PDB-3g0m: Crystal structure of cysteine desulfuration protein SufE from Sal...

ID or keywords:

Entry

Database: PDB / ID: 3g0m

Title

Crystal structure of cysteine desulfuration protein SufE from Salmonella typhimurium LT2

Components

Cysteine desulfuration protein sufE

Keywords

HYDROLASE / cysteine desulfuration protein SufE / ynhA / CSGID / National Institute of Allergy and Infectious Diseases / NIAID / Structural Genomics / Center for Structural Genomics of Infectious Diseases

Function / homology

Function and homology information

sulfur compound metabolic process / iron-sulfur cluster assembly / cytoplasm
Similarity search - Function

Biological species

Salmonella typhimurium LT2 (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 1.76 Å

Authors

Nocek, B. / Maltseva, N. / Stam, J. / Anderson, W. / Joachimiak, A. / Center for Structural Genomics of Infectious Diseases (CSGID)

Citation

Journal: To be Published
Title: Crystal structure of cysteine desulfuration protein SufE from Salmonella typhimurium LT2
Authors: Nocek, B. / Maltseva, N. / Stam, J. / Anderson, W. / Joachimiak, A.

History

Deposition	Jan 28, 2009	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Feb 17, 2009	Provider: repository / Type: Initial release
Revision 1.1	Jul 13, 2011	Group: Advisory / Version format compliance
Revision 1.2	Sep 6, 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_conn / struct_ref_seq_dif / struct_site Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details / _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	3g0m.cif.gz	44.9 KB	Display	PDBx/mmCIF format
PDB format	pdb3g0m.ent.gz	31.3 KB	Display	PDB format
PDBx/mmJSON format	3g0m.json.gz		Tree view	PDBx/mmJSON format
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Validation report

Summary document	3g0m_validation.pdf.gz	450.2 KB	Display	wwPDB validaton report
Full document	3g0m_full_validation.pdf.gz	451.1 KB	Display
Data in XML	3g0m_validation.xml.gz	8.4 KB	Display
Data in CIF	3g0m_validation.cif.gz	10.8 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/g0/3g0m ftp://data.pdbj.org/pub/pdb/validation_reports/g0/3g0m	HTTPS FTP

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Related structure data

Related structure data	1mzgS S: Starting model for refinement
Similar structure data	5rso-1 7bf5-2 7bf4-d 5rsw-1 1ws1-d 5rvf-1 4bvm-d 5rsq-1 5s1o-1 6bsx-2 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: IDP00875

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Links

PDB pages	PDBj / wwPDB / NCBI
Related items in Molecule of the Month	#234 - Jun 2019 MDM2 and Cancer similarity (1) #252 - Dec 2020 Hepatitis C Virus Protease/Helicase similarity (1) #9 - Sep 2000 Lysozyme similarity (1)

Deposited unit

A: Cysteine desulfuration protein sufE

hetero molecules

16.3 kDa, 1 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

Idetical with deposited unit
defined by software

Unit cell

Length a, b, c (Å)	31.791, 42.617, 45.006
Angle α, β, γ (deg.)	90.00, 98.15, 90.00
Int Tables number	4
Space group name H-M	P12₁1

#1: Protein	Cysteine desulfuration protein sufE Mass: 16052.532 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Salmonella typhimurium LT2 (bacteria) / Strain: LT2 / SGSC1412 / Gene: gi:16764724, NP_460339, STM1374, sufE / Plasmid: pMCSG7 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q8ZPQ1
#2: Chemical	ChemComp-BME / BETA-MERCAPTOETHANOL Mass: 78.133 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C₂H₆OS
#3: Chemical	ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C₂H₆O₂
#4: Chemical	ChemComp-PEG / DI(HYDROXYETHYL)ETHER Mass: 106.120 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C₄H₁₀O₃
#5: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 62 / 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: 1.88 Å³/Da / Density % sol: 34.58 %
Crystal grow	Temperature: 292 K / Method: vapor diffusion, hanging drop / pH: 6.5 Details: 30% PEG 400, 0.1M Li2SO4, 0.1M Cacodylate, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 292K

