PDB-5ha5: Crystal structure of an NAD-bound oxidoreductase from Brucella ovis

ID or keywords:

Entry

Database: PDB / ID: 5ha5

Title

Crystal structure of an NAD-bound oxidoreductase from Brucella ovis

Components

Brucella ovis oxidoreductase

Keywords

OXIDOREDUCTASE / SSGCID / short chain dehydrogenase/reductase family / Brucella ovis / NAD / Structural Genomics / Seattle Structural Genomics Center for Infectious Disease / PSI-2 / Protein Structure Initiative

Function / homology

Function and homology information

oxidoreductase activity / nucleotide binding
Similarity search - Function

Biological species

Brucella ovis IntaBari-2002-82-58 (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 1.95 Å

Authors

Seattle Structural Genomics Center for Infectious Disease (SSGCID)

Citation

Journal: to be published
Title: Crystal structure of an NAD-bound oxidoreductase from Brucella ovis
Authors: Mayclin, S.J. / Dranow, D.M. / Lorimer, D.D. / Edwards, T.E.

History

Deposition	Dec 30, 2015	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Feb 10, 2016	Provider: repository / Type: Initial release
Revision 1.1	Oct 11, 2017	Group: Data collection / Derived calculations / Category: pdbx_struct_oper_list / reflns_shell Item: _pdbx_struct_oper_list.symmetry_operation / _reflns_shell.percent_possible_all
Revision 1.2	Mar 6, 2024	Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2 Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	5ha5.cif.gz	373.9 KB	Display	PDBx/mmCIF format
PDB format	pdb5ha5.ent.gz	306.1 KB	Display	PDB format
PDBx/mmJSON format	5ha5.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/ha/5ha5 ftp://data.pdbj.org/pub/pdb/validation_reports/ha/5ha5	HTTPS FTP

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Related structure data

Similar structure data	4oyr-d 4d0s-d 4rf2-1 1nff-1 1nfq-d 4za2-d 5wuw-1 1nfr-d 4bqp-2 5t5q-d 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-BrovA.00010.a

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Links

PDB pages	PDBj / wwPDB / NCBI
Related items in Molecule of the Month	#188 - Aug 2015 Tetrahydrobiopterin Biosynthesis similarity (2) #216 - Dec 2017 Biodegradable Plastic similarity (2) #77 - May 2006 Glucose Oxidase similarity (2) #90 - Jun 2007 Fatty Acid Synthase similarity (2) #134 - Feb 2011 Integrin similarity (1) #172 - Apr 2014 RecA and Rad51 similarity (1) #194 - Feb 2016 Designer Insulins similarity (1) #234 - Jun 2019 MDM2 and Cancer similarity (1) #259 - Jul 2021 Designed Proteins and Citizen Science similarity (1)

PDB pages

PDBj /

wwPDB /

NCBI

Related items in Molecule of the Month

#188 - Aug 2015
Tetrahydrobiopterin Biosynthesis
similarity (2)
#216 - Dec 2017
Biodegradable Plastic
similarity (2)
#77 - May 2006
Glucose Oxidase
similarity (2)
#90 - Jun 2007
Fatty Acid Synthase
similarity (2)
#134 - Feb 2011
Integrin
similarity (1)
#172 - Apr 2014
RecA and Rad51
similarity (1)
#194 - Feb 2016
Designer Insulins
similarity (1)
#234 - Jun 2019
MDM2 and Cancer
similarity (1)
#259 - Jul 2021
Designed Proteins and Citizen Science
similarity (1)

Deposited unit

A: Brucella ovis oxidoreductase

B: Brucella ovis oxidoreductase

C: Brucella ovis oxidoreductase

D: Brucella ovis oxidoreductase

hetero molecules

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

1

Idetical with deposited unit
defined by author&software

Unit cell

Length a, b, c (Å)	52.500, 96.820, 101.900
Angle α, β, γ (deg.)	90.000, 100.750, 90.000
Int Tables number	4
Space group name H-M	P12₁1

#1: Protein	Brucella ovis oxidoreductase Mass: 25616.438 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Brucella ovis IntaBari-2002-82-58 (bacteria) Gene: H715_02246 / Plasmid: BrovA.00010.a.B1 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: N8N848
#2: Chemical	ChemComp-IMD / IMIDAZOLE Mass: 69.085 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C₃H₅N₂
#3: Chemical	ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL Mass: 62.068 Da / Num. of mol.: 15 / Source method: obtained synthetically / Formula: C₂H₆O₂
#4: Chemical	ChemComp-NAD / NICOTINAMIDE-ADENINE-DINUCLEOTIDE Mass: 663.425 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C₂₁H₂₇N₇O₁₄P₂ / Comment: NAD*YM
#5: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 711 / 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: 2.54 Å³/Da / Density % sol: 52 %
Crystal grow	Temperature: 290 K / Method: vapor diffusion, sitting drop Details: MORPHEUS H2: 10% PEG8000, 20%EG, 20mM each amino acid, 100mM MES/imidazole pH6.5, 5mM NADP; protein conc. 24.8mg/mL; direct cryo; puck yum7-6

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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: Dec 11, 2015

Radiation

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

Radiation wavelength

Wavelength: 0.97872 Å / Relative weight: 1

Reflection

Resolution: 1.9→50 Å / Num. obs: 78788 / % possible obs: 99.9 % / Observed criterion σ(I): -3 / B_iso Wilson estimate: 19.24 Å² / R_merge F obs: 0.998 / R_merge(I) obs: 0.07 / R_rim(I) all: 0.082 / Χ²: 0.983 / Net I/σ(I): 15.52 / Num. measured all: 296987

Reflection shell

Diffraction-ID: 1 / Rejects: _

Resolution (Å)	Highest resolution (Å)	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
1.9-1.95		0.828	0.48	2.72	21837	5816	5808	0.56	99.9
1.95-2		0.88	0.387	3.4	21352	5667	5671	0.451	100
2-2.06		0.914	0.321	4.11	20578	5471	5462	0.375	99.8
2.06-2.12		0.939	0.256	5.17	20362	5397	5389	0.299	99.9
2.12-2.19		0.96	0.202	6.57	19634	5195	5192	0.236	99.9
2.19-2.27		0.972	0.17	7.78	18975	5023	5014	0.198	99.8
2.27-2.36		0.978	0.146	9.02	18145	4796	4797	0.17	100
2.36-2.45		0.983	0.127	10.11	17724	4683	4677	0.149	99.9
2.45-2.56		0.988	0.106	12.11	16907	4469	4463	0.124	99.9
2.56-2.69		0.992	0.087	14.48	16316	4305	4300	0.102	99.9
2.69-2.83		0.994	0.073	16.97	15306	4043	4042	0.086	100
2.83-3		0.996	0.06	20.3	14656	3876	3872	0.07	99.9
3-3.21		0.997	0.05	23.78	13638	3599	3599	0.059	100
3.21-3.47		0.998	0.04	29.36	12803	3413	3409	0.047	99.9
3.47-3.8		0.998	0.033	35.47	11611	3120	3114	0.038	99.8
3.8-4.25		0.999	0.029	38.59	10510	2812	2812	0.034	100
4.25-4.91		0.999	0.025	42.1	9284	2496	2491	0.029	99.8
4.91-6.01		0.999	0.026	40.27	7929	2106	2105	0.03	100
6.01-8.5		0.999	0.022	42.17	6187	1656	1655	0.026	99.9
	8.5	0.999	0.017	50.2	3233	929	916	0.02	98.6

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Processing

Software

Name	Version	Classification
PHENIX		refinement
XSCALE		data scaling
PDB_EXTRACT	3.15	data extraction

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT / Resolution: 1.95→48.41 Å / SU ML: 0.16 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 17.64 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.19	2005	2.55 %	Random selection
R_work	0.1509	76752	-	-
obs	0.1519	78757	99.9 %	-

Solvent computation

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

Displacement parameters

B_iso max: 98.05 Å² / B_iso mean: 24.2788 Å² / B_iso min: 8.37 Å²

Refinement step

Cycle: final / Resolution: 1.95→48.41 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	6901	0	256	711	7868
B_iso mean	-	-	35.33	34.52	-
Num. residues	-	-	-	-	972

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.007	7312
X-RAY DIFFRACTION	f_angle_d	0.897	9942
X-RAY DIFFRACTION	f_chiral_restr	0.056	1197
X-RAY DIFFRACTION	f_plane_restr	0.005	1269
X-RAY DIFFRACTION	f_dihedral_angle_d	15.547	4293

LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 14 / % reflection obs: 100 %

Resolution (Å)	R_factor R_free	Num. reflection R_free	R_factor R_work	Num. reflection R_work	Num. reflection all
1.9-1.9475	0.2179	140	0.1948	5474	5614
1.9475-2.0002	0.2181	139	0.1792	5442	5581
2.0002-2.0591	0.2316	144	0.1753	5416	5560
2.0591-2.1255	0.2006	143	0.1644	5519	5662
2.1255-2.2015	0.2295	148	0.1572	5474	5622
2.2015-2.2896	0.2128	138	0.1535	5443	5581
2.2896-2.3938	0.1855	143	0.1517	5479	5622
2.3938-2.52	0.2122	148	0.1527	5451	5599
2.52-2.6779	0.1898	144	0.1499	5476	5620
2.6779-2.8847	0.2077	145	0.1545	5477	5622
2.8847-3.1749	0.1716	136	0.152	5493	5629
3.1749-3.6342	0.1899	147	0.1452	5504	5651
3.6342-4.5781	0.1624	142	0.1304	5514	5656
4.5781-48.4257	0.1667	148	0.1448	5590	5738

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	5.2756	0.9251	2.4641	5.0179	1.322	7.6447	0.0118	0.2029	-0.0037	-0.2016	-0.0074	0.1295	-0.1239	-0.0617	-0.0465	0.0735	0.0213	-0.0005	0.1065	0.0172	0.1468	-28.6976	16.3638	23.0168
2	2.8717	-0.2564	1.6255	3.23	0.1043	5.4644	-0.0868	0.1274	0.2578	-0.1601	0.0271	0.0653	-0.4315	0.0029	0.0368	0.135	-0.0024	-0.0157	0.1126	0.0158	0.1587	-26.6717	22.4871	24.917
3	2.1817	-1.2439	2.616	2.3631	-1.0996	3.2936	-0.0802	-0.1911	0.0237	0.1189	-0.0001	0.3061	-0.2091	-0.245	0.0863	0.1128	0.0441	0.0179	0.1567	-0.0369	0.1973	-33.51	18.523	34.5524
4	1.0286	-0.4926	0.4343	1.1581	-0.2632	1.1925	-0.0462	0.0672	0.0184	0.0506	0.0285	0.0504	-0.0894	-0.0092	0.0305	0.0688	-0.012	0.0197	0.1149	0.0116	0.1202	-20.4278	6.9614	35.0998
5	0.7643	-0.603	-0.0272	1.3213	-0.0436	2.0494	-0.0543	0.0029	0.2628	-0.0547	0.02	-0.0201	-0.1086	0.0583	0.0074	0.0782	-0.001	-0.0049	0.1021	0.0219	0.1382	-20.2617	4.5872	29.0966
6	2.8769	-0.0007	0.5088	1.4142	-0.0216	1.1869	0.0122	0.0051	0.242	-0.1003	-0.0174	-0.0805	-0.08	0.0696	0.0119	0.1083	-0.0146	0.0032	0.1233	0.0053	0.092	-13.6881	6.2864	19.3887
7	0.6166	-0.3979	0.2679	1.1061	-0.4018	1.0741	-0.0435	-0.0737	-0.0662	0.1608	0.0654	0.057	0.0127	-0.0243	-0.0129	0.1024	-0.0012	0.0181	0.1202	0.0142	0.1096	-11.0483	-11.0016	49.3391
8	0.3948	-0.2871	0.8968	2.3931	0.1672	2.3917	0.0754	-0.1961	-0.1159	0.0627	-0.0353	0.3284	0.2276	-0.3059	-0.0428	0.1136	-0.0084	0.0206	0.1466	0.0209	0.1552	-14.569	-20.4507	37.0343
9	0.6313	-0.2802	0.2691	1.0645	-0.0985	1.546	0.0541	0.1429	-0.05	-0.4016	-0.0244	0.155	0.0778	-0.0917	-0.0302	0.2681	-0.0164	-0.0532	0.1825	-0.0167	0.1412	-19.7234	-8.5037	-1.148
10	1.2347	-0.565	-0.117	2.7919	-0.1429	3.1195	0.0955	0.0552	-0.0941	-0.2365	-0.0696	0.3672	0.1635	-0.255	-0.027	0.1539	0.0078	-0.034	0.1529	-0.0104	0.1229	-16.972	-9.5475	11.4969
11	2.0324	0.2001	0.1935	1.2097	-0.3587	2.0754	-0.0358	0.1231	-0.0451	-0.2101	0.1085	0.2871	0.159	-0.2067	-0.0573	0.1304	-0.0063	-0.0405	0.1108	-0.0106	0.1403	-25.9958	-3.4508	15.1426
12	6.6553	1.8249	-3.2053	5.8952	-1.5515	2.4112	-0.0198	-0.256	-0.2841	0.1537	-0.0901	-0.2797	0.3475	0.3627	0.1596	0.2457	0.0868	-0.0032	0.1565	-0.01	0.1965	1.405	-35.194	28.2736
13	2.0343	-0.932	-0.2951	1.7724	0.2571	0.723	-0.0428	0.0058	-0.1765	-0.2679	0.0468	-0.2899	0.5678	0.4081	-0.0112	0.3185	0.1166	0.0704	0.2263	-0.0061	0.2357	7.0893	-36.2041	21.5605
14	0.8055	-0.2256	0.2167	1.6918	-0.0839	0.9963	0.0419	0.1086	-0.1209	-0.1954	-0.0187	-0.0968	0.2709	0.1465	-0.0189	0.2347	0.0259	0.0184	0.1586	-0.0248	0.1313	-4.3512	-27.0418	13.9901
15	6.3592	4.6941	-4.3797	4.7158	-4.1337	4.1277	-0.0458	0.1334	-0.0145	-0.2257	0.1381	0.1942	0.2936	-0.0814	-0.1114	0.1783	-0.0011	-0.0251	0.0991	-0.0334	0.1216	-12.4092	-22.7045	18.2745
16	1.1706	-0.7821	0.6138	1.8422	0.6164	2.9229	-0.2061	0.2447	-0.3895	-0.3326	0.0268	-1.1821	0.2402	0.6178	0.211	0.2072	0.0377	0.0399	0.2704	0.0357	0.3583	0.631	-19.9782	22.6374
17	1.649	0.1513	0.7873	3.0465	0.3717	0.9833	0.0029	0.0974	-0.0474	-0.0897	-0.0182	-0.3299	0.0847	0.2441	0.0223	0.1034	0.0236	0.0255	0.16	0.0091	0.1114	-0.5966	-16.4124	29.7658

