PDB-8hty: Candida boidinii Formate Dehydrogenase Crystal Structure at 1.4 A...

ID or keywords:

Entry

Database: PDB / ID: 8hty

Title

Candida boidinii Formate Dehydrogenase Crystal Structure at 1.4 Angstrom Resolution

Components

Formate dehydrogenase

Keywords

OXIDOREDUCTASE / formate dehydrogenase / Candida boidinii

Function / homology

Function and homology information

formate catabolic process / formate dehydrogenase / formate dehydrogenase (NAD+) activity / oxidoreductase activity, acting on the CH-OH group of donors, NAD or NADP as acceptor / NAD binding / mitochondrion / cytosol
Similarity search - Function

Biological species

[Candida] boidinii (fungus)

Method

X-RAY DIFFRACTION /

MOLECULAR REPLACEMENT / Resolution: 1.4 Å

Authors

Gul, M. / Yuksel, B. / Bulut, H. / DeMirci, H.

Funding support

1items

Citation

Journal: Acta Crystallogr D Struct Biol / Year: 2023
Title: Structural analysis of wild-type and Val120Thr mutant Candida boidinii formate dehydrogenase by X-ray crystallography.
Authors: Gul, M. / Yuksel, B. / Bulut, H. / DeMirci, H.

History

Deposition	Dec 22, 2022	Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0	Jan 18, 2023	Provider: repository / Type: Initial release
Revision 1.1	Nov 8, 2023	Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / citation Item: _citation.journal_abbrev / _citation.journal_id_CSD ..._citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year

Structure viewer	Molecule: MolmilJmol/JSmol

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PDBx/mmCIF format	8hty.cif.gz	837.6 KB	Display	PDBx/mmCIF format
PDB format	pdb8hty.ent.gz	704.7 KB	Display	PDB format
PDBx/mmJSON format	8hty.json.gz		Tree view	PDBx/mmJSON format
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Validation report

Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/ht/8hty ftp://data.pdbj.org/pub/pdb/validation_reports/ht/8hty	HTTPS FTP

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Related structure data

Related structure data	8iq7C 8ivjC 5dnaS S: Starting model for refinement C: citing same article (ref.)
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

Deposited unit

A: Formate dehydrogenase

B: Formate dehydrogenase

C: Formate dehydrogenase

D: Formate dehydrogenase

hetero molecules

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

1

A: Formate dehydrogenase

B: Formate dehydrogenase

hetero molecules

defined by author&software
Evidence: native gel electrophoresis
81.7 kDa, 2 polymers
Search similar-shape structures of this assembly by Omokage search (details)

2

C: Formate dehydrogenase

D: Formate dehydrogenase

hetero molecules

defined by author&software
81.1 kDa, 2 polymers
Search similar-shape structures of this assembly by Omokage search (details)

Unit cell

Length a, b, c (Å)	54.132, 68.959, 109.792
Angle α, β, γ (deg.)	78.14, 89.48, 81.11
Int Tables number	1
Space group name H-M	P1

#1: Protein	Formate dehydrogenase Mass: 40364.969 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) [Candida] boidinii (fungus) / Gene: FDH / Production host: Escherichia coli BL21 (bacteria) / References: UniProt: A0A0A1EQY0
#2: Chemical	ChemComp-SO4 / SULFATE ION Mass: 96.063 Da / Num. of mol.: 14 / Source method: obtained synthetically / Formula: SO₄
#3: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 2179 / Source method: isolated from a natural source / Formula: H₂O
Has ligand of interest	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: 2.45 Å³/Da / Density % sol: 49.87 %
Crystal grow	Temperature: 277 K / Method: vapor diffusion, sitting drop / pH: 6.5 Details: 30% (w/v) PEG 5000 MME, 100 mM MES/Sodium hydroxide pH 6.5, 200 mM Ammonium sulfate

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Data collection

Diffraction	Mean temperature: 100 K / Serial crystal experiment: N
Diffraction source	Source: ROTATING ANODE / Type: RIGAKU PhotonJet-R / Wavelength: 1.54 Å
Detector	Type: RIGAKU HyPix-3000 / Detector: PIXEL / Date: Mar 31, 2022
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 1.54 Å / Relative weight: 1
Reflection	Resolution: 1.39→24.75 Å / Num. obs: 301717 / % possible obs: 98.82 % / Redundancy: 151.46 % / CC_1/2: 0.999 / CC star: 1 / Net I/σ(I): 11.74
Reflection shell	Resolution: 1.39→1.51 Å / Num. unique obs: 18691 / CC_1/2: 0.34 / CC star: 0.708 / % possible all: 86

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Processing

Software

Name	Version	Classification
PHENIX	1.20.1	refinement
PHASER	2.8.3	phasing
CrysalisPro	1.171.42.35a	data reduction
CrysalisPro	1.171.42.35a	data scaling

