PDB-4tqt: Crystal structure of Dihydropyrimidinase from Brucella suis

ID or keywords:

Entry

Database: PDB / ID: 4tqt

Title

Crystal structure of Dihydropyrimidinase from Brucella suis

Components

D-hydantoinase

Keywords

HYDROLASE / SSGCID /

Dihydropyrimidinase /

Structural Genomics / Seattle Structural Genomics Center for Infectious Disease

Function / homology

Function and homology information

dihydropyrimidinase /

dihydropyrimidinase activity /

metal ion binding /

cytoplasm
Similarity search - Function

Biological species

Brucella suis (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT /

molecular replacement / Resolution: 2.15 Å

Authors

Seattle Structural Genomics Center for Infectious Disease (SSGCID)

Citation

Journal: to be published
Title: Crystal structure of Dihydropyrimidinase from Brucella suis
Authors: Seattle Structural Genomics Center for Infectious Disease (SSGCID) / Abendroth, J. / Davies, D.R. / Lorimer, D. / Edwards, T.E.

History

Deposition	Jun 12, 2014	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Aug 6, 2014	Provider: repository / Type: Initial release
Revision 1.1	Nov 22, 2017	Group: Database references / Derived calculations ...Database references / Derived calculations / Other / Refinement description / Source and taxonomy Category: citation / entity_src_gen ...citation / entity_src_gen / pdbx_database_status / pdbx_struct_oper_list / software Item: _citation.journal_id_CSD / _entity_src_gen.pdbx_alt_source_flag ..._citation.journal_id_CSD / _entity_src_gen.pdbx_alt_source_flag / _pdbx_database_status.pdb_format_compatible / _pdbx_struct_oper_list.symmetry_operation
Revision 1.2	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 / refine_hist / struct_conn / struct_conn_type Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _refine_hist.number_atoms_total / _refine_hist.pdbx_number_atoms_nucleic_acid / _refine_hist.pdbx_number_atoms_protein / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_conn_type.id
Revision 1.3	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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Download

PDBx/mmCIF format	4tqt.cif.gz	1.1 MB	Display	PDBx/mmCIF format
PDB format	pdb4tqt.ent.gz	926.6 KB	Display	PDB format
PDBx/mmJSON format	4tqt.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/tq/4tqt ftp://data.pdbj.org/pub/pdb/validation_reports/tq/4tqt	HTTPS FTP

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Related structure data

Related structure data	3dc8S S: Starting model for refinement
Similar structure data	3dc8-1 5mkv-d 4b3z-d 4cns-d 2vm8-d 4lcs-1 4lcq-1 2vr2-1 2gse-d 4cnu-2 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.01123.b

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Links

PDB pages	PDBj / wwPDB / NCBI
Related items in Molecule of the Month	#215 - Nov 2017 Aspartate Transcarbamoylase similarity (4) #158 - Feb 2013 Proton-Gated Urea Channel similarity (4)

Deposited unit

A: D-hydantoinase

B: D-hydantoinase

C: D-hydantoinase

D: D-hydantoinase

E: D-hydantoinase

F: D-hydantoinase

hetero molecules

331 kDa, 6 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

A: D-hydantoinase

B: D-hydantoinase

C: D-hydantoinase

D: D-hydantoinase

hetero molecules

defined by author&software
221 kDa, 4 polymers
Search similar-shape structures of this assembly by Omokage search (details)

2

E: D-hydantoinase

F: D-hydantoinase

hetero molecules

E: D-hydantoinase

F: D-hydantoinase

hetero molecules

defined by author&software
221 kDa, 4 polymers
Search similar-shape structures of this assembly by Omokage search (details)

Unit cell

Length a, b, c (Å)	156.690, 88.830, 221.240
Angle α, β, γ (deg.)	90.000, 91.170, 90.000
Int Tables number	5
Space group name H-M	C121

Components on special symmetry positions

ID	Model	Components
1	1	B-610- HOH
2	1	E-621- HOH
3	1	F-616- HOH
4	1	F-617- HOH

Noncrystallographic symmetry (NCS)

NCS domain:

ID	Ens-ID	Details
1	1	chain A and segid
2	1	chain B and segid
3	1	chain C and segid
4	1	chain D and segid
5	1	chain E and segid
6	1	chain F and segid

NCS domain segments:

Dom-ID	Component-ID	Ens-ID	Selection details	Auth asym-ID
1	1	1	chain A and segid	A
2	1	1	chain B and segid	B
3	1	1	chain C and segid	C
4	1	1	chain D and segid	D
5	1	1	chain E and segid	E
6	1	1	chain F and segid	F

Details

biological unit is a tetramer: chains A, B, C, D; a second tetramer is generated by chains E and F with symmetry mates -x+1, y, -z+1

#1: Protein	D-hydantoinase / Phenylhydantoinase Mass: 54750.781 Da / Num. of mol.: 6 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Brucella suis (bacteria) / Strain: 1330 / Gene: dhT, BR0278, BS1330_I0279 / Plasmid: BrsuA.01123.b.B1 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) References: UniProt: Q8G2P0, UniProt: A0A0H3G9X2*PLUS, dihydropyrimidinase
#2: Chemical	ChemComp-ZN / ZINC ION Mass: 65.409 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: Zn
#3: Chemical	... ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol Mass: 62.068 Da / Num. of mol.: 24 / Source method: obtained synthetically / Formula: C₂H₆O₂
#4: Water	ChemComp-HOH / water / Water Mass: 18.015 Da / Num. of mol.: 1238 / 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: 2.35 Å³/Da / Density % sol: 47.7 %
Crystal grow	Temperature: 290 K / Method: vapor diffusion, sitting drop / pH: 6.5 Details: Microlytics MCSG 1 screen, B6: 20% PEG 8000, 100mM MES pH 6.5, 200mM CaOAc2; cryo: 25% EG; BrsuA.01123.b.B1.PS01876 at 19.16mg/ml, tray 247701b6, puck dbd6-4

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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: RAYONIX MX-225 / Detector: CCD / Date: Jan 29, 2014

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: 2.15→50 Å / Num. obs: 165022 / % possible obs: 99.9 % / Observed criterion σ(I): -3 / Redundancy: 4.65 % / B_iso Wilson estimate: 32.15 Å² / R_merge F obs: 0.999 / R_merge(I) obs: 0.065 / R_rim(I) all: 0.073 / Χ²: 0.999 / Net I/σ(I): 16.38 / Num. measured all: 767858

Reflection shell

Diffraction-ID: 1 / Rejects: 0

Resolution (Å)	Highest resolution (Å)	Redundancy (%)	R_merge F obs	R_merge(I) obs	Mean I/σ(I) obs	Num. measured obs	Num. possible	Num. unique obs	R_rim(I) all	% possible all
2.15-2.21		4.68	0.874	0.541	2.99	57015	12175	12172	0.61	100
2.21-2.27			0.92	0.416	3.89	55389	11819	11819	0.469	100
2.27-2.33			0.932	0.359	4.4	53964	11501	11497	0.404	100
2.33-2.4			0.954	0.281	5.49	52731	11224	11221	0.317	100
2.4-2.48			0.972	0.234	6.49	50752	10825	10819	0.263	99.9
2.48-2.57			0.977	0.194	7.77	49535	10550	10550	0.218	100
2.57-2.67			0.984	0.16	9.22	47673	10133	10132	0.18	100
2.67-2.78			0.989	0.129	11.28	45870	9740	9738	0.145	100
2.78-2.9			0.993	0.106	13.14	43923	9389	9384	0.12	99.9
2.9-3.04			0.995	0.086	16.06	41980	8954	8953	0.097	100
3.04-3.21			0.996	0.07	19.16	39994	8553	8549	0.079	100
3.21-3.4			0.997	0.055	23.62	37447	8048	8045	0.062	100
3.4-3.63			0.998	0.045	28.48	34963	7583	7579	0.051	99.9
3.63-3.93			0.998	0.038	33.23	32537	7111	7110	0.043	100
3.93-4.3			0.999	0.035	36.36	29607	6517	6511	0.039	99.9
4.3-4.81			0.999	0.031	39.53	26838	5910	5904	0.035	99.9
4.81-5.55			0.999	0.031	38.57	23903	5246	5243	0.035	99.9
5.55-6.8			0.999	0.029	38.63	20166	4435	4433	0.033	100
6.8-9.62			0.999	0.023	43.55	15447	3449	3449	0.026	100
	9.62		0.999	0.02	45.06	8124	1968	1914	0.023	97.3

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Phasing

Phasing

Method:

molecular replacement

Phasing MR

Model details: Phaser MODE: MR_AUTO

	Highest resolution	Lowest resolution
Rotation	5.83 Å	45.02 Å
Translation	5.83 Å	45.02 Å

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Processing

Software

Name	Version	Classification
XDS		data reduction
XSCALE		data scaling
PHASER		phasing
ARP		model building
PHENIX	(phenix.refine: dev_1702)	refinement
PDB_EXTRACT		data extraction

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: 3dc8

3dc8

Resolution: 2.15→44.239 Å / SU ML: 0.2 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 18.68 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.1818	8375	5.08 %	Random selection
R_work	0.1347	156605	-	-
obs	0.1372	164980	99.93 %	-

Solvent computation

Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL

Displacement parameters

B_iso max: 107.57 Å² / B_iso mean: 38.8919 Å² / B_iso min: 16.52 Å²

Refinement step

Cycle: final / Resolution: 2.15→44.239 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	21830	0	108	1238	23176
B_iso mean	-	-	45	40.43	-
Num. residues	-	-	-	-	2869

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.007	22482
X-RAY DIFFRACTION	f_angle_d	1.041	30473
X-RAY DIFFRACTION	f_chiral_restr	0.044	3336
X-RAY DIFFRACTION	f_plane_restr	0.005	4050
X-RAY DIFFRACTION	f_dihedral_angle_d	12.37	8174

Refine LS restraints NCS

Ens-ID	Dom-ID	Auth asym-ID	Number	Refine-ID	Rms	Type
1	1	A	13299	X-RAY DIFFRACTION	3.298	TORSIONAL
1	2	B	13299	X-RAY DIFFRACTION	3.298	TORSIONAL
1	3	C	13299	X-RAY DIFFRACTION	3.298	TORSIONAL
1	4	D	13299	X-RAY DIFFRACTION	3.298	TORSIONAL
1	5	E	13299	X-RAY DIFFRACTION	3.298	TORSIONAL
1	6	F	13299	X-RAY DIFFRACTION	3.298	TORSIONAL

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 (%)
2.15-2.1744	0.2488	259	0.1973	5183	X-RAY DIFFRACTION	100
2.1744-2.2	0.229	278	0.1867	5201	X-RAY DIFFRACTION	100
2.2-2.2269	0.2377	263	0.1759	5180	X-RAY DIFFRACTION	100
2.2269-2.255	0.2234	295	0.1729	5211	X-RAY DIFFRACTION	100
2.255-2.2847	0.25	276	0.1754	5176	X-RAY DIFFRACTION	100
2.2847-2.316	0.218	259	0.1731	5240	X-RAY DIFFRACTION	100
2.316-2.3491	0.218	312	0.1588	5144	X-RAY DIFFRACTION	100
2.3491-2.3842	0.2063	316	0.1519	5161	X-RAY DIFFRACTION	100
2.3842-2.4214	0.2261	289	0.1535	5212	X-RAY DIFFRACTION	100
2.4214-2.4611	0.2236	286	0.1526	5147	X-RAY DIFFRACTION	100
2.4611-2.5035	0.2231	269	0.1479	5245	X-RAY DIFFRACTION	100
2.5035-2.5491	0.2343	286	0.1466	5162	X-RAY DIFFRACTION	100
2.5491-2.5981	0.2161	268	0.1471	5193	X-RAY DIFFRACTION	100
2.5981-2.6511	0.2185	234	0.1553	5321	X-RAY DIFFRACTION	100
2.6511-2.7087	0.2197	266	0.1479	5192	X-RAY DIFFRACTION	100
2.7087-2.7717	0.2124	271	0.1437	5201	X-RAY DIFFRACTION	100
2.7717-2.841	0.2066	233	0.1448	5243	X-RAY DIFFRACTION	100
2.841-2.9178	0.2024	281	0.1445	5266	X-RAY DIFFRACTION	100
2.9178-3.0037	0.1926	300	0.1431	5180	X-RAY DIFFRACTION	100
3.0037-3.1006	0.2064	277	0.1511	5209	X-RAY DIFFRACTION	100
3.1006-3.2114	0.2077	272	0.1495	5234	X-RAY DIFFRACTION	100
3.2114-3.3399	0.1885	309	0.1477	5200	X-RAY DIFFRACTION	100
3.3399-3.4919	0.196	309	0.1434	5166	X-RAY DIFFRACTION	100
3.4919-3.6759	0.1693	318	0.1326	5212	X-RAY DIFFRACTION	100
3.6759-3.9061	0.1451	299	0.1182	5225	X-RAY DIFFRACTION	100
3.9061-4.2075	0.144	275	0.1134	5235	X-RAY DIFFRACTION	100
4.2075-4.6305	0.1299	252	0.0984	5287	X-RAY DIFFRACTION	100
4.6305-5.2995	0.1495	273	0.1073	5300	X-RAY DIFFRACTION	100
5.2995-6.6732	0.1618	285	0.1219	5275	X-RAY DIFFRACTION	100
6.6732-50	0.1398	265	0.1161	5404	X-RAY DIFFRACTION	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	0.812	0.0359	0.1205	0.8852	0.2684	1.1541	-0.0553	0.1106	-0.2657	0.2015	0.0681	0.0441	0.4407	0.1103	0.0033	0.359	0.0644	0.0282	0.2565	-0.0865	0.3064	33.4086	-9.6944	26.694
2	0.6293	-0.0234	0.1207	0.6044	0.151	1.418	-0.1118	0.2202	0.0903	-0.0412	-0.0004	0.095	-0.1392	-0.1474	0.1059	0.1624	0.0122	-0.0383	0.321	-0.0115	0.2495	17.9234	21.9195	13.9657
3	0.8134	0.0894	0.1877	0.9021	0.3301	1.068	-0.1098	0.0913	0.0956	0.175	0.1489	-0.1995	-0.0756	0.4034	-0.0256	0.2734	0.0427	-0.0827	0.3836	-0.0717	0.2772	56.2738	24.8724	48.358
4	0.595	0.087	0.0033	0.564	0.2311	1.277	-0.0827	-0.113	0.0865	0.2255	-0.0229	0.1241	-0.0434	-0.1746	0.0942	0.3403	0.0996	0.0158	0.2504	-0.0675	0.2752	20.8225	27.3664	60.0682
5	0.5997	0.0574	-0.2335	0.8346	-0.0589	1.5859	-0.0373	0.1065	-0.2075	-0.2192	-0.0742	-0.0722	0.1384	0.0009	0.1005	0.2486	0.034	0.0466	0.2019	-0.0628	0.3085	81.1537	15.2207	87.857
6	0.7544	0.1233	-0.3582	0.9082	-0.0019	1.2615	0.1204	-0.0728	0.0896	-0.0158	-0.1087	-0.2645	-0.5261	0.3785	-0.002	0.4392	-0.1434	0.0242	0.3126	0.0126	0.3221	97.1207	45.9093	101.6485

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details	Auth asym-ID	Auth seq-ID
1	X-RAY DIFFRACTION	1	chain 'A'	A	6 - 503
2	X-RAY DIFFRACTION	2	chain 'B'	B	6 - 503
3	X-RAY DIFFRACTION	3	chain 'C'	C	6 - 503
4	X-RAY DIFFRACTION	4	chain 'D'	D	6 - 503
5	X-RAY DIFFRACTION	5	chain 'E'	E	6 - 503
6	X-RAY DIFFRACTION	6	chain 'F'	F	6 - 503

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