PDB-6t92: NAD+-dependent fungal formate dehydrogenase from Chaetomium therm...

ID or keywords:

Entry

Database: PDB / ID: 6t92

Title

NAD+-dependent fungal formate dehydrogenase from Chaetomium thermophilum: A complex of N120C mutant protein with the reduced form of the cofactor NADH and the substrate formate at a secondary site.

Components

Formate dehydrogenase

Keywords

CYTOSOLIC PROTEIN /

NAD+

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 /

cytoplasm
Similarity search - Function

Biological species

Chaetomium thermophilum (fungus)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 1.12 Å

Authors

Isupov, M.N. / Yelmazer, B. / De Rose, S.A. / Littlechild, J.A.

Citation

Journal: J.Struct.Biol. / Year: 2020
Title: Structural insights into the NAD + -dependent formate dehydrogenase mechanism revealed from the NADH complex and the formate NAD + ternary complex of the Chaetomium thermophilum enzyme.
Authors: Yilmazer, B. / Isupov, M.N. / De Rose, S.A. / Bulut, H. / Benninghoff, J.C. / Binay, B. / Littlechild, J.A.

History

Deposition	Oct 25, 2019	Deposition site: PDBE / Processing site: PDBE
Revision 1.0	Nov 18, 2020	Provider: repository / Type: Initial release
Revision 1.1	Jun 2, 2021	Group: Database references / Category: citation / citation_author Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _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 / _citation_author.name
Revision 1.2	Jan 24, 2024	Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description Category: atom_type / chem_comp_atom ...atom_type / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model Item: _atom_type.pdbx_N_electrons / _atom_type.pdbx_scat_Z ..._atom_type.pdbx_N_electrons / _atom_type.pdbx_scat_Z / _database_2.pdbx_DOI / _database_2.pdbx_database_accession

Structure viewer	Molecule: MolmilJmol/JSmol

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PDBx/mmCIF format	6t92.cif.gz	616.6 KB	Display	PDBx/mmCIF format
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Validation report

Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/t9/6t92 ftp://data.pdbj.org/pub/pdb/validation_reports/t9/6t92	HTTPS FTP

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Related structure data

Related structure data	6t8yC 6t8zC 6t94C 5dnaS S: Starting model for refinement C: citing same article (ref.)
Similar structure data	6t8y-2 6t94-1 4gmg-2 6t8y-1 4r5m-d 5kvq-d 6bfq-2 6t8z-2 6i5z-1 5e70-3 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

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Links

PDB pages	PDBj / wwPDB / NCBI
Related items in Molecule of the Month	#102 - Jun 2008 Lactate Dehydrogenase similarity (1) #93 - Sep 2007 Citrate Synthase similarity (1)

Deposited unit

AAA: Formate dehydrogenase

BBB: Formate dehydrogenase

CCC: Formate dehydrogenase

DDD: Formate dehydrogenase

hetero molecules

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

1

AAA: Formate dehydrogenase

BBB: Formate dehydrogenase

hetero molecules

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

2

CCC: Formate dehydrogenase

DDD: Formate dehydrogenase

hetero molecules

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

Unit cell

Length a, b, c (Å)	50.731, 94.606, 94.614
Angle α, β, γ (deg.)	85.627, 89.880, 81.618
Int Tables number	1
Space group name H-M	P1

Noncrystallographic symmetry (NCS)

NCS domain:

ID	Ens-ID	Details
1	1	Chains A B
2	2	Chains A C
3	3	Chains A D
4	4	Chains B C
5	5	Chains B D
6	6	Chains C D

NCS ensembles :

ID
1
2
3
4
5
6

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Protein , 1 types, 4 molecules AAABBBCCCDDD

#1: Protein	Formate dehydrogenase / / FDH / NAD-dependent formate dehydrogenase Mass: 45630.441 Da / Num. of mol.: 4 / Mutation: N120C Source method: isolated from a genetically manipulated source Source: (gene. exp.) Chaetomium thermophilum (strain DSM 1495 / CBS 144.50 / IMI 039719) (fungus) Strain: DSM 1495 / CBS 144.50 / IMI 039719 / Gene: FDH, CTHT_0067590 / Production host: Escherichia coli BL21 (bacteria) / References: UniProt: G0SGU4, formate dehydrogenase

#1: Protein

Formate dehydrogenase /

/ FDH / NAD-dependent formate dehydrogenase

Mass: 45630.441 Da / Num. of mol.: 4 / Mutation: N120C
Source method: isolated from a genetically manipulated source
Source: (gene. exp.)