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: 5DNA

5dna

Resolution: 1.4→21.83 Å / SU ML: 0.18 / Cross valid method: FREE R-VALUE / σ(F): 1.96 / Phase error: 23.65 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection
R_free	0.1904	1992	-
R_work	0.1674	-	-
obs	0.1675	300000	98.82 %

Solvent computation

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

Refinement step

Cycle: LAST / Resolution: 1.4→21.83 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	11069	0	70	2179	13318

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.015
X-RAY DIFFRACTION	f_angle_d	1.422
X-RAY DIFFRACTION	f_dihedral_angle_d	6.228	1545
X-RAY DIFFRACTION	f_chiral_restr	0.099	1737
X-RAY DIFFRACTION	f_plane_restr	0.014	1992

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 (%)
1.4-1.43	0.3728	126		18691	X-RAY DIFFRACTION	86
1.43-1.47	0.3471	143	0.3424		X-RAY DIFFRACTION	99
1.47-1.51	0.3556	142	0.3002		X-RAY DIFFRACTION	99
1.51-1.56	0.2948	143	0.2595		X-RAY DIFFRACTION	100
1.56-1.62	0.2546	144	0.2242		X-RAY DIFFRACTION	100
1.62-1.68	0.2419	145	0.2056		X-RAY DIFFRACTION	100
1.68-1.76	0.2285	143	0.1844		X-RAY DIFFRACTION	100
1.76-1.85	0.1894	143	0.1701		X-RAY DIFFRACTION	100
1.85-1.97	0.1959	144	0.1719		X-RAY DIFFRACTION	100
1.97-2.12	0.181	145	0.1475		X-RAY DIFFRACTION	100
2.12-2.33	0.1653	143	0.1441		X-RAY DIFFRACTION	100
2.33-2.67	0.1524	144	0.1419		X-RAY DIFFRACTION	100
2.67-3.36	0.1722	144	0.1486		X-RAY DIFFRACTION	100
3.36-10	0.1624	143	0.1415		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	1.3923	-1.0971	0.0019	2.1949	0.1906	1.4155	0.0011	0.0441	-0.0214	-0.06	-0.0315	0.1021	-0.0404	-0.0793	0.0304	0.1546	-0.0018	-0.0074	0.1348	0.0044	0.1154	9.2348	-15.1847	-6.1486
2	0.3961	-0.093	-0.3282	0.8449	0.7279	2.2311	0.0148	-0.037	0.0192	0.0867	-0.0624	0.1101	0.1101	-0.1491	0.0407	0.1532	0.0057	0.0005	0.1221	-0.0041	0.1328	8.1204	-13.6257	23.4616
3	1.0139	0.0574	0.2373	1.9116	0.4693	1.8302	0.0234	-0.0122	-0.1465	0.0934	0.0106	-0.1161	0.4473	0.1495	-0.0291	0.2599	0.0641	-0.0094	0.1301	0.002	0.109	20.5175	-25.7379	25.7465
4	0.8916	0.1292	-0.9984	0.6425	0.0242	2.1266	-0.0134	0.0231	-0.0379	0.0291	-0.0335	0.041	0.1758	-0.1292	0.0513	0.167	-0.003	-0.037	0.1269	-0.0041	0.125	11.5309	-19.5693	11.0996
5	1.9828	1.1381	0.5521	3.1482	0.8303	4.2073	0.0894	-0.0809	-0.1006	0.1749	-0.1448	0.2098	0.4731	-0.4528	0.046	0.2315	-0.0444	0.0245	0.2427	-0.0128	0.164	3.4006	-10.3708	59.2526
6	0.2773	-0.0331	0.1567	0.5082	0.4835	2.4556	-0.003	-0.083	0.0327	0.0774	-0.0184	0.0743	-0.0675	-0.1506	0.036	0.132	0.0197	0.0113	0.1154	-0.0112	0.1217	8.0625	-2.5606	42.4999
7	1.263	-0.1313	-0.1959	1.2767	0.4447	1.3854	0.0012	-0.102	0.1977	0.0243	-0.0298	0.0291	-0.2407	-0.0512	0.0304	0.1942	0.0167	-0.01	0.1258	-0.021	0.1306	12.3226	4.7804	30.5701
8	1.4207	0.2892	0.267	1.49	0.8029	3.5185	0.0393	-0.0292	-0.0675	0.0594	0.0688	-0.1871	0.2807	0.3556	-0.1045	0.1977	0.0568	-0	0.2123	0.0039	0.1199	19.0958	-6.6346	58.3367
9	2.1991	-0.3074	0.0849	1.7795	0.3055	2.1838	0.0538	-0.0984	-0.0816	0.0038	-0.0134	0.176	0.205	-0.2631	-0.0466	0.175	-0.0157	-0.0192	0.1815	-0.0052	0.124	-20.0601	-2.7058	-57.5191
10	0.4162	-0.2265	0.2179	0.7888	0.5303	0.671	-0.008	0.0191	-0.0436	-0.0184	0.0491	-0.0418	-0.0351	0.084	-0.0416	0.0997	0.0029	0.0107	0.1138	0.0019	0.1414	-8.6336	8.4083	-31.0295
11	2.7819	-0.7079	-1.1434	2.7547	-0.0311	2.9791	0.055	0.3955	0.2576	-0.6601	0.179	-0.5826	-0.2822	0.4338	-0.118	0.2406	-0.1183	0.1353	0.3012	-0.0197	0.3623	6.2856	17.2844	-38.0631
12	1.2547	-0.4416	0.1096	1.838	0.5908	2.0574	0.0361	0.062	-0.0111	-0.1451	0.0689	-0.3136	0.0968	0.3206	-0.0872	0.111	0.0218	0.0281	0.1381	-0.0198	0.1559	2.0437	-0.5744	-33.3069
13	0.5094	-0.2438	0.2938	0.5513	-0.272	3.2296	0.0077	0.08	-0.024	-0.1031	-0.0056	0.0022	-0.0939	-0.014	0.0156	0.146	-0.0111	0.0022	0.1211	-0.0228	0.1562	-12.6548	4.529	-48.2478
14	0.8298	-0.8325	0.1225	2.3488	0.0655	1.4984	-0.1692	-0.1824	-0.0654	0.6533	0.2127	-0.055	0.2772	0.091	-0.0449	0.3669	0.0643	-0.0318	0.1679	-0.0018	0.1374	-9.533	16.0963	5.6135
15	0.4571	-0.2419	0.0733	0.7164	0.2725	1.3783	-0.0084	-0.0014	-0.0356	0.035	0.011	0.0077	-0.0527	-0.0604	0.0004	0.0647	0.0054	0.0127	0.0776	0.0065	0.0939	-15.7752	14.7451	-24.7082
16	3.2614	-1.5752	-2.3495	2.3995	2.0552	4.1713	0.1078	-0.05	0.3618	-0.1245	-0.0404	-0.2536	-0.5167	0.0438	-0.111	0.2604	0.0226	-0.0057	0.1163	0.0369	0.1767	-16.9186	33.026	-27.4162
17	0.9403	-0.2602	0.0073	1.5362	0.2666	1.2414	-0.0584	-0.062	-0.0466	0.1319	0.0182	0.2402	-0.1099	-0.2355	0.0397	0.1271	0.0251	0.0301	0.1475	0.0047	0.1381	-27.4422	16.8591	-20.2224
18	1.0412	0.1202	-0.2782	2.6381	2.0607	3.8199	0.0359	-0.0682	0.1694	0.3372	0.1941	-0.5133	-0.0891	0.1938	-0.2286	0.1973	0.0143	-0.0569	0.1412	-0.0104	0.1858	-3.0527	27.4392	-1.1906

