PDB-5i7w: Crystal Structure of a Cysteine Synthase from Brucella suis

ID or keywords:

Entry

Database: PDB / ID: 5i7w

Title

Crystal Structure of a Cysteine Synthase from Brucella suis

Components

Cysteine synthase A

Keywords

TRANSFERASE / SSGCID / Cysteine synthase / Structural Genomics / Seattle Structural Genomics Center for Infectious Disease

Function / homology

Function and homology information

cysteine synthase / cysteine synthase activity / cysteine biosynthetic process from serine / cytoplasm
Similarity search - Function

Biological species

Brucella suis biovar 1 (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT /

molecular replacement / Resolution: 1.95 Å

Authors

Seattle Structural Genomics Center for Infectious Disease (SSGCID)

Citation

Journal: to be published
Title: Crystal Structure of a Cysteine Synthase from Brucella suis
Authors: Dranow, D.M. / Lorimer, D. / Edwards, T.E.

History

Deposition	Feb 18, 2016	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Mar 2, 2016	Provider: repository / Type: Initial release
Revision 1.1	Sep 27, 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 / pdbx_struct_oper_list Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_oper_list.symmetry_operation
Revision 1.2	Nov 15, 2023	Group: Data collection / Category: chem_comp_atom / chem_comp_bond / Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_2

Structure viewer	Molecule: MolmilJmol/JSmol

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PDBx/mmCIF format	5i7w.cif.gz	281.4 KB	Display	PDBx/mmCIF format
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Validation report

Summary document	5i7w_validation.pdf.gz	453.7 KB	Display	wwPDB validaton report
Full document	5i7w_full_validation.pdf.gz	455.7 KB	Display
Data in XML	5i7w_validation.xml.gz	30.2 KB	Display
Data in CIF	5i7w_validation.cif.gz	44.2 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/i7/5i7w ftp://data.pdbj.org/pub/pdb/validation_reports/i7/5i7w	HTTPS FTP

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Related structure data

Related structure data	1ve1S S: Starting model for refinement
Similar structure data	2xkb-9 5vu3-4 5vu3-2 6r15-d 2xkb-8 5vu3-1 6h55-d 2bat-d 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
Other databases	TargetTrack: SSGCID-BrsuA.01147.a

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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

B: Cysteine synthase A

hetero molecules

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

1

A: Cysteine synthase A

hetero molecules

defined by author&software
39.5 kDa, 1 polymers
Search similar-shape structures of this assembly by Omokage search (details)

2

B: Cysteine synthase A

hetero molecules

defined by author&software
39.4 kDa, 1 polymers
Search similar-shape structures of this assembly by Omokage search (details)

Unit cell

Length a, b, c (Å)	60.020, 71.860, 201.600
Angle α, β, γ (deg.)	90.000, 90.000, 90.000
Int Tables number	19
Space group name H-M	P2₁2₁2₁

#1: Protein	Cysteine synthase A Mass: 39284.117 Da / Num. of mol.: 2 / Fragment: BrsuA.01147.A1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Brucella suis biovar 1 (strain 1330) (bacteria) Strain: 1330 / Gene: BS1330_I1049 / Plasmid: BrsuA.01147.A1 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: A0A0H3G350, cysteine synthase
#2: Chemical	ChemComp-MLI / MALONATE ION Mass: 102.046 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C₃H₂O₄
#3: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 468 / 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: 2.77 Å³/Da / Density % sol: 55.54 %
Crystal grow	Temperature: 290 K / Method: vapor diffusion, sitting drop / pH: 6.5 Details: BrsuA.01147.a.A1.PS01448 at 20 mg/ml was mixed 1:1 with JCSG+(g6): 0.2 M sodium malonate, pH = 7.0, 20% (w/v) PEG-3350, cryoprotected with 20% glycerol, in 2 steps

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Data collection

Diffraction

Mean temperature: 100 K

Diffraction source

Source:

SYNCHROTRON / Site:

APS

/ Beamline: 21-ID-F / Wavelength: 0.97872 Å

Detector

Type: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Feb 3, 2016 / Details: Beryllium Lenses

Radiation

Monochromator: Diamond [111] / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray

Radiation wavelength

Wavelength: 0.97872 Å / Relative weight: 1

Reflection

Resolution: 1.95→50 Å / Num. obs: 64412 / % possible obs: 99.8 % / Observed criterion σ(I): -3 / Redundancy: 13.1 % / B_iso Wilson estimate: 20.3 Å² / CC_1/2: 0.994 / R_merge(I) obs: 0.123 / Net I/σ(I): 9.82

Reflection shell

Resolution (Å)	R_merge(I) obs	Mean I/σ(I) obs	Diffraction-ID	% possible all
1.95-2	0.529	3.67	1	100
2-2.06	0.426	4.42	1	100
2.06-2.12	0.353	5.1	1	100
2.12-2.18	0.308	5.76	1	100
2.18-2.25	0.261	6.64	1	100
2.25-2.33	0.24	7.19	1	100
2.33-2.42	0.206	8.03	1	99.9
2.42-2.52	0.183	9.06	1	99.9
2.52-2.63	0.161	9.93	1	99.8
2.63-2.76	0.145	11.03	1	99.8
2.76-2.91	0.13	11.91	1	99.8
2.91-3.08	0.118	13.09	1	99.8
3.08-3.3	0.108	14.21	1	99.6
3.3-3.56	0.097	15.23	1	99.5
3.56-3.9	0.087	16.47	1	99.7
3.9-4.36	0.081	16.81	1	99.7
4.36-5.03	0.076	17.13	1	99.7
5.03-6.17	0.07	16.76	1	99.9
6.17-8.72	0.059	17.03	1	99.4
8.72-50	0.052	16.55	1	97.1

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Phasing

Phasing	Method: molecular replacement

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Processing

Software

Name	Version	Classification
XSCALE		data scaling
PHENIX		refinement
PDB_EXTRACT	3.2	data extraction
XDS		data reduction

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: 1VE1

1ve1

Resolution: 1.95→46.066 Å / SU ML: 0.19 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 20.86

	R_factor	Num. reflection	% reflection
R_free	0.2155	1978	3.07 %
R_work	0.1768	-	-
obs	0.178	64404	99.82 %

Solvent computation

Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å

Displacement parameters

B_iso max: 97.88 Å² / B_iso mean: 28.6533 Å² / B_iso min: 10.22 Å²

Refinement step

Cycle: final / Resolution: 1.95→46.066 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	5043	0	21	477	5541
B_iso mean	-	-	40.04	34.6	-
Num. residues	-	-	-	-	677

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.006	5224
X-RAY DIFFRACTION	f_angle_d	0.768	7122
X-RAY DIFFRACTION	f_chiral_restr	0.053	812
X-RAY DIFFRACTION	f_plane_restr	0.005	946
X-RAY DIFFRACTION	f_dihedral_angle_d	15.303	3111

LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 14

Resolution (Å)	R_factor R_free	Num. reflection R_free	R_factor R_work	Num. reflection R_work	Num. reflection all	% reflection obs (%)
1.95-1.9988	0.2879	152	0.2264	4400	4552	100
1.9988-2.0528	0.287	140	0.2098	4387	4527	100
2.0528-2.1132	0.2506	119	0.1971	4410	4529	100
2.1132-2.1814	0.246	123	0.1921	4425	4548	100
2.1814-2.2594	0.2131	137	0.1825	4410	4547	100
2.2594-2.3499	0.2276	147	0.1898	4416	4563	100
2.3499-2.4568	0.2287	141	0.1854	4433	4574	100
2.4568-2.5863	0.2318	142	0.1804	4436	4578	100
2.5863-2.7483	0.2042	135	0.1831	4453	4588	100
2.7483-2.9605	0.2602	143	0.1847	4431	4574	100
2.9605-3.2584	0.1997	148	0.1851	4473	4621	100
3.2584-3.7297	0.2058	146	0.1689	4491	4637	100
3.7297-4.6983	0.1942	150	0.1429	4533	4683	100
4.6983-46.0784	0.1761	155	0.1689	4728	4883	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	2.2864	1.0497	-1.7906	1.9596	-1.0303	2.7894	-0.1643	0.2664	-0.0464	-0.4322	0.1523	-0.0834	0.1974	-0.3483	0.0354	0.1707	-0.0027	0.0309	0.1656	0.0076	0.1157	4.8648	-23.5531	-23.5384
2	1.255	0.5572	-0.0519	0.8976	0.1755	4.4238	0.0028	-0.0457	0.0367	-0.1332	0.0471	-0.0872	0.1008	0.2542	-0.027	0.1532	0.0082	0.0618	0.1188	0.004	0.1367	17.695	-5.6613	-18.6236
3	0.997	0.6173	-0.272	1.2078	-0.1352	1.4366	0.0521	0.0488	0.0841	-0.1003	0.0106	0.0857	-0.1568	-0.1863	-0.0498	0.1361	0.0467	0.0365	0.1493	0.0127	0.1464	2.5302	-10.4507	-14.2943
4	0.9445	-0.1184	-0.7472	2.7733	0.5529	1.461	-0.0272	-0.0496	0.0182	0.0542	0.0311	-0.0666	0.1019	-0.0461	-0.0109	0.0932	-0.0021	0.0117	0.1579	0.0154	0.1137	3.9851	-24.2313	-8.2277
5	0.7576	-0.9726	-1.4956	1.3536	1.8283	2.8481	-0.1897	-0.0599	0.0371	0.1189	0.1361	-0.1468	0.3472	0.3062	0.0358	0.1513	0.0026	0.0094	0.2352	-0.0061	0.2621	23.581	-33.5823	-11.9259
6	1.043	-0.0865	-0.5371	2.2161	-1.1957	1.4633	-0.0395	0.1014	-0.1106	-0.0379	0.0871	0.1916	0.0708	-0.0806	-0.0694	0.2687	-0.0328	0.0876	0.1755	-0.0292	0.1658	15.4308	-30.4095	-35.9539
7	2.0963	-1.4179	-1.2365	1.2517	0.8419	1.2397	0.3123	-0.5637	0.5094	-0.0044	0.0625	-0.1829	-0.4036	0.4807	-0.2834	0.3594	-0.0998	0.135	0.2672	-0.0775	0.2535	27.9412	-37.931	-25.8934
8	1.0636	-0.3918	0.0352	1.6754	-1.0242	1.2652	0.0571	0.1825	-0.1082	-0.3	-0.0052	0.1374	0.2075	0.0194	-0.0418	0.3033	-0.0476	0.0761	0.1636	-0.0407	0.1487	19.8841	-35.5376	-43.1149
9	0.6133	-0.0222	-0.1652	1.4115	-0.0816	1.8895	-0.0255	0.1079	0.0161	-0.1187	0.0228	-0.2756	0.1131	0.0694	0.0169	0.322	-0.0109	0.1344	0.1952	0.0085	0.1931	28.4724	-22.2436	-44.8082
10	1.8139	-1.8613	-3.4621	3.9639	5.2294	8.4911	0.1888	-0.3894	0.2248	0.2005	0.4871	-0.7622	0.5031	0.8016	-0.6756	0.2735	-0.0066	-0.065	0.3491	-0.0497	0.3844	34.3597	-8.7994	-23.9436

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details	Auth asym-ID	Auth seq-ID
1	X-RAY DIFFRACTION	1	chain 'A' and (resid 1 through 43 )	A	1 - 43
2	X-RAY DIFFRACTION	2	chain 'A' and (resid 44 through 124 )	A	44 - 124
3	X-RAY DIFFRACTION	3	chain 'A' and (resid 125 through 220 )	A	125 - 220
4	X-RAY DIFFRACTION	4	chain 'A' and (resid 221 through 302 )	A	221 - 302
5	X-RAY DIFFRACTION	5	chain 'A' and (resid 303 through 342 )	A	303 - 342
6	X-RAY DIFFRACTION	6	chain 'B' and (resid 2 through 71 )	B	2 - 71
7	X-RAY DIFFRACTION	7	chain 'B' and (resid 72 through 124 )	B	72 - 124
8	X-RAY DIFFRACTION	8	chain 'B' and (resid 125 through 209 )	B	125 - 209
9	X-RAY DIFFRACTION	9	chain 'B' and (resid 210 through 309 )	B	210 - 309
10	X-RAY DIFFRACTION	10	chain 'B' and (resid 310 through 342 )	B	310 - 342

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