PDB-2q3d: 2.2 A Resolution Crystal Structure of O-Acetylserine Sulfhydrylas...

ID or keywords:

Entry

Database: PDB / ID: 2q3d

Title

2.2 A Resolution Crystal Structure of O-Acetylserine Sulfhydrylase (OASS) From MYCOBACTERIUM TUBERCULOSIS in Complex with the Reaction Intermediate ALPHA-AMINOACRYLATE

Components

Cysteine synthase A

Keywords

TRANSFERASE / Mycobacterium tuberculosis / Pyridoxal-5'-phosphate / sulphur metabolism / cysteine biosynthesis / alpha-aminoacrylate intermediate

Function / homology

Function and homology information

Cysteine synthesis from O-acetylserine / cysteine synthase / L-cysteine desulfhydrase activity / cysteine biosynthetic process / cysteine synthase activity / cysteine biosynthetic process from serine / pyridoxal phosphate binding / extracellular region / cytosol / cytoplasm
Similarity search - Function

Biological species

Mycobacterium tuberculosis (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 2.2 Å

Authors

Schneider, G. / Schnell, R.

Citation

Journal: J.Biol.Chem. / Year: 2007
Title: Structural Insights into Catalysis and Inhibition of O-Acetylserine Sulfhydrylase from Mycobacterium tuberculosis: CRYSTAL STRUCTURES OF THE ENZYME {alpha}-AMINOACRYLATE INTERMEDIATE AND AN ...
Authors: Schnell, R. / Oehlmann, W. / Singh, M. / Schneider, G.

History

Deposition	May 30, 2007	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Jun 12, 2007	Provider: repository / Type: Initial release
Revision 1.1	May 1, 2008	Group: Version format compliance
Revision 1.2	Jul 13, 2011	Group: Advisory / Derived calculations / Version format compliance
Revision 1.3	Mar 7, 2018	Group: Data collection / Category: diffrn_source / Item: _diffrn_source.pdbx_synchrotron_site
Revision 1.4	Aug 30, 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_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_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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Download

PDBx/mmCIF format	2q3d.cif.gz	74.8 KB	Display	PDBx/mmCIF format
PDB format	pdb2q3d.ent.gz	55.9 KB	Display	PDB format
PDBx/mmJSON format	2q3d.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	2q3d_validation.pdf.gz	797 KB	Display	wwPDB validaton report
Full document	2q3d_full_validation.pdf.gz	803 KB	Display
Data in XML	2q3d_validation.xml.gz	14 KB	Display
Data in CIF	2q3d_validation.cif.gz	18.8 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/q3/2q3d ftp://data.pdbj.org/pub/pdb/validation_reports/q3/2q3d	HTTPS FTP

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Related structure data

Related structure data	2q3bSC 2q3cC S: Starting model for refinement C: citing same article (ref.)
Similar structure data	6v77-d 3vc3-3 5the-1 1ve1-1 2q3c-1 2eco-1 4lmb-1 2bhs-1 2qe2-1 4rg4-d 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
Related items in Molecule of the Month	#228 - Dec 2018 Directed Evolution of Enzymes similarity (3)

Deposited unit

A: Cysteine synthase A

hetero molecules

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

1

A: Cysteine synthase A

hetero molecules

A: Cysteine synthase A

hetero molecules

defined by author&software
67 kDa, 2 polymers
Search similar-shape structures of this assembly by Omokage search (details)

Unit cell

Length a, b, c (Å)	71.785, 71.785, 181.179
Angle α, β, γ (deg.)	90.00, 90.00, 90.00
Int Tables number	92
Space group name H-M	P4₁2₁2

Details

The OASS forms a dimer, the second part of the biological assembly is generated by the two fold axis: -y+1, -x+1, -z+1/2.

#1: Protein	Cysteine synthase A / O-acetylserine sulfhydrylase A / O-acetylserine Thiol / lyase A / CSase A Mass: 33067.891 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mycobacterium tuberculosis (bacteria) / Strain: Rv2334 / Gene: cysK / Plasmid: pET28a / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) References: UniProt: P0A534, UniProt: P9WP55*PLUS, cysteine synthase
#2: Chemical	ChemComp-PDA / 2-[(3-HYDROXY-2-METHYL-5-PHOSPHONOOXYMETHYL-PYRIDIN-4-YLMETHYL)-AMINO]-PROPIONIC ACID / PYRIDOXYL-ALANINE-5-PHOSPHATE Mass: 320.236 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C₁₁H₁₇N₂O₇P
#3: Chemical	ChemComp-MPD / (4S)-2-METHYL-2,4-PENTANEDIOL Mass: 118.174 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C₆H₁₄O₂ / Comment: precipitant*YM
#4: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 42 / 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: 3.6 Å³/Da / Density % sol: 65.85 %
Crystal grow	Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8.2 Details: 0.1 M HEPES, 80% MPD. SOAKED WITH 1 mM O-ACETYL-SERINE FOR 30 MINUTES BEFORE FREEZING., pH 8.2, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

Diffraction	Mean temperature: 110 K
Diffraction source	Source: SYNCHROTRON / Site: MAX II / Beamline: I911-3 / Wavelength: 1 Å
Detector	Type: MAR CCD 165 mm / Detector: CCD / Date: Oct 19, 2006 Details: First mirror: Water-cooled vertically collimating cylindrical mirror (R = 7300 m). Second mirror: Toroid mirror for horizontal and vertical focusing (R=3300m, R=27mm).
Radiation	Monochromator: Double crystal monochromator, Si(111). The first crystal is water cooled. Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 1 Å / Relative weight: 1
Reflection	Resolution: 2.2→71.8 Å / Num. all: 24607 / Num. obs: 24607 / % possible obs: 98.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 5.4 % / B_iso Wilson estimate: 43 Å² / R_merge(I) obs: 0.091 / Net I/σ(I): 14.2
Reflection shell	Resolution: 2.2→2.32 Å / Redundancy: 5.3 % / R_merge(I) obs: 0.499 / Mean I/σ(I) obs: 2.4 / Num. unique all: 3550 / % possible all: 99.8

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Processing

Software

Name	Version	Classification
REFMAC	5.2.0005	refinement
MARCCD-mxCube		data collection
MOSFLM		data reduction
SCALA		data scaling
MOLREP		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: PDB entry 2Q3B, Holoenzyme

2q3b

Resolution: 2.2→28.35 Å / Cor.coef. F_o:F_c: 0.962 / Cor.coef. F_o:F_c free: 0.937 / SU B: 13.344 / SU ML: 0.158 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.181 / ESU R Free: 0.179 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.24943	1245	5.1 %	RANDOM
R_work	0.19379	-	-	-
all	0.19641	23287	-	-
obs	0.19641	23287	98.49 %	-

Solvent computation

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

Displacement parameters

B_iso mean: 30.42 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	3.56 Å²	0 Å²	0 Å²
2-	-	3.56 Å²	0 Å²
3-	-	-	-7.12 Å²

Refinement step

Cycle: LAST / Resolution: 2.2→28.35 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	2271	0	29	42	2342

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.012	0.022	2363
X-RAY DIFFRACTION	r_angle_refined_deg	1.419	1.999	3221
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	5.487	5	313
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	28.28	23.441	93
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	16.682	15	391
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	14.801	15	23
X-RAY DIFFRACTION	r_chiral_restr	0.092	0.2	382
X-RAY DIFFRACTION	r_gen_planes_refined	0.005	0.02	1778
X-RAY DIFFRACTION	r_nbd_refined	0.211	0.2	1158
X-RAY DIFFRACTION	r_nbtor_refined	0.31	0.2	1623
X-RAY DIFFRACTION	r_xyhbond_nbd_refined	0.508	0.2	125
X-RAY DIFFRACTION	r_symmetry_vdw_refined	0.233	0.2	46
X-RAY DIFFRACTION	r_symmetry_hbond_refined	0.221	0.2	11
X-RAY DIFFRACTION	r_mcbond_it	0.581	1.5	1564
X-RAY DIFFRACTION	r_mcangle_it	0.97	2	2473
X-RAY DIFFRACTION	r_scbond_it	1.739	3	870
X-RAY DIFFRACTION	r_scangle_it	2.668	4.5	744

