PDB-6t8z: NAD+-dependent fungal formate dehydrogenase from Chaetomium therm...

ID or keywords:

Entry

Database: PDB / ID: 6t8z

Title

NAD+-dependent fungal formate dehydrogenase from Chaetomium thermophilum: A ternary complex with the oxidised form of the cofactor NAD+ and the substrate formate both at a primary and secondary sites.

Components

Formate dehydrogenase

Keywords

CYTOSOLIC PROTEIN / NAD+ dependent formate dehydrogenase

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 / cytosol
Similarity search - Function

Biological species

Chaetomium thermophilum (fungus)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 1.21 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	6t8z.cif.gz	631.9 KB	Display	PDBx/mmCIF format
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Validation report

Summary document	6t8z_validation.pdf.gz	3.8 MB	Display	wwPDB validaton report
Full document	6t8z_full_validation.pdf.gz	3.8 MB	Display
Data in XML	6t8z_validation.xml.gz	78.8 KB	Display
Data in CIF	6t8z_validation.cif.gz	119.5 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/t8/6t8z ftp://data.pdbj.org/pub/pdb/validation_reports/t8/6t8z	HTTPS FTP

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Related structure data

Related structure data	6t8yC 6t92C 6t94C 5dnaS C: citing same article (ref.) S: Starting model for refinement
Similar structure data	6t94-1 6t8y-1 6t8y-2 6t92-2 4r5m-d 6bfq-3 3n7u-5 6j11-2 2ome-4 6bfq-1 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

Deposited unit

AAA: Formate dehydrogenase

BBB: Formate dehydrogenase

CCC: Formate dehydrogenase

DDD: Formate dehydrogenase

hetero molecules

187 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
93.5 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
93.3 kDa, 2 polymers
Search similar-shape structures of this assembly by Omokage search (details)

Unit cell

Length a, b, c (Å)	50.395, 94.515, 94.330
Angle α, β, γ (deg.)	85.689, 89.927, 81.939
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: 45641.398 Da / Num. of mol.: 4 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: 45641.398 Da / Num. of mol.: 4
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, 1991 molecules

#2: Chemical	ChemComp-PEG / DI(HYDROXYETHYL)ETHER Mass: 106.120 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: C₄H₁₀O₃
#3: Chemical	ChemComp-FMT / FORMIC ACID Mass: 46.025 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: CH₂O₂ / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical	ChemComp-NAD / NICOTINAMIDE-ADENINE-DINUCLEOTIDE Mass: 663.425 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C₂₁H₂₇N₇O₁₄P₂ / Feature type: SUBJECT OF INVESTIGATION / Comment: NAD*YM
#5: Chemical	ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL Mass: 62.068 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: C₂H₆O₂
#6: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 1965 / 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: 2.43 Å³/Da / Density % sol: 49.38 %
Crystal grow	Temperature: 291 K / Method: microbatch / pH: 5.5 Details: 0.1M Bis-Tris, pH 5.5, 25 % w/v PEG 3350, 2.5 mM NAD+

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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: 1.21→47.03 Å / Num. obs: 467507 / % possible obs: 89.1 % / Redundancy: 1.8 % / B_iso Wilson estimate: 17.8 Å² / CC_1/2: 0.998 / Net I/σ(I): 5.8
Reflection shell	Resolution: 1.21→1.23 Å / Redundancy: 1.8 % / Num. unique obs: 22684 / CC_1/2: 0.25 / Χ²: 0.7 / % possible all: 87.1

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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: 1.21→47.03 Å / Cor.coef. F_o:F_c: 0.97 / Cor.coef. F_o:F_c free: 0.963 / Cross valid method: FREE R-VALUE / ESU R: 0.047 / ESU R Free: 0.049
Details: Hydrogens have been added in their riding positions

	R_factor	Num. reflection	% reflection
R_free	0.2107	23228	4.969 %
R_work	0.1882	-	-
all	0.189	-	-
obs	-	467501	89.117 %

Solvent computation

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

Displacement parameters

B_iso mean: 19.293 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	-0.089 Å²	0.364 Å²	-0.141 Å²
2-	-	0.014 Å²	-0.241 Å²
3-	-	-	0.141 Å²

Refinement step

Cycle: LAST / Resolution: 1.21→47.03 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	11621	0	277	1965	13863

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.012	0.013	12988
X-RAY DIFFRACTION	r_bond_other_d	0.034	0.017	12444
X-RAY DIFFRACTION	r_angle_refined_deg	1.663	1.656	17679
X-RAY DIFFRACTION	r_angle_other_deg	2.296	1.588	28974
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	6.704	5	1719
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	30.341	21.26	738
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	12.523	15	2390
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	13.945	15	125
X-RAY DIFFRACTION	r_chiral_restr	0.095	0.2	1659
X-RAY DIFFRACTION	r_gen_planes_refined	0.012	0.02	14767
X-RAY DIFFRACTION	r_gen_planes_other	0.02	0.02	2780
X-RAY DIFFRACTION	r_nbd_refined	0.214	0.2	2538
X-RAY DIFFRACTION	r_symmetry_nbd_other	0.212	0.2	11320
X-RAY DIFFRACTION	r_nbtor_refined	0.166	0.2	6091
X-RAY DIFFRACTION	r_symmetry_nbtor_other	0.069	0.2	5535
X-RAY DIFFRACTION	r_xyhbond_nbd_refined	0.182	0.2	1462
X-RAY DIFFRACTION	r_symmetry_xyhbond_nbd_other	0.038	0.2	4
X-RAY DIFFRACTION	r_symmetry_nbd_refined	0.223	0.2	14
X-RAY DIFFRACTION	r_nbd_other	0.157	0.2	66
X-RAY DIFFRACTION	r_symmetry_xyhbond_nbd_refined	0.207	0.2	41
X-RAY DIFFRACTION	r_mcbond_it	3.226	4.642	6246
X-RAY DIFFRACTION	r_mcbond_other	3.226	4.643	6247
X-RAY DIFFRACTION	r_mcangle_it	4.049	7.828	7867
X-RAY DIFFRACTION	r_mcangle_other	4.049	7.828	7867
X-RAY DIFFRACTION	r_scbond_it	4.501	5.5	6742
X-RAY DIFFRACTION	r_scbond_other	4.501	5.5	6743
X-RAY DIFFRACTION	r_scangle_it	5.826	8.849	9700
X-RAY DIFFRACTION	r_scangle_other	5.826	8.85	9701
X-RAY DIFFRACTION	r_lrange_it	6.848	25.29	15358
X-RAY DIFFRACTION	r_lrange_other	6.848	25.291	15359
X-RAY DIFFRACTION	r_ncsr_local_group_1	0.073	0.05	12615
X-RAY DIFFRACTION	r_ncsr_local_group_2	0.073	0.05	12570
X-RAY DIFFRACTION	r_ncsr_local_group_3	0.062	0.05	12719
X-RAY DIFFRACTION	r_ncsr_local_group_4	0.065	0.05	12579
X-RAY DIFFRACTION	r_ncsr_local_group_5	0.072	0.05	12549
X-RAY DIFFRACTION	r_ncsr_local_group_6	0.076	0.05	12593

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 (%)
1.21-1.241	0.353	1684	0.345	32279	X-RAY DIFFRACTION	87.3646
1.241-1.275	0.337	1724	0.333	31956	X-RAY DIFFRACTION	89.2682
1.275-1.312	0.319	1602	0.313	31444	X-RAY DIFFRACTION	89.8917
1.312-1.353	0.309	1604	0.297	30734	X-RAY DIFFRACTION	90.4585
1.353-1.397	0.297	1537	0.281	29897	X-RAY DIFFRACTION	90.6062
1.397-1.446	0.272	1499	0.267	28981	X-RAY DIFFRACTION	91.1511
1.446-1.501	0.267	1537	0.242	27917	X-RAY DIFFRACTION	91.1465
1.501-1.562	0.247	1428	0.22	26769	X-RAY DIFFRACTION	90.8291
1.562-1.631	0.229	1367	0.2	25716	X-RAY DIFFRACTION	90.6878
1.631-1.711	0.238	1306	0.199	24423	X-RAY DIFFRACTION	90.3438
1.711-1.804	0.219	1222	0.191	23222	X-RAY DIFFRACTION	90.0564
1.804-1.913	0.202	1069	0.177	21540	X-RAY DIFFRACTION	88.3061
1.913-2.045	0.206	1055	0.176	20179	X-RAY DIFFRACTION	88.2287
2.045-2.209	0.199	954	0.167	18389	X-RAY DIFFRACTION	86.2333
2.209-2.419	0.177	893	0.155	16893	X-RAY DIFFRACTION	85.8937
2.419-2.705	0.184	779	0.153	15067	X-RAY DIFFRACTION	85.3358
2.705-3.123	0.191	623	0.158	13392	X-RAY DIFFRACTION	85.1199
3.123-3.823	0.181	557	0.153	11285	X-RAY DIFFRACTION	85.2986
3.823-5.403	0.144	484	0.137	9044	X-RAY DIFFRACTION	88.8309
5.403-47.03	0.172	304	0.171	5146	X-RAY DIFFRACTION	92.3572

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