PDB-6ovw: Crystal structure of ornithine carbamoyltransferase from Salmonel...

ID or keywords:

Entry

Database: PDB / ID: 6ovw

Title

Crystal structure of ornithine carbamoyltransferase from Salmonella enterica

Components

Ornithine carbamoyltransferase

Ornithine transcarbamylase

Keywords

ISOMERASE /

structural genomics / CSGID / Center for Structural Genomics of Infectious Diseases

Function / homology

Function and homology information

ornithine carbamoyltransferase /

ornithine carbamoyltransferase activity /

amino acid binding /

cytoplasm
Similarity search - Function

Biological species

Salmonella typhimurium (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 1.903 Å

Authors

Chang, C. / Mesa, N. / Skarina, T. / Savchenko, A. / Joachimiak, A. / Center for Structural Genomics of Infectious Diseases (CSGID)

Citation

Journal: To Be Published
Title: Crystal structure of ornithine carbamoyltransferase from Salmonella enterica
Authors: Chang, C. / Mesa, N. / Skarina, T. / Savchenko, A. / Joachimiak, A. / Center for Structural Genomics of Infectious Diseases (CSGID)

History

Deposition	May 8, 2019	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	May 22, 2019	Provider: repository / Type: Initial release
Revision 1.1	Oct 11, 2023	Group: Data collection / Database references / Refinement description Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

Structure viewer	Molecule: MolmilJmol/JSmol

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PDBx/mmCIF format	6ovw.cif.gz	147.8 KB	Display	PDBx/mmCIF format
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Validation report

Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/ov/6ovw ftp://data.pdbj.org/pub/pdb/validation_reports/ov/6ovw	HTTPS FTP

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Related structure data

Related structure data	1duvS S: Starting model for refinement
Similar structure data	4am8-1 4jqo-d 3txx-2 2otc-1 4jfr-d 6ypo-1 4a8h-1 2otc-2 4jhx-d 6ywj-2 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: CSGID-IDP97163

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Links

PDB pages	PDBj / wwPDB / NCBI
Related items in Molecule of the Month	#215 - Nov 2017 Aspartate Transcarbamoylase similarity (7)

Deposited unit

A: Ornithine carbamoyltransferase

hetero molecules

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

1

A: Ornithine carbamoyltransferase

hetero molecules

A: Ornithine carbamoyltransferase

hetero molecules

A: Ornithine carbamoyltransferase

hetero molecules

defined by author&software
111 kDa, 3 polymers
Search similar-shape structures of this assembly by Omokage search (details)

Unit cell

Length a, b, c (Å)	139.214, 139.214, 139.214
Angle α, β, γ (deg.)	90.000, 90.000, 90.000
Int Tables number	212
Space group name H-M	P4₃32

Components on special symmetry positions

ID	Model	Components
1	1	A-589- HOH
2	1	A-724- HOH
3	1	A-726- HOH

#1: Protein	Ornithine carbamoyltransferase / Ornithine transcarbamylase Mass: 36782.953 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Salmonella typhimurium (strain SL1344) (bacteria) Strain: SL1344 / Gene: argI, SL1344_4399 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) References: UniProt: A0A0H3NPU3, ornithine carbamoyltransferase
#2: Chemical	ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C₃H₈O₃
#3: Chemical	ChemComp-PO4 / PHOSPHATE ION / Phosphate Mass: 94.971 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: PO₄
#4: Water	ChemComp-HOH / water / Water Mass: 18.015 Da / Num. of mol.: 275 / 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: 3.06 Å³/Da / Density % sol: 59.75 %
Crystal grow	Temperature: 289 K / Method: vapor diffusion, hanging drop / pH: 8.5 / Details: 2.0 M ammonium dihydrogen phosphate, 0.1 M Tris-Cl

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Data collection

Diffraction

Mean temperature: 100 K / Serial crystal experiment: N

Diffraction source

Source:

SYNCHROTRON / Site:

APS

/ Beamline: 19-ID / Wavelength: 0.97927 Å

Detector

Type: DECTRIS PILATUS3 X 6M / Detector: PIXEL / Date: Nov 13, 2018

Radiation

Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray

Radiation wavelength

Wavelength: 0.97927 Å / Relative weight: 1

Reflection

Resolution: 1.9→50 Å / Num. obs: 36844 / % possible obs: 100 % / Redundancy: 30.2 % / R_merge(I) obs: 0.079 / R_pim(I) all: 0.014 / R_rim(I) all: 0.08 / Χ²: 1.009 / Net I/σ(I): 7.3 / Num. measured all: 1111728

Reflection shell

Diffraction-ID: 1

Resolution (Å)	Redundancy (%)	R_merge(I) obs	Num. unique obs	CC_1/2	R_pim(I) all	R_rim(I) all	Χ²	% possible all
1.9-1.93	9.7	1.686	1803	0.435	0.56	1.78	1.114	99.7
1.93-1.97	16.6	1.429	1796	0.702	0.357	1.475	0.965	100
1.97-2.01	25.9	1.177	1793	0.855	0.234	1.2	0.94	100
2.01-2.05	31.1	0.986	1815	0.916	0.179	1.002	0.96	100
2.05-2.09	32.6	0.787	1806	0.946	0.139	0.799	1.092	100
2.09-2.14	33.1	0.662	1804	0.963	0.116	0.672	0.995	100
2.14-2.19	33	0.498	1803	0.979	0.087	0.506	0.99	100
2.19-2.25	32	0.444	1815	0.984	0.079	0.451	1.205	100
2.25-2.32	30.4	0.352	1836	0.989	0.064	0.358	1.066	100
2.32-2.39	34	0.275	1803	0.994	0.048	0.28	1.018	100
2.39-2.48	33.9	0.218	1828	0.996	0.038	0.221	1.001	100
2.48-2.58	33.4	0.176	1818	0.997	0.031	0.179	1.01	100
2.58-2.7	32.7	0.145	1840	0.998	0.026	0.147	1.041	100
2.7-2.84	30.6	0.115	1847	0.998	0.021	0.117	0.991	100
2.84-3.02	34	0.088	1840	0.999	0.015	0.09	0.945	100
3.02-3.25	33.5	0.069	1851	0.999	0.012	0.07	0.926	100
3.25-3.58	32.4	0.059	1877	0.999	0.01	0.06	0.95	100
3.58-4.09	32.2	0.051	1880	0.999	0.009	0.052	0.978	100
4.09-5.16	32.3	0.049	1919	0.999	0.009	0.05	0.984	100
5.16-50	29.4	0.048	2070	0.999	0.009	0.049	1.071	100

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Processing

Software

Name	Version	Classification
SCALEPACK		data scaling
PHENIX	1.15.2_3472	refinement
PDB_EXTRACT	3.25	data extraction
HKL-3000		data reduction
HKL-3000		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: 1DUV

1duv

Resolution: 1.903→41.975 Å / SU ML: 0.17 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 17.81

	R_factor	Num. reflection	% reflection
R_free	0.1862	1721	4.87 %
R_work	0.1668	-	-
obs	0.1678	35311	96.12 %

Solvent computation

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

Displacement parameters

B_iso max: 128.27 Å² / B_iso mean: 25.1092 Å² / B_iso min: 1.28 Å²

Refinement step

Cycle: final / Resolution: 1.903→41.975 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	2572	0	21	275	2868
B_iso mean	-	-	58.8	34.43	-
Num. residues	-	-	-	-	334

LS refinement shell

Refine-ID: X-RAY DIFFRACTION / R_factor R_free error: 0 / Total num. of bins used: 12