LS refinement shell

Resolution: 2.2→2.257 Å / Total num. of bins used: 20

	R_factor	Num. reflection	% reflection
R_free	0.318	103	-
R_work	0.302	1684	-
obs	-	1684	99.61 %

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	19.8513	10.4344	8.5097	7.2998	1.6284	17.7702	0.1209	1.5252	-0.3784	0.5415	0.4199	-0.5056	0.5381	0.2559	-0.5408	0.2803	0.1373	0.0297	0.1557	-0.0343	0.2486	58.231	14.607	32.469
2	2.4137	1.5807	-2.6971	5.6058	1.3633	36.4197	-0.0411	-0.0416	-0.3756	0.1316	-0.0178	-0.1037	-0.2941	0.9382	0.0588	0.1685	0.2117	0.0091	0.2749	-0.0084	0.4407	52.454	12.1281	50.9402
3	0.4956	-0.9001	1.4495	5.5624	-4.1342	4.8136	-0.0397	-0.1391	-0.3574	0.6327	0.0429	-0.1482	0.1278	0.2299	-0.0032	0.249	0.0625	0.0049	0.1564	0.0121	0.1586	46.283	12.0956	66.0708
4	2.7153	-0.5827	-1.0241	0.125	0.2198	0.3863	0.0043	0.3695	0.1826	-0.1499	0.0887	-0.2296	-0.0647	-0.0497	-0.093	0.1541	0.0918	-0.0234	0.2429	-0.0243	0.32	45.541	12.9055	40.0606
5	3.774	-4.8055	-4.826	11.6089	6.62	6.7379	-0.288	0.1172	-0.0618	-0.2029	0.3795	-0.0197	-0.4263	0.1315	-0.0915	0.1731	0.0022	-0.0246	0.3311	-0.0423	0.1211	38.5804	10.7399	22.6538
6	1.5295	-0.1213	2.4556	2.9976	1.0519	4.4626	-0.348	0.6019	-0.0092	-0.2128	0.3548	-0.1863	0.1064	-0.1678	-0.0068	0.1502	0.0416	0.015	0.2284	-0.0106	0.2765	39.6614	17.7894	34.7048
7	4.5192	-0.5856	-1.6354	2.8452	2.6384	7.9895	-0.0792	0.0188	0.0298	-0.642	-0.01	0.429	-0.5877	-0.3638	0.0892	0.1022	0.1544	-0.0376	0.3737	0.0241	0.3986	34.7538	22.7374	35.2097
8	15.1958	3.2065	-1.913	5.9197	0.3882	2.5805	-0.1717	0.2324	0.4225	-0.3298	0.0634	0.6692	-0.1564	-0.9369	0.1082	0.1283	0.162	-0.0485	0.4283	0.0143	0.3555	30.6834	23.1481	34.914
9	25.4607	-7.7222	8.4637	2.6173	-6.782	67.3821	0.214	0.2338	-0.3852	-0.0522	-0.283	1.3741	0.4183	-2.6388	0.069	0.0849	-0.0479	-0.0917	0.5366	-0.0382	0.5299	24.0483	13.9755	33.2245
10	5.8014	-2.2846	4.2299	4.8327	-1.6637	8.7764	0.1026	0.7386	-0.1136	-0.433	-0.1017	0.4348	0.1853	-0.353	-0.0009	0.0908	0.0175	0.013	0.3246	-0.0599	0.1648	34.6856	8.2368	31.5755
11	8.1599	-1.7967	-0.9813	15.0603	-21.1803	31.3361	0.2076	0.3161	-0.4782	0.2406	-0.0255	-1.2104	0.7262	0.7929	-0.1821	0.3373	0.2491	-0.0327	0.1095	-0.072	0.42	51.2713	0.862	48.5392
12	26.6951	9.3276	-9.9147	19.9725	-5.371	3.8999	0.4166	-0.0302	-0.5888	0.5915	-0.4066	-0.8137	1.204	0.9182	-0.0099	0.3551	0.2433	-0.0828	0.3452	-0.0022	0.2904	51.9994	0.3817	55.3418
13	4.7605	-0.4932	-1.2235	0.8021	1.39	2.4392	-0.0202	-0.3103	-0.2544	-0.3731	0.2451	-0.0544	0.9781	-0.4461	-0.2249	0.2169	0.1149	0.0513	0.1975	-0.0134	0.2759	39.7829	1.8474	48.2921
14	13.3616	-8.1024	-4.7098	10.5845	3.0531	2.9421	0.3592	0.3808	-0.9485	-0.1857	-0.5398	0.146	0.8852	-0.3396	0.1806	0.316	0.0368	-0.0007	0.091	-0.0397	0.2467	40.9159	-2.6265	53.9198
15	1.7404	-0.0523	0.6441	6.9684	0.6841	4.7666	-0.0453	0.0855	0.0316	0.1622	-0.1653	0.4344	0.4366	-1.2377	0.2106	0.0694	-0.0049	0.0513	0.4052	-0.041	0.2759	26.3063	9.6763	48.7351
16	1.5415	-2.0805	-1.4793	8.6741	1.6208	6.7566	0.1902	0.0435	-0.2901	0.3438	-0.2123	0.0672	1.2819	-0.8247	0.0221	0.1889	0.0278	0.0542	0.1314	-0.0266	0.2412	31.9117	1.2052	54.4186
17	34.3385	7.5609	2.9345	1.8011	-0.3762	7.9184	0.4788	-0.5975	1.9258	0.6566	-0.408	0.7301	-0.5187	-0.6609	-0.0708	0.3721	0.1606	0.1185	0.2428	-0.0534	0.3653	36.9664	21.7461	61.0242
18	3.7417	1.131	-2.7634	2.4307	1.1555	4.1105	0.0721	0.0064	0.1034	0.3982	-0.056	0.2348	-0.0897	-0.0374	-0.0161	0.2306	0.1457	0.0376	0.2132	0.0253	0.3071	41.0989	16.9404	58.1638
19	2.3878	-0.1063	1.3431	0.2603	0.8783	4.1992	0.2176	-0.1386	-0.0791	0.3766	-0.25	0.1978	0.3917	0.289	0.0324	0.2799	0.1477	0.0487	0.2008	-0.0503	0.3416	41.6921	11.1132	58.2472
20	30.5569	-32.1898	7.4806	34.018	-5.4771	55.3639	-0.8026	-2.3003	0.7415	0.9565	1.2654	-0.0952	-2.0814	-1.1126	-0.4628	0.1785	0.1347	0.1112	0.2545	-0.0496	0.3502	34.6274	28.8728	53.4579

