PDB-9y83: Crystal structure of Ornithine carbamoyltransferase from Burkhold...

ID or keywords:

Entry

Database: PDB / ID: 9y83

Title

Crystal structure of Ornithine carbamoyltransferase from Burkholderia xenovorans

Components

Ornithine carbamoyltransferase

Keywords

TRANSFERASE / SSGCID / STRUCTURAL GENOMICS / SEATTLE STRUCTURAL GENOMICS CENTER FOR INFECTIOUS DISEASE

Function / homology

Function and homology information

ornithine carbamoyltransferase / ornithine carbamoyltransferase activity / citrulline biosynthetic process / L-arginine biosynthetic process via ornithine / L-arginine biosynthetic process / amino acid binding / cytoplasm
Similarity search - Function

Biological species

Paraburkholderia xenovorans LB400 (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 2.55 Å

Authors

Seattle Structural Genomics Center for Infectious Disease (SSGCID)

Funding support

United States, 2items

Organization	Grant number	Country
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)	75N93022C00036	United States
National Institutes of Health/Office of the Director	S10OD030394	United States

Citation

Journal: To be published
Title: Crystal structure of Ornithine carbamoyltransferase from Burkholderia xenovorans
Authors: Liu, L. / Lovell, S. / Battaile, K.P.

History

Deposition	Sep 11, 2025	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Sep 24, 2025	Provider: repository / Type: Initial release

Structure viewer	Molecule: MolmilJmol/JSmol

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PDBx/mmCIF format	9y83.cif.gz	516.1 KB	Display	PDBx/mmCIF format
PDB format	pdb9y83.ent.gz	429 KB	Display	PDB format
PDBx/mmJSON format	9y83.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	9y83_validation.pdf.gz	450.9 KB	Display	wwPDB validaton report
Full document	9y83_full_validation.pdf.gz	459.7 KB	Display
Data in XML	9y83_validation.xml.gz	49.3 KB	Display
Data in CIF	9y83_validation.cif.gz	63.1 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/y8/9y83 ftp://data.pdbj.org/pub/pdb/validation_reports/y8/9y83	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
Related items in Molecule of the Month	#215 - Nov 2017 Aspartate Transcarbamoylase similarity (7)

Deposited unit

A: Ornithine carbamoyltransferase

B: Ornithine carbamoyltransferase

C: Ornithine carbamoyltransferase

D: Ornithine carbamoyltransferase

hetero molecules

153 kDa, 4 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

A: Ornithine carbamoyltransferase

B: Ornithine carbamoyltransferase

C: Ornithine carbamoyltransferase

D: Ornithine carbamoyltransferase

hetero molecules

A: Ornithine carbamoyltransferase

B: Ornithine carbamoyltransferase

C: Ornithine carbamoyltransferase

D: Ornithine carbamoyltransferase

hetero molecules

A: Ornithine carbamoyltransferase

B: Ornithine carbamoyltransferase

C: Ornithine carbamoyltransferase

D: Ornithine carbamoyltransferase

hetero molecules

defined by author&software
Evidence: gel filtration
459 kDa, 12 polymers
Search similar-shape structures of this assembly by Omokage search (details)

Unit cell

Length a, b, c (Å)	157.570, 157.570, 138.457
Angle α, β, γ (deg.)	90.00, 90.00, 120.00
Int Tables number	150
Space group name H-M	P321

#1: Protein	Ornithine carbamoyltransferase / OTCase Mass: 38211.285 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Paraburkholderia xenovorans LB400 (bacteria) Gene: argF, Bxe_C0747 / Plasmid: BuxeA.00088.a.B2 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q13H08, ornithine carbamoyltransferase
#2: Chemical	ChemComp-CL / CHLORIDE ION Mass: 35.453 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: Cl
#3: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 20 / Source method: isolated from a natural source / Formula: H₂O
Has ligand of interest	N
Has protein modification	N

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Experiment

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

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Sample preparation

Crystal	Density Matthews: 3.25 Å³/Da / Density % sol: 62.11 %
Crystal grow	Temperature: 291 K / Method: vapor diffusion, sitting drop / pH: 7.5 Details: Index F12: 100 mM HEPES, pH 7.5, 25% PEG 3350, 200 mM NaCl. BuxeA.00088.a.B2.PW39423 at 24.5 mg/mL. plate 20257 F12 drop 1, Puck: PSL-0410, Cryo: 20% glycerol + 80% crystallant

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Data collection

Diffraction	Mean temperature: 100 K / Serial crystal experiment: N
Diffraction source	Source: SYNCHROTRON / Site: NSLS-II / Beamline: 19-ID / Wavelength: 0.9786 Å
Detector	Type: DECTRIS EIGER2 XE 9M / Detector: PIXEL / Date: Aug 9, 2025
Radiation	Monochromator: Double Crystal Si 111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.9786 Å / Relative weight: 1
Reflection	Resolution: 2.55→48.6 Å / Num. obs: 64960 / % possible obs: 100 % / Redundancy: 20.3 % / CC_1/2: 1 / R_merge(I) obs: 0.111 / R_pim(I) all: 0.025 / R_rim(I) all: 0.114 / Χ²: 1.1 / Net I/σ(I): 24.4 / Num. measured all: 1319401
Reflection shell	Resolution: 2.55→2.62 Å / % possible obs: 100 % / Redundancy: 21.1 % / R_merge(I) obs: 2.204 / Num. measured all: 100406 / Num. unique obs: 4751 / CC_1/2: 0.667 / R_pim(I) all: 0.49 / R_rim(I) all: 2.258 / Χ²: 0.93 / Net I/σ(I) obs: 1.6

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Processing

Software

Name	Version	Classification
PHENIX	(2.0_5806: ???)	refinement
Aimless		data scaling
XDS		data reduction
PHASER		phasing
PDB_EXTRACT		data extraction

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT / Resolution: 2.55→48.6 Å / SU ML: 0.31 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 24.2 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection
R_free	0.2265	3313	5.1 %
R_work	0.1902	-	-
obs	0.192	64945	99.98 %

Solvent computation

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

Refinement step

Cycle: LAST / Resolution: 2.55→48.6 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	10243	0	5	20	10268

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.003	10472
X-RAY DIFFRACTION	f_angle_d	0.527	14236
X-RAY DIFFRACTION	f_dihedral_angle_d	17.916	3778
X-RAY DIFFRACTION	f_chiral_restr	0.041	1595
X-RAY DIFFRACTION	f_plane_restr	0.006	1860

