PDB-8kg1: Crystal structure of the cargo cysteine desulfurase from Mycobact...

ID or keywords:

Entry

Database: PDB / ID: 8kg1

Title

Crystal structure of the cargo cysteine desulfurase from Mycobacterium smegmatis

Components

cysteine desulfurase

Keywords

TRANSFERASE / cargo protein / cysteine desulfurase

Function / homology

Function and homology information

cysteine desulfurase / cysteine desulfurase activity / cysteine metabolic process / pyridoxal phosphate binding
Similarity search - Function

Biological species

Mycolicibacterium smegmatis (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 2.1 Å

Authors

Liu, X. / Tang, Y. / Liu, Y. / Ma, M. / Gao, Y.

Funding support

China, 2items

Citation

Journal: To be published
Title: Crystal structure of the cargo cysteine desulfurase from Mycobacterium smegmatis
Authors: Liu, X. / Tang, Y.

History

Deposition	Aug 17, 2023	Deposition site: PDBJ / Processing site: PDBC
Revision 1.0	Nov 20, 2024	Provider: repository / Type: Initial release

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	8kg1.cif.gz	343.9 KB	Display	PDBx/mmCIF format
PDB format	pdb8kg1.ent.gz	277.1 KB	Display	PDB format
PDBx/mmJSON format	8kg1.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/kg/8kg1 ftp://data.pdbj.org/pub/pdb/validation_reports/kg/8kg1	HTTPS FTP

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Related structure data

Similar structure data	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: cysteine desulfurase

B: cysteine desulfurase

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

1

Idetical with deposited unit
defined by author&software
Evidence: gel filtration

Unit cell

Length a, b, c (Å)	112.092, 112.092, 120.813
Angle α, β, γ (deg.)	90.00, 90.00, 120.00
Int Tables number	152
Space group name H-M	P3₁21

Components on special symmetry positions

ID	Model	Components
1	1	B-702- HOH
2	1	B-808- HOH

#1: Protein	cysteine desulfurase Mass: 46524.297 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mycolicibacterium smegmatis (strain ATCC 700084 / mc(2)155) (bacteria) Gene: MSMEI_4425 Production host: Mycolicibacterium smegmatis (strain ATCC 700084 / mc(2)155) (bacteria) References: UniProt: I7GDP6, cysteine desulfurase
#2: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 529 / Source method: isolated from a natural source / Formula: H₂O
Has ligand of interest	Y
Has protein modification	Y

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Experiment

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

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Sample preparation

Crystal	Density Matthews: 2.35 Å³/Da / Density % sol: 47.76 %
Crystal grow	Temperature: 289 K / Method: vapor diffusion, sitting drop / pH: 6.5 Details: The reservoir solution consisted of 0.1mM Bis-Tris pH6.5 and 9-24%w/v PEG10000. Protein crystals grew by vapor diffusion at 16℃ in sitting drops. Yellow crystals with a hexagonal ...Details: The reservoir solution consisted of 0.1mM Bis-Tris pH6.5 and 9-24%w/v PEG10000. Protein crystals grew by vapor diffusion at 16℃ in sitting drops. Yellow crystals with a hexagonal morphology appeared within 24 h and reached their full size after 5-7 days. PH range: 6.5-7.5

Crystal

Density Matthews: 2.35 Å³/Da / Density % sol: 47.76 %

Crystal grow

Temperature: 289 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: The reservoir solution consisted of 0.1mM Bis-Tris pH6.5 and 9-24%w/v PEG10000. Protein crystals grew by vapor diffusion at 16℃ in sitting drops. Yellow crystals with a hexagonal ...
PH range: 6.5-7.5

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Data collection

Diffraction

Mean temperature: 100 K / Serial crystal experiment: N

Diffraction source

Source:

SYNCHROTRON / Site:

SSRF

/ Beamline: BL18U1 / Wavelength: 1.03845 Å

Detector

Type: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Apr 12, 2023

Radiation

Monochromator: LN2-cooled DCM with Si(111) crystals / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray

Radiation wavelength

Wavelength: 1.03845 Å / Relative weight: 1

Reflection

Resolution: 2.1→50 Å / Num. obs: 51350 / % possible obs: 100 % / Redundancy: 18.6 % / CC_1/2: 0.995 / CC star: 0.999 / R_merge(I) obs: 0.137 / R_pim(I) all: 0.032 / R_rim(I) all: 0.141 / Χ²: 0.943 / Net I/σ(I): 7.8 / Num. measured all: 957416