Resolution (Å)	R_factor R_free	Num. reflection R_free	R_factor R_work	Num. reflection R_work	Num. reflection all	% reflection obs (%)
1.9026-1.9586	0.2999	94	0.2698	1504	1598	53
1.9586-2.0218	0.2391	139	0.2059	2849	2988	100
2.0218-2.094	0.2256	134	0.1786	2872	3006	100
2.094-2.1779	0.1735	137	0.1584	2872	3009	100
2.1779-2.277	0.2	127	0.153	2865	2992	100
2.277-2.397	0.1949	152	0.1593	2881	3033	100
2.397-2.5472	0.1848	150	0.1685	2877	3027	100
2.5472-2.7438	0.2088	145	0.1713	2894	3039	100
2.7438-3.0199	0.2157	150	0.1763	2925	3075	100
3.0199-3.4567	0.183	170	0.1692	2917	3087	100
3.4567-4.3543	0.145	152	0.1426	2976	3128	100
4.3543-41.9848	0.1698	171	0.1679	3158	3329	100

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	0.0775	-0.0283	0.0051	0.0248	0.007	0.0458	-0.0794	-0.0993	0.0151	0.0541	0.0311	0.011	-0.1164	-0.0474	-0.0444	0.098	0.0126	0.0009	0.0918	-0.0345	0.0506	64.2119	81.5775	88.3523
2	0.011	0.003	0.0062	0.0188	-0.006	0.0126	-0.0719	-0.0069	-0.0633	-0.0117	-0.0278	0.0099	0.0521	-0.0112	-0.0312	0.077	-0.0164	0.0316	0.0799	-0.0064	0.0946	67.956	63.6801	82.7292
3	0.1114	0.0268	-0.0011	0.0943	0.0283	0.0733	-0.0731	-0.2487	-0.011	0.0825	0.0432	0.0576	-0.0483	-0.2105	-0.0877	0.0514	0.0497	0.0259	0.1822	-0.0207	0.0915	46.5254	79.0321	87.5435
4	0.0176	0.0024	0.0004	0.0023	0.0024	0.0007	0.0112	-0.0192	-0.0081	-0.0153	-0.0033	0.0109	0.0688	-0.0034	-0.0034	0.2033	-0.028	-0.0672	0.1579	0.0623	0.1377	38.5922	73.7494	68.5612
5	0.0257	0.01	-0.0012	0.0103	-0.0061	0.0216	-0.0595	0.007	0.1123	-0.0237	0.0127	0.0792	-0.03	0.003	-0.0161	0.1036	0.0807	-0.1024	0.1084	0.0498	0.2287	42.6906	89.9368	72.7477
6	0.0055	-0.0014	0.0006	-0.0004	-0.0004	0.0021	-0.0399	0.0567	0.0421	-0.0295	0.0162	-0.0093	0.0084	-0.034	-0.02	0.1488	0.0364	-0.1829	0.0793	0.1214	0.1313	43.8092	85.2929	64.3977
7	0.0206	0.0085	-0.0122	0.0257	0.016	0.0278	-0.0101	-0.0342	0.0366	0.0229	0.0136	0.0086	-0.0097	0.0305	0.0144	0.0724	0.0119	-0.0071	0.0898	-0.0277	0.0461	62.1242	84.8264	85.7102

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 69 )	A	1 - 69
2	X-RAY DIFFRACTION	2	chain 'A' and (resid 70 through 100 )	A	70 - 100
3	X-RAY DIFFRACTION	3	chain 'A' and (resid 101 through 231 )	A	101 - 231
4	X-RAY DIFFRACTION	4	chain 'A' and (resid 232 through 254 )	A	232 - 254
5	X-RAY DIFFRACTION	5	chain 'A' and (resid 255 through 283 )	A	255 - 283
6	X-RAY DIFFRACTION	6	chain 'A' and (resid 284 through 312 )	A	284 - 312
7	X-RAY DIFFRACTION	7	chain 'A' and (resid 313 through 334 )	A	313 - 334

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