / Center for Structural Genomics of Infectious Diseases / CSGID

Function / homology

Heavy-metal resistance protein / Heavy-metal resistance / Four Helix Bundle (Hemerythrin (Met), subunit A) - #1490 / Four Helix Bundle (Hemerythrin (Met), subunit A) / periplasmic space / Up-down Bundle / zinc ion binding / Mainly Alpha / Signaling pathway modulator ZraP

Function and homology information

Biological species

Salmonella enterica subsp. enterica serovar Typhimurium (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON / MOLECULAR REPLACMENT / Resolution: 2.7 Å

Authors

Filippova, E.V. / Minasov, G. / Shuvalova, L. / Winsor, J. / Dubrovska, I. / Anderson, W.F. / Center for Structural Genomics of Infectious Diseases (CSGID)

Citation

Journal: To be Published
Title: Alpha-Helical barrel formed by the decamer of the zinc resistance-associated protein (STM4172) from Salmonella enterica subsp. enterica serovar Typhimurium str. LT2
Authors: Filippova, E.V. / Minasov, G. / Shuvalova, L. / Winsor, J. / Dubrovska, I. / Papazisi, L. / Anderson, W.F.

History

Deposition	Jan 7, 2010	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Jan 19, 2010	Provider: repository / Type: Initial release
Revision 1.1	Jul 13, 2011	Group: Advisory / Version format compliance
Revision 1.2	Nov 1, 2017	Group: Refinement description / Category: software / Item: _software.name
Revision 1.3	Feb 21, 2024	Group: Data collection / Database references Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ref_seq_dif Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	3lay.cif.gz	172.1 KB	Display	PDBx/mmCIF format
PDB format	pdb3lay.ent.gz	132.3 KB	Display	PDB format
PDBx/mmJSON format	3lay.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	3lay_validation.pdf.gz	517.3 KB	Display	wwPDB validaton report
Full document	3lay_full_validation.pdf.gz	525.1 KB	Display
Data in XML	3lay_validation.xml.gz	26.8 KB	Display
Data in CIF	3lay_validation.cif.gz	38.9 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/la/3lay ftp://data.pdbj.org/pub/pdb/validation_reports/la/3lay	HTTPS FTP

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Related structure data

Similar structure data	6tjm-1 3wx6-1 2v9u-d 4jt3-3 3txs-1 Search similar-shape structures by Omokage search (details) Similarity search - Function & homologyF&H Search Similarity search - FunctionF&H Search Similarity search - HomologyF&H Search
Other databases	TargetDB: IDP01826

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Links

PDB pages	PDBj / wwPDB / NCBI

Deposited unit

A: Zinc resistance-associated protein

B: Zinc resistance-associated protein

C: Zinc resistance-associated protein

D: Zinc resistance-associated protein

E: Zinc resistance-associated protein

F: Zinc resistance-associated protein

G: Zinc resistance-associated protein

H: Zinc resistance-associated protein

I: Zinc resistance-associated protein

J: Zinc resistance-associated protein

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

1

Idetical with deposited unit
defined by author

Unit cell

Length a, b, c (Å)	100.795, 148.910, 74.536
Angle α, β, γ (deg.)	90.00, 90.00, 90.00
Int Tables number	18
Space group name H-M	P2₁2₁2

#1: Protein	Zinc resistance-associated protein Mass: 18892.006 Da / Num. of mol.: 10 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Salmonella enterica subsp. enterica serovar Typhimurium (bacteria) Strain: LT2 / Gene: STM4172, STMF1.61, zraP / Plasmid: pMCSG7 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)-Magic / References: UniProt: Q9L9I0
#2: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 64 / Source method: isolated from a natural source / Formula: H₂O

#1: Protein

Zinc resistance-associated protein

Mass: 18892.006 Da / Num. of mol.: 10
Source method: isolated from a genetically manipulated source
Source: (gene. exp.)

Salmonella enterica subsp. enterica serovar Typhimurium (bacteria)
Strain: LT2 / Gene: STM4172, STMF1.61, zraP / Plasmid: pMCSG7 / Production host:

Escherichia coli (E. coli) / Strain (production host): BL21(DE3)-Magic / References: UniProt: Q9L9I0

#2: Water

ChemComp-HOH / water

Mass: 18.015 Da / Num. of mol.: 64 / 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 grow	Temperature: 295 K / Method: vapor diffusion, sitting drop / pH: 6.5 Details: 0.2 M Sodium chloride, 0.1 M Bis-tris, 25 % (w/v) PEG 3350, 0.2 mM Zn acetate, pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 295K

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Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: SYNCHROTRON / Site: APS / Beamline: 21-ID-G / Wavelength: 0.97872 Å
Detector	Type: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Nov 25, 2009 / Details: beryllium lenses
Radiation	Monochromator: diamond / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.97872 Å / Relative weight: 1
Reflection	Resolution: 2.7→83.33 Å / Num. all: 31571 / Num. obs: 31571 / % possible obs: 99.9 % / Observed criterion σ(I): -3 / Redundancy: 7.3 % / B_iso Wilson estimate: 65.8 Å² / R_merge(I) obs: 0.07 / Net I/σ(I): 40.9
Reflection shell	Resolution: 2.7→2.75 Å / Redundancy: 6.4 % / R_merge(I) obs: 0.48 / Mean I/σ(I) obs: 3.9 / % possible all: 100

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Processing

Software

Name	Version	Classification
Blu-Ice	Max	data collection
MLPHARE		phasing
DM		model building
SHELXD		phasing
RESOLVE		model building
CCP4		model building
ARP/wARP		model building
Coot		model building
REFMAC	5.5.0051	refinement
HKL-2000		data reduction
HKL-3000		data scaling
DM		phasing
RESOLVE		phasing
CCP4		phasing

Refinement

Method to determine structure: MOLECULAR REPLACMENT / Resolution: 2.7→30 Å / Cor.coef. F_o:F_c: 0.94 / Cor.coef. F_o:F_c free: 0.92 / SU B: 25.215 / SU ML: 0.252 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.631 / ESU R Free: 0.33 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.2672	1586	5 %	RANDOM
R_work	0.22263	-	-	-
obs	0.22486	29891	99.71 %	-
all	-	31571	-	-

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: 29.7 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	-0.49 Å²	0 Å²	0 Å²
2-	-	1.63 Å²	0 Å²
3-	-	-	-1.14 Å²

Refine analyze

Luzzati coordinate error obs: 0.45 Å

Refinement step

Cycle: LAST / Resolution: 2.7→30 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	5936	0	0	64	6000

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.018	0.022	6009
X-RAY DIFFRACTION	r_bond_other_d	0.001	0.02	3885
X-RAY DIFFRACTION	r_angle_refined_deg	1.622	1.969	8141
X-RAY DIFFRACTION	r_angle_other_deg	0.92	3	9573
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	2.602	5	781
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	32.365	25.795	264
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	15.526	15	1041
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	18.532	15	32
X-RAY DIFFRACTION	r_chiral_restr	0.09	0.2	964
X-RAY DIFFRACTION	r_gen_planes_refined	0.006	0.02	6761
X-RAY DIFFRACTION	r_gen_planes_other	0.001	0.02	1079
X-RAY DIFFRACTION	r_mcbond_it	1.417	1.5	3936
X-RAY DIFFRACTION	r_mcbond_other	0.259	1.5	1572
X-RAY DIFFRACTION	r_mcangle_it	2.657	2	6274
X-RAY DIFFRACTION	r_scbond_it	3.564	3	2073
X-RAY DIFFRACTION	r_scangle_it	5.908	4.5	1867