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Auth asym-ID	Label asym-ID	Auth seq-ID	Label seq-ID
1	X-RAY DIFFRACTION	1	A	A	1 - 9	4 - 12
2	X-RAY DIFFRACTION	2	A	A	10 - 20	13 - 23
3	X-RAY DIFFRACTION	3	A	A	21 - 32	24 - 35
4	X-RAY DIFFRACTION	4	A	A	33 - 55	36 - 58
5	X-RAY DIFFRACTION	5	A	A	56 - 69	59 - 72
6	X-RAY DIFFRACTION	6	A	A	70 - 85	73 - 88
7	X-RAY DIFFRACTION	7	A	A	86 - 105	89 - 108
8	X-RAY DIFFRACTION	8	A	A	106 - 122	109 - 125
9	X-RAY DIFFRACTION	9	A	A	123 - 130	126 - 133
10	X-RAY DIFFRACTION	10	A	A	131 - 158	134 - 161
11	X-RAY DIFFRACTION	11	A	A	159 - 163	162 - 166
12	X-RAY DIFFRACTION	12	A	A	164 - 172	167 - 175
13	X-RAY DIFFRACTION	13	A	A	173 - 191	176 - 194
14	X-RAY DIFFRACTION	14	A	A	192 - 203	195 - 206
15	X-RAY DIFFRACTION	15	A	A	204 - 233	207 - 236
16	X-RAY DIFFRACTION	16	A	A	234 - 244	237 - 247
17	X-RAY DIFFRACTION	17	A	A	245 - 257	248 - 260
18	X-RAY DIFFRACTION	18	A	A	258 - 275	261 - 278
19	X-RAY DIFFRACTION	19	A	A	276 - 300	279 - 303
20	X-RAY DIFFRACTION	20	A	A	301 - 306	304 - 309

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