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 (%)
2.55-2.59	0.3395	150	0.2976	2532	X-RAY DIFFRACTION	100
2.59-2.63	0.336	150	0.2573	2516	X-RAY DIFFRACTION	100
2.63-2.67	0.3009	150	0.252	2514	X-RAY DIFFRACTION	100
2.67-2.71	0.2561	108	0.2346	2571	X-RAY DIFFRACTION	100
2.71-2.76	0.27	162	0.2399	2543	X-RAY DIFFRACTION	100
2.76-2.81	0.2927	122	0.2481	2533	X-RAY DIFFRACTION	100
2.81-2.86	0.3683	122	0.2837	2573	X-RAY DIFFRACTION	100
2.86-2.92	0.3614	115	0.2664	2575	X-RAY DIFFRACTION	100
2.92-2.98	0.2608	122	0.2536	2537	X-RAY DIFFRACTION	100
2.98-3.05	0.2944	133	0.2412	2557	X-RAY DIFFRACTION	100
3.05-3.13	0.2994	154	0.2424	2557	X-RAY DIFFRACTION	100
3.13-3.21	0.3037	127	0.2396	2564	X-RAY DIFFRACTION	100
3.21-3.31	0.2411	143	0.237	2521	X-RAY DIFFRACTION	100
3.31-3.41	0.2604	152	0.2255	2554	X-RAY DIFFRACTION	100
3.41-3.54	0.2619	122	0.2224	2582	X-RAY DIFFRACTION	100
3.54-3.68	0.2431	161	0.1925	2548	X-RAY DIFFRACTION	100
3.68-3.84	0.2316	146	0.181	2549	X-RAY DIFFRACTION	100
3.84-4.05	0.22	166	0.1628	2552	X-RAY DIFFRACTION	100
4.05-4.3	0.1829	121	0.1646	2592	X-RAY DIFFRACTION	100
4.3-4.63	0.1693	148	0.1457	2582	X-RAY DIFFRACTION	100
4.63-5.1	0.1907	118	0.1483	2605	X-RAY DIFFRACTION	100
5.1-5.83	0.1952	154	0.1795	2590	X-RAY DIFFRACTION	100
5.84-7.35	0.2188	147	0.1964	2625	X-RAY DIFFRACTION	100
7.35-48.6	0.1718	120	0.1559	2760	X-RAY DIFFRACTION	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	2.7469	1.124	-1.5419	2.1556	-1.2123	3.6764	-0.0047	0.108	0.0853	0.0015	0.1879	0.0722	0.0952	-0.2739	-0.1451	0.5166	0.0105	-0.04	0.4591	0.0133	0.4714	-88.6484	22.2744	15.3647
2	1.5549	-0.247	0.1583	1.3463	-0.1583	1.5714	0.0919	0.1768	-0.2048	-0.3367	0.0146	0.0099	-0.0551	0.0595	-0.1199	0.5686	-0.0337	-0.0182	0.4386	-0.0624	0.4784	-76.9742	21.0597	-6.3487
3	4.5044	-0.6587	0.5876	1.4478	0.0523	1.0686	-0.0443	-0.1164	-0.1167	-0.0077	0.1714	-0.0727	-0.003	-0.0197	-0.1337	0.6196	-0.0265	-0.0768	0.4918	0.0663	0.4754	-82.8034	12.9834	43.0112
4	1.7655	0.8079	0.0458	2.5366	-0.3026	1.9225	-0.0213	0.1639	-0.1813	-0.1224	0.0286	0.1046	0.5197	-0.0102	-0.0072	0.6741	-0.0491	-0.0216	0.5615	0.1314	0.5844	-105.0516	3.1008	39.7667
5	1.5652	-0.8141	0.5049	2.036	-0.3924	4.2935	0.0137	-0.0476	0.0912	0.0108	0.1305	-0.0426	0.0513	0.355	-0.1296	0.5054	-0.0353	-0.0523	0.504	-0.0819	0.5356	-60.4353	20.6525	24.7461
6	2.4546	-0.1872	0.0309	2.0987	-0.6787	2.1258	-0.1106	0.0221	-0.5964	0.0428	0.2033	-0.4798	0.5682	0.1217	-0.0501	0.6291	0.1023	-0.1689	0.5229	-0.1616	0.7478	-48.2121	6.1313	40.7995
7	1.9678	-1.3359	0.4107	1.2747	0.3285	2.418	-0.1712	0.4682	-0.5869	-0.3491	0.2922	0.3127	0.5323	-0.096	-0.153	0.6986	-0.0345	-0.1319	0.6797	-0.1015	0.8234	-62.7411	25.1965	58.9006
8	3.9562	1.9693	-1.5286	2.542	-1.2916	2.2025	0.1134	-0.2671	-0.3379	0.2774	-0.1218	-0.305	-0.1447	0.1645	0.046	0.5936	0.0173	-0.0964	0.5981	0.0281	0.7072	-76.031	31.6105	68.9359
9	3.1235	-0.4773	0.6777	2.7294	-0.1452	2.5562	0.1731	-0.0446	-0.3426	0.1554	-0.0879	0.1662	0.4423	0.161	-0.061	0.5702	0.0163	-0.1647	0.5908	-0.0236	0.6088	-48.0364	24.7128	72.8621
10	2.444	-0.0257	0.3849	1.4316	0.0791	1.5677	0.1356	-0.2963	0.061	0.3916	-0.0223	-0.0611	-0.0352	0.2113	-0.1111	0.6173	-0.0455	-0.0744	0.6819	-0.0413	0.615	-49.9927	38.7678	77.0585

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	chain 'A' and (resid 1 through 134 )
2	X-RAY DIFFRACTION	2	chain 'A' and (resid 135 through 332 )
3	X-RAY DIFFRACTION	3	chain 'B' and (resid 1 through 134 )
4	X-RAY DIFFRACTION	4	chain 'B' and (resid 135 through 332 )
5	X-RAY DIFFRACTION	5	chain 'C' and (resid 1 through 134 )
6	X-RAY DIFFRACTION	6	chain 'C' and (resid 135 through 332 )
7	X-RAY DIFFRACTION	7	chain 'D' and (resid 1 through 36 )
8	X-RAY DIFFRACTION	8	chain 'D' and (resid 37 through 134 )
9	X-RAY DIFFRACTION	9	chain 'D' and (resid 135 through 239 )
10	X-RAY DIFFRACTION	10	chain 'D' and (resid 240 through 332 )

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