Chaetomium thermophilum (strain DSM 1495 / CBS 144.50 / IMI 039719) (fungus)
Strain: DSM 1495 / CBS 144.50 / IMI 039719 / Gene: FDH, CTHT_0067590 / Production host:

Escherichia coli BL21 (bacteria) / References: UniProt: G0SGU4,

formate dehydrogenase

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Non-polymers , 5 types, 1781 molecules

#2: Chemical	ChemComp-PEG / DI(HYDROXYETHYL)ETHER / Diethylene glycol Mass: 106.120 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C₄H₁₀O₃
#3: Chemical	ChemComp-NAI / 1,4-DIHYDRONICOTINAMIDE ADENINE DINUCLEOTIDE / NADH / Nicotinamide adenine dinucleotide Mass: 665.441 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C₂₁H₂₉N₇O₁₄P₂ / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical	ChemComp-FMT / FORMIC ACID / Formic acid Mass: 46.025 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: CH₂O₂ / Feature type: SUBJECT OF INVESTIGATION
#5: Chemical	ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol Mass: 62.068 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C₂H₆O₂
#6: Water	ChemComp-HOH / water / Water Mass: 18.015 Da / Num. of mol.: 1759 / Source method: isolated from a natural source / Formula: H₂O

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Details

Has ligand of interest	Y

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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: 49.88 %
Crystal grow	Temperature: 291 K / Method: microbatch / pH: 7.5 Details: 0.2 M Magnesium chloride hexahydrate, 0.1 M Tris pH 7.5, 10 % w/v PEG 1000, 10 % w/v PEG 8000

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Data collection

Diffraction	Mean temperature: 100 K / Serial crystal experiment: N
Diffraction source	Source: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.9763 Å
Detector	Type: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Feb 26, 2018
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.9763 Å / Relative weight: 1
Reflection	Resolution: 1.12→63.93 Å / Num. obs: 548213 / % possible obs: 82.1 % / Redundancy: 1.7 % / B_iso Wilson estimate: 15.7 Å² / CC_1/2: 0.998 / Net I/σ(I): 5.7
Reflection shell	Resolution: 1.12→1.14 Å / Redundancy: 1.4 % / Mean I/σ(I) obs: 0.8 / Num. unique obs: 17604 / CC_1/2: 0.291 / % possible all: 53.2

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Processing

Software

Name	Version	Classification
REFMAC	5.8.0257	refinement
XDS		data reduction
XDS		data scaling
MoRDa		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: 5dna

5dna

Resolution: 1.12→63.93 Å / Cor.coef. F_o:F_c: 0.966 / Cor.coef. F_o:F_c free: 0.958 / Cross valid method: FREE R-VALUE / ESU R: 0.044 / ESU R Free: 0.046
Details: Hydrogens have been added in their riding positions

	R_factor	Num. reflection	% reflection
R_free	0.2276	27331	4.985 %
R_work	0.2069	-	-
all	0.208	-	-
obs	-	548212	82.101 %

Solvent computation

Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å

Displacement parameters

B_iso mean: 18.109 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	-0.172 Å²	-0.052 Å²	-0.041 Å²
2-	-	0.793 Å²	0.069 Å²
3-	-	-	-0.651 Å²

Refinement step

Cycle: LAST / Resolution: 1.12→63.93 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	11503	0	256	1759	13518