LS refinement shell

Resolution: 2.7→2.77 Å / Total num. of bins used: 20

	R_factor	Num. reflection	% reflection
R_free	0.395	106	-
R_work	0.333	2210	-
obs	-	2210	99.83 %

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	11.1503	-1.7856	-4.1831	2.3365	-0.161	1.9121	0.5659	0.0177	0.1258	-0.033	-0.4334	0.2113	-0.2056	0.2122	-0.1324	0.2287	0.1691	-0.089	0.4683	-0.1289	0.4044	30.579	139.092	97.801
2	21.6324	-7.604	-8.8745	4.7216	2.9514	4.0376	0.5356	-0.0298	0.7523	-0.0308	-0.1756	0.0186	-0.3572	0.2663	-0.3599	0.1325	-0.0527	-0.0191	0.1908	-0.0707	0.2321	27.801	145.938	91.702
3	4.8506	3.7778	0.6623	8.0385	-1.255	2.0989	0.3033	0.3122	0.5899	0.8451	-0.6703	-0.5829	-0.2234	0.8802	0.3671	0.2675	-0.1826	-0.1044	0.4432	0.1133	0.5338	16.742	119.907	119.229
4	2.8719	4.566	0.5686	9.4179	-1.2844	3.5498	0.5201	-0.2323	0.3849	1.0127	-0.69	0.1402	-0.3061	0.2967	0.17	0.306	-0.0988	0.0176	0.1958	-0.0781	0.4435	10.741	126.47	119.823
5	4.4133	0.8438	-2.3657	0.5246	-0.0636	3.6297	0.1316	0.0136	0.5064	-0.1714	-0.0478	0.2931	0.0252	-0.7491	-0.0838	0.1895	-0.0475	-0.0879	0.2751	-0.0532	0.617	16.552	139.091	79.092
6	19.8749	-0.5195	-7.2471	0.5496	-0.3961	4.2786	0.0897	-0.1315	0.0017	-0.2054	0.0148	0.2044	-0.2606	-0.15	-0.1044	0.2864	0.0769	-0.0932	0.0352	-0.0211	0.3146	21.534	145.501	83.504
7	9.7415	7.8803	0.8255	6.5197	1.0696	1.2887	0.2478	0.339	0.4177	0.236	0.2717	0.2311	0.078	0.113	-0.5194	0.1199	-0.0262	-0.1241	0.0385	-0.0336	0.7537	2.622	129.631	104.376
8	10.1029	10.7935	1.7376	13.382	1.9218	1.7083	0.5237	-0.0675	0.7758	0.997	-0.0341	0.878	-0.1501	0.0429	-0.4896	0.2011	-0.0061	0.1137	0.0246	-0.0466	0.4728	3.397	129.957	113.908
9	0.6641	-1.2911	0.9536	2.6855	-2.9621	9.4442	-0.0981	0.1639	0.1695	0.0863	-0.2585	-0.2837	-0.0543	-0.2188	0.3566	0.1589	-0.0546	-0.1452	0.1099	0.1717	0.4802	12.927	87.797	80.387
10	1.5999	-2.3622	2.923	7.4857	-9.0072	15.682	-0.2507	0.1014	0.0569	-0.2427	-0.0929	-0.4907	0.5241	-0.1945	0.3437	0.1606	-0.0502	-0.0154	0.0325	0.0465	0.2734	20.592	82.692	78.434
11	0.6985	0.1141	1.2621	4.9456	-5.1422	9.7695	0.1991	-0.3938	-0.1044	0.0248	-0.3872	-0.5808	0.0755	0.2484	0.1882	0.1638	-0.1895	-0.1054	0.4602	0.0419	0.4537	35.645	90.981	82.878
12	1.1184	-1.0951	2.8962	3.1394	-6.418	29.9597	-0.2768	-0.1671	-0.0002	-0.2996	-0.1917	-0.5152	0.681	-0.458	0.4685	0.2923	0.0807	0.0422	0.1625	0.0963	0.3797	30.271	84.079	79.34
13	2.4304	0.2949	-1.518	3.6466	3.4735	4.6963	-0.0606	-0.806	0.8646	0.3528	0.3593	0.1807	0.4633	0.9374	-0.2986	0.3008	-0.0095	-0.1731	0.3609	-0.1512	0.8793	19.824	88.893	108.42
14	2.9418	5.1494	5.0139	9.9789	10.3367	11.8652	0.012	-0.2498	0.2664	0.5286	-0.1973	0.158	0.7775	0.1386	0.1853	0.3064	0.068	-0.1696	0.1776	-0.033	0.2993	11.969	87.872	112.842
15	0.994	1.5786	2.0187	2.9909	4.2949	8.4827	0.095	-0.0692	0.2703	0.1549	-0.2385	0.2022	0.1232	-0.1305	0.1436	0.229	0.0092	-0.1061	0.0901	0.0278	0.3527	0.45	99.139	105.037
16	1.2994	2.3361	3.2971	5.6776	9.2446	17.0427	0.0623	-0.1813	0.0496	0.3522	-0.2136	0.1895	0.4975	-0.0321	0.1513	0.1589	-0.0439	-0.0676	0.0657	0.0086	0.2013	3.146	91.939	110.544
17	4.6412	-5.1183	2.308	9.5762	-1.5944	2.3603	0.0498	-0.7056	0.3546	0.3002	0.153	-0.6419	0.312	-0.1814	-0.2029	0.3793	-0.0433	-0.0937	0.3569	0.0092	0.4613	40.909	121.246	75.94
18	7.092	-8.8081	4.1363	15.5269	-6.1877	3.0439	0.241	0.2136	0.0437	-0.4809	-0.231	-0.3596	-0.0263	0.255	-0.0101	0.1622	-0.0868	-0.0027	0.0656	0.0007	0.22	39.22	118.813	66.969
19	4.6548	-3.8297	0.225	7.0432	-2.1069	1.0257	0.0366	-0.4748	0.0345	-0.2901	0.2883	0.2437	0.1563	-0.0715	-0.325	0.2624	-0.0562	-0.0803	0.2869	0.0225	0.5537	22.735	112.104	65.239
20	9.3644	-9.8622	-0.095	13.7264	-0.9728	0.936	0.0473	0.4366	0.1088	-0.3277	-0.2178	-0.2277	0.0824	0.0633	0.1706	0.0942	-0.054	-0.0261	0.1	0.0096	0.1949	31.163	115.607	62.064

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Auth asym-ID	Auth seq-ID
1	X-RAY DIFFRACTION	1	C	46 - 83
2	X-RAY DIFFRACTION	2	C	86 - 120
3	X-RAY DIFFRACTION	3	A	46 - 83
4	X-RAY DIFFRACTION	4	A	86 - 120
5	X-RAY DIFFRACTION	5	D	46 - 83
6	X-RAY DIFFRACTION	6	D	86 - 120
7	X-RAY DIFFRACTION	7	B	46 - 83
8	X-RAY DIFFRACTION	8	B	86 - 120
9	X-RAY DIFFRACTION	9	H	46 - 83
10	X-RAY DIFFRACTION	10	H	86 - 120
11	X-RAY DIFFRACTION	11	G	46 - 83
12	X-RAY DIFFRACTION	12	G	86 - 120
13	X-RAY DIFFRACTION	13	I	46 - 83
14	X-RAY DIFFRACTION	14	I	86 - 120
15	X-RAY DIFFRACTION	15	J	46 - 83
16	X-RAY DIFFRACTION	16	J	86 - 120
17	X-RAY DIFFRACTION	17	E	46 - 83
18	X-RAY DIFFRACTION	18	E	86 - 120
19	X-RAY DIFFRACTION	19	F	46 - 83
20	X-RAY DIFFRACTION	20	F	86 - 120

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