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	chain 'A' and (resid 1 through 106 )
2	X-RAY DIFFRACTION	2	chain 'A' and (resid 107 through 158 )
3	X-RAY DIFFRACTION	3	chain 'A' and (resid 159 through 255 )
4	X-RAY DIFFRACTION	4	chain 'A' and (resid 256 through 356 )
5	X-RAY DIFFRACTION	5	chain 'B' and (resid 1 through 75 )
6	X-RAY DIFFRACTION	6	chain 'B' and (resid 76 through 158 )
7	X-RAY DIFFRACTION	7	chain 'B' and (resid 159 through 316 )
8	X-RAY DIFFRACTION	8	chain 'B' and (resid 317 through 353 )
9	X-RAY DIFFRACTION	9	chain 'C' and (resid 1 through 106 )
10	X-RAY DIFFRACTION	10	chain 'C' and (resid 107 through 186 )
11	X-RAY DIFFRACTION	11	chain 'C' and (resid 187 through 207 )
12	X-RAY DIFFRACTION	12	chain 'C' and (resid 208 through 291 )
13	X-RAY DIFFRACTION	13	chain 'C' and (resid 292 through 354 )
14	X-RAY DIFFRACTION	14	chain 'D' and (resid 1 through 106 )
15	X-RAY DIFFRACTION	15	chain 'D' and (resid 107 through 186 )
16	X-RAY DIFFRACTION	16	chain 'D' and (resid 187 through 207 )
17	X-RAY DIFFRACTION	17	chain 'D' and (resid 208 through 316 )
18	X-RAY DIFFRACTION	18	chain 'D' and (resid 317 through 356 )

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