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.013	0.013	12784
X-RAY DIFFRACTION	r_bond_other_d	0.034	0.017	12225
X-RAY DIFFRACTION	r_angle_refined_deg	1.92	1.675	17408
X-RAY DIFFRACTION	r_angle_other_deg	2.339	1.598	28432
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	6.819	5	1691
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	31.156	21.193	729
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	13.08	15	2342
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	14.201	15	124
X-RAY DIFFRACTION	r_chiral_restr	0.103	0.2	1628
X-RAY DIFFRACTION	r_gen_planes_refined	0.018	0.02	14492
X-RAY DIFFRACTION	r_gen_planes_other	0.032	0.02	2787
X-RAY DIFFRACTION	r_nbd_refined	0.216	0.2	2489
X-RAY DIFFRACTION	r_symmetry_nbd_other	0.212	0.2	11279
X-RAY DIFFRACTION	r_nbtor_refined	0.167	0.2	5909
X-RAY DIFFRACTION	r_symmetry_nbtor_other	0.071	0.2	5422
X-RAY DIFFRACTION	r_xyhbond_nbd_refined	0.163	0.2	1247
X-RAY DIFFRACTION	r_symmetry_nbd_refined	0.253	0.2	15
X-RAY DIFFRACTION	r_nbd_other	0.248	0.2	58
X-RAY DIFFRACTION	r_symmetry_xyhbond_nbd_refined	0.248	0.2	47
X-RAY DIFFRACTION	r_xyhbond_nbd_other	0.135	0.2	1
X-RAY DIFFRACTION	r_mcbond_it	3.013	4.412	6156
X-RAY DIFFRACTION	r_mcbond_other	3.013	4.412	6157
X-RAY DIFFRACTION	r_mcangle_it	3.785	7.457	7749
X-RAY DIFFRACTION	r_mcangle_other	3.785	7.458	7750
X-RAY DIFFRACTION	r_scbond_it	3.963	5.216	6628
X-RAY DIFFRACTION	r_scbond_other	3.963	5.217	6629
X-RAY DIFFRACTION	r_scangle_it	5.084	8.422	9551
X-RAY DIFFRACTION	r_scangle_other	5.083	8.423	9552
X-RAY DIFFRACTION	r_lrange_it	6.112	23.691	14892
X-RAY DIFFRACTION	r_lrange_other	6.113	23.692	14893
X-RAY DIFFRACTION	r_ncsr_local_group_1	0.066	0.05	12339
X-RAY DIFFRACTION	r_ncsr_local_group_2	0.066	0.05	12351
X-RAY DIFFRACTION	r_ncsr_local_group_3	0.063	0.05	12479
X-RAY DIFFRACTION	r_ncsr_local_group_4	0.069	0.05	12449
X-RAY DIFFRACTION	r_ncsr_local_group_5	0.074	0.05	12353
X-RAY DIFFRACTION	r_ncsr_local_group_6	0.072	0.05	12317

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 (%)
1.12-1.149	0.349	1421	0.354	26518	X-RAY DIFFRACTION	56.5224
1.149-1.181	0.355	1839	0.348	34471	X-RAY DIFFRACTION	75.2913
1.181-1.215	0.336	1850	0.333	36830	X-RAY DIFFRACTION	82.745
1.215-1.252	0.33	1935	0.317	37123	X-RAY DIFFRACTION	85.9797
1.252-1.293	0.306	1966	0.303	36963	X-RAY DIFFRACTION	88.0667
1.293-1.339	0.303	1822	0.293	36070	X-RAY DIFFRACTION	88.9066
1.339-1.389	0.287	1873	0.272	35001	X-RAY DIFFRACTION	89.709
1.389-1.446	0.258	1761	0.253	33680	X-RAY DIFFRACTION	89.4117
1.446-1.51	0.251	1707	0.23	31630	X-RAY DIFFRACTION	87.8677
1.51-1.584	0.244	1619	0.22	29784	X-RAY DIFFRACTION	86.5406
1.584-1.669	0.219	1464	0.197	27651	X-RAY DIFFRACTION	84.4721
1.669-1.771	0.23	1374	0.194	25958	X-RAY DIFFRACTION	83.8174
1.771-1.893	0.223	1195	0.191	23532	X-RAY DIFFRACTION	80.4653
1.893-2.044	0.213	1123	0.189	21724	X-RAY DIFFRACTION	80.0778
2.044-2.24	0.211	1013	0.182	19165	X-RAY DIFFRACTION	76.8569
2.24-2.504	0.196	953	0.169	17594	X-RAY DIFFRACTION	78.1025
2.504-2.891	0.202	760	0.169	15715	X-RAY DIFFRACTION	78.7223
2.891-3.54	0.187	709	0.174	13820	X-RAY DIFFRACTION	82.2474
3.54-5.002	0.199	562	0.167	11146	X-RAY DIFFRACTION	85.6036
5.002-63.93	0.185	385	0.19	6506	X-RAY DIFFRACTION	91.8678

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