Reflection shell

Diffraction-ID: 1 / % possible all: 100

Resolution (Å)	Redundancy (%)	R_merge(I) obs	Num. unique obs	CC_1/2	CC star	R_pim(I) all	R_rim(I) all	Χ²
2.1-2.14	17.4	1.74	2550	0.89	0.971	0.429	1.793	0.841
2.14-2.18	18.4	1.493	2530	0.916	0.978	0.359	1.536	0.856
2.18-2.22	17.9	1.183	2532	0.932	0.982	0.287	1.218	0.856
2.22-2.26	17.7	0.982	2504	0.954	0.988	0.24	1.011	0.898
2.26-2.31	19	0.791	2571	0.962	0.99	0.187	0.813	0.888
2.31-2.37	18.9	0.74	2518	0.973	0.993	0.171	0.76	0.937
2.37-2.42	18.7	0.541	2548	0.974	0.993	0.129	0.557	0.894
2.42-2.49	18.4	0.438	2573	0.983	0.996	0.105	0.451	0.907
2.49-2.56	17.6	0.35	2520	0.986	0.996	0.086	0.361	0.914
2.56-2.65	19	0.295	2556	0.984	0.996	0.07	0.304	0.933
2.65-2.74	18.2	0.237	2558	0.991	0.998	0.057	0.244	0.919
2.74-2.85	19.2	0.194	2552	0.993	0.998	0.045	0.199	0.941
2.85-2.98	19.5	0.165	2544	0.993	0.998	0.038	0.169	0.941
2.98-3.14	19.4	0.143	2562	0.995	0.999	0.033	0.147	1.002
3.14-3.33	18.6	0.128	2578	0.994	0.998	0.03	0.132	1.044
3.33-3.59	19.2	0.117	2588	0.996	0.999	0.027	0.12	1.088
3.59-3.95	19.7	0.104	2577	0.995	0.999	0.024	0.107	1.047
3.95-4.52	19.4	0.097	2596	0.996	0.999	0.022	0.099	0.983
4.52-5.7	18.6	0.087	2645	0.996	0.999	0.021	0.09	0.856
5.7-50	18.1	0.075	2748	0.996	0.999	0.018	0.077	1.078

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Processing

Software

Name	Version	Classification
PHENIX	(1.20.1_4487: ???)	refinement
HKL-2000		data scaling
HKL-2000		data reduction
MOLREP		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT / Resolution: 2.1→45.04 Å / SU ML: 0.15 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 17.23 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection
R_free	0.1855	2605	5.08 %
R_work	0.1492	-	-
obs	0.1511	51305	99.76 %

Solvent computation

Shrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL

Refinement step

Cycle: LAST / Resolution: 2.1→45.04 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	6225	0	0	529	6754

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.007	6412
X-RAY DIFFRACTION	f_angle_d	0.843	8737
X-RAY DIFFRACTION	f_dihedral_angle_d	7.826	906
X-RAY DIFFRACTION	f_chiral_restr	0.053	977
X-RAY DIFFRACTION	f_plane_restr	0.009	1153

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 (%)
2.1-2.14	0.2164	95	0.1769	2467	X-RAY DIFFRACTION	95
2.14-2.18	0.2052	164	0.1763	2495	X-RAY DIFFRACTION	100
2.18-2.23	0.2219	160	0.1661	2527	X-RAY DIFFRACTION	100
2.23-2.28	0.2163	150	0.1594	2524	X-RAY DIFFRACTION	100
2.28-2.33	0.1977	127	0.1568	2557	X-RAY DIFFRACTION	100
2.33-2.39	0.204	161	0.1559	2511	X-RAY DIFFRACTION	100
2.39-2.45	0.2059	136	0.1561	2549	X-RAY DIFFRACTION	100
2.45-2.52	0.2101	140	0.1571	2528	X-RAY DIFFRACTION	100
2.52-2.6	0.1714	125	0.15	2596	X-RAY DIFFRACTION	100
2.6-2.7	0.1988	123	0.1476	2539	X-RAY DIFFRACTION	100
2.7-2.81	0.1864	151	0.1482	2550	X-RAY DIFFRACTION	100
2.81-2.93	0.1916	114	0.1535	2575	X-RAY DIFFRACTION	100
2.93-3.09	0.1881	135	0.1458	2566	X-RAY DIFFRACTION	100
3.09-3.28	0.2164	150	0.1502	2553	X-RAY DIFFRACTION	100
3.28-3.53	0.1755	112	0.1449	2589	X-RAY DIFFRACTION	100
3.53-3.89	0.1691	156	0.1353	2583	X-RAY DIFFRACTION	100
3.89-4.45	0.1458	136	0.1293	2615	X-RAY DIFFRACTION	100
4.45-5.6	0.1491	114	0.1421	2651	X-RAY DIFFRACTION	100
5.61-45.04	0.1956	156	0.1619	2725	X-RAY DIFFRACTION	100

Refinement TLS params.

Method: refined / Origin x: -45.7343 Å / Origin y: 60.2486 Å / Origin z: -18.4209 Å

	11	12	13	21	22	23	31	32	33
T	0.0912 Å²	0.0477 Å²	0.0229 Å²	-	0.166 Å²	0.0062 Å²	-	-	0.1118 Å²
L	1.0103 °²	0.3908 °²	0.0264 °²	-	0.5468 °²	0.0124 °²	-	-	0.7538 °²
S	0.0539 Å °	-0.0636 Å °	-0.0785 Å °	0.0381 Å °	-0.0284 Å °	-0.0087 Å °	-0.1692 Å °	-0.0882 Å °	-0.0154 Å °

Refinement TLS group

Selection details: all

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