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Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.9794 Å
Detector	Type: ADSC QUANTUM 315 / Detector: CCD / Date: Dec 3, 2008 / Details: mirrors
Radiation	Monochromator: double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.9794 Å / Relative weight: 1
Reflection	Resolution: 1.76→40 Å / Num. all: 11960 / Num. obs: 11678 / % possible obs: 97.6 % / Observed criterion σ(I): 2 / Redundancy: 3.5 % / R_merge(I) obs: 0.042 / Net I/σ(I): 31.6
Reflection shell	Resolution: 1.76→1.79 Å / Redundancy: 2.2 % / R_merge(I) obs: 0.293 / Mean I/σ(I) obs: 3.1 / Num. unique all: 465 / % possible all: 79.1

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Processing

Software

Name	Version	Classification
SBC-Collect		data collection
CCP4		model building
MOLREP		phasing
REFMAC	5.5.0054	refinement
HKL-3000		data reduction
HKL-3000		data scaling
CCP4		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: PDB entry 1MZG

1mzg

Resolution: 1.76→40 Å / Cor.coef. F_o:F_c: 0.963 / Cor.coef. F_o:F_c free: 0.941 / SU B: 6.347 / SU ML: 0.093 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 2 / ESU R: 0.144 / ESU R Free: 0.141 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.23972	558	4.8 %	RANDOM
R_work	0.18503	-	-	-
all	0.1878	11663	-	-
obs	0.18774	11105	97.65 %	-

Solvent computation

Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK

Displacement parameters

B_iso mean: 16.174 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	-2.9 Å²	0 Å²	0.1 Å²
2-	-	2.22 Å²	0 Å²
3-	-	-	0.71 Å²

Refinement step

Cycle: LAST / Resolution: 1.76→40 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	1101	0	15	62	1178

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.02	0.022	1143
X-RAY DIFFRACTION	r_bond_other_d	0.002	0.02	800
X-RAY DIFFRACTION	r_angle_refined_deg	1.638	1.95	1539
X-RAY DIFFRACTION	r_angle_other_deg	0.945	3	1937
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	4.714	5	139
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	36.966	23.455	55
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	13.872	15	205
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	16.864	15	11
X-RAY DIFFRACTION	r_chiral_restr	0.099	0.2	170
X-RAY DIFFRACTION	r_gen_planes_refined	0.007	0.02	1252
X-RAY DIFFRACTION	r_gen_planes_other	0.001	0.02	232
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	0.911	1.5	691
X-RAY DIFFRACTION	r_mcbond_other	0.306	1.5	277
X-RAY DIFFRACTION	r_mcangle_it	1.493	2	1110
X-RAY DIFFRACTION	r_scbond_it	2.685	3	452
X-RAY DIFFRACTION	r_scangle_it	4.286	4.5	428
X-RAY DIFFRACTION	r_rigid_bond_restr
X-RAY DIFFRACTION	r_sphericity_free
X-RAY DIFFRACTION	r_sphericity_bonded

LS refinement shell

Resolution: 1.76→1.81 Å / Total num. of bins used: 20

	R_factor	Num. reflection	% reflection
R_free	0.275	38	-
R_work	0.258	708	-
obs	-	-	84.68 %

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	8.1249	-3.8068	-1.1793	6.9875	7.8817	10.5028	-0.2986	-0.554	0.7836	-0.0669	0.4362	-0.3518	-0.2547	0.292	-0.1376	0.5029	-0.031	0.0553	0.2927	-0.0105	0.4627	26.2231	30.0077	31.5264
2	9.9364	-6.4586	2.119	7.6575	0.1004	2.973	0.1857	0.7551	0.1591	-0.3374	-0.0782	-0.192	-0.0242	0.3308	-0.1075	0.1722	-0.0138	0.0014	0.2032	0.0259	0.1555	29.6665	22.1061	23.5365
3	0.7785	-0.5654	2.3008	9.5827	-1.5313	6.8029	0.1103	0.0607	0.0142	-0.3295	-0.1429	0.0345	0.314	0.1642	0.0326	0.2046	-0.0004	0.0229	0.248	0.0101	0.2187	34.7784	11.8627	30.0326
4	6.3208	-2.1129	-1.0134	2.8497	2.8417	3.6268	-0.1456	0.0658	-0.0011	0.2831	-0.0126	0.0227	0.1073	0.208	0.1582	0.1722	-0.0376	0.0085	0.2299	0.0211	0.1974	31.1091	18.1216	36.2676
5	11.671	-4.5387	-2.0042	9.9569	0.2146	5.6069	0.1097	-0.145	0.5987	0.0361	-0.0592	-0.3117	-0.2438	0.0968	-0.0505	0.2279	-0.0287	-0.0309	0.2096	-0.0278	0.2275	26.5968	26.7835	41.9033
6	10.2438	7.2295	0.0162	9.2824	2.2387	5.8284	0.3108	-0.3525	0.0029	0.0239	-0.2432	0.2195	0.2427	-0.7564	-0.0676	0.2616	0.0203	-0.0047	0.3561	-0.0549	0.1926	14.1206	27.5228	49.3265
7	7.7795	0.0145	1.9896	7.5117	0.7887	8.211	0.0601	-0.9348	-0.4069	0.4575	-0.1765	0.2966	0.254	-0.1896	0.1164	0.2035	-0.0541	0.0207	0.2402	0.0615	0.0906	12.7656	17.5452	44.4913
8	2.8034	-2.3024	3.1225	18.0425	-8.3873	5.6189	-0.225	-0.3596	0.0501	0.3992	0.1784	0.0128	-0.4094	-0.4366	0.0466	0.295	0.0675	0.0254	0.2954	-0.048	0.2459	8.6207	33.4673	36.228
9	6.032	-6.7928	5.8126	9.5581	-9.329	9.8394	-0.2831	-0.1034	0.3406	0.6647	0.0164	-0.2831	-0.6782	-0.0877	0.2667	0.2387	-0.038	-0.0128	0.152	-0.0601	0.1809	14.046	30.8628	36.1472
10	4.1632	-1.6317	2.2418	2.3627	-1.3602	2.8647	-0.05	-0.1746	0.1065	0.0857	-0.0199	-0.1004	-0.035	0.0461	0.07	0.1508	-0.0227	0.0042	0.1388	0.0077	0.1534	20.8401	21.4769	35.6578
11	4.5077	-3.7317	-1.4553	9.879	2.717	5.0082	0.2135	0.3635	0.0806	-0.1913	-0.1819	0.2105	-0.0418	-0.1561	-0.0316	0.133	0.0014	-0.0041	0.1145	0.0176	0.1307	10.9184	23.6052	24.3439
12	8.9568	-1.6659	1.8359	8.0051	-0.7638	5.0714	-0.0314	-0.1466	-0.1969	-0.0374	0.1783	-0.1047	0.1149	0.2243	-0.1469	0.1623	0.0373	0.0116	0.153	-0.017	0.1591	22.6724	15.0242	23.935
13	11.1989	1.1858	-1.1183	6.1671	-1.2204	0.3153	-0.0957	-0.0913	-0.4454	0.0048	0.0525	-0.0584	0.0318	0.007	0.0432	0.2762	0.0199	-0.0025	0.1995	0.0148	0.2456	23.1984	6.8534	34.1381
14	8.8068	-3.132	-0.9539	10.8849	1.8876	5.0773	0.031	0.0165	-0.6125	-0.1514	-0.0361	0.133	0.4995	-0.045	0.0051	0.1657	-0.0051	-0.0055	0.1618	0.0172	0.1794	15.2579	12.285	34.884
15	9.329	-2.8423	0.5704	5.0094	-1.5286	4.385	-0.0352	-0.0207	-0.0216	0.0078	0.0644	0.2693	-0.2365	-0.1004	-0.0291	0.1807	-0.0126	0.0081	0.1365	0.0152	0.1511	6.5374	21.8552	32.5435

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Auth asym-ID	Auth seq-ID
1	X-RAY DIFFRACTION	1	A	1 - 6
2	X-RAY DIFFRACTION	2	A	7 - 16
3	X-RAY DIFFRACTION	3	A	17 - 23
4	X-RAY DIFFRACTION	4	A	24 - 31
5	X-RAY DIFFRACTION	5	A	32 - 36
6	X-RAY DIFFRACTION	6	A	37 - 43
7	X-RAY DIFFRACTION	7	A	44 - 58
8	X-RAY DIFFRACTION	8	A	59 - 63
9	X-RAY DIFFRACTION	9	A	64 - 72
10	X-RAY DIFFRACTION	10	A	73 - 91
11	X-RAY DIFFRACTION	11	A	92 - 103
12	X-RAY DIFFRACTION	12	A	104 - 112
13	X-RAY DIFFRACTION	13	A	113 - 120
14	X-RAY DIFFRACTION	14	A	121 - 126
15	X-RAY DIFFRACTION	15	A	127 - 138

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