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details	Auth asym-ID
1	X-RAY DIFFRACTION	1	chain 'A' and (resid 9 through 24 )	A
2	X-RAY DIFFRACTION	2	chain 'A' and (resid 25 through 60 )	A
3	X-RAY DIFFRACTION	3	chain 'A' and (resid 61 through 89 )	A
4	X-RAY DIFFRACTION	4	chain 'A' and (resid 90 through 160 )	A
5	X-RAY DIFFRACTION	5	chain 'A' and (resid 161 through 205 )	A
6	X-RAY DIFFRACTION	6	chain 'A' and (resid 206 through 258 )	A
7	X-RAY DIFFRACTION	7	chain 'B' and (resid 9 through 184 )	B
8	X-RAY DIFFRACTION	8	chain 'B' and (resid 185 through 258 )	B
9	X-RAY DIFFRACTION	9	chain 'C' and (resid 9 through 160 )	C
10	X-RAY DIFFRACTION	10	chain 'C' and (resid 161 through 215 )	C
11	X-RAY DIFFRACTION	11	chain 'C' and (resid 216 through 258 )	C
12	X-RAY DIFFRACTION	12	chain 'D' and (resid 9 through 24 )	D
13	X-RAY DIFFRACTION	13	chain 'D' and (resid 25 through 74 )	D
14	X-RAY DIFFRACTION	14	chain 'D' and (resid 75 through 160 )	D
15	X-RAY DIFFRACTION	15	chain 'D' and (resid 161 through 184 )	D
16	X-RAY DIFFRACTION	16	chain 'D' and (resid 185 through 211 )	D
17	X-RAY DIFFRACTION	17	chain 'D' and (resid 212 through 258 )	D

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