PDB-6t94: NAD+-dependent fungal formate dehydrogenase from Chaetomium therm...

ID or keywords:

Entry

Database: PDB / ID: 6t94

Title

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

Components

Formate dehydrogenase

Keywords

CYTOSOLIC PROTEIN / NADH

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: 1.15 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 / Refinement description / Category: citation / citation_author / struct_ncs_dom_lim 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 / Refinement description Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ncs_dom_lim Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

Structure viewer	Molecule: MolmilJmol/JSmol

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PDBx/mmCIF format	6t94.cif.gz	622.9 KB	Display	PDBx/mmCIF format
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Validation report

Summary document	6t94_validation.pdf.gz	1.6 MB	Display	wwPDB validaton report
Full document	6t94_full_validation.pdf.gz	1.6 MB	Display
Data in XML	6t94_validation.xml.gz	77.4 KB	Display
Data in CIF	6t94_validation.cif.gz	118 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/t9/6t94 ftp://data.pdbj.org/pub/pdb/validation_reports/t9/6t94	HTTPS FTP

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Related structure data

Related structure data	6t8yC 6t8zC 6t92C 5dnaS S: Starting model for refinement C: citing same article (ref.)
Similar structure data	6t8z-2 6t8y-1 6t8y-2 6t8z-1 6t92-2 4r5m-d 6t92-1 1ztx-d 1oxq-d 6bfq-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
93.1 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
93.1 kDa, 2 polymers
Search similar-shape structures of this assembly by Omokage search (details)

Unit cell

Length a, b, c (Å)	50.730, 94.745, 94.604
Angle α, β, γ (deg.)	85.964, 89.972, 81.577
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 domain segments:

Dom-ID	Component-ID	Ens-ID	Beg auth comp-ID	Beg label comp-ID	End auth comp-ID	End label comp-ID	Auth asym-ID	Label asym-ID	Auth seq-ID	Label seq-ID
1	1	1	THR	THR	GLN	GLN	AAA	A	-4 - 361	30 - 395
1	2	1	THR	THR	GLN	GLN	BBB	B	-4 - 361	30 - 395
2	1	2	ALA	ALA	GLN	GLN	AAA	A	-3 - 361	31 - 395
2	2	2	ALA	ALA	GLN	GLN	CCC	C	-3 - 361	31 - 395
3	1	3	THR	THR	ARG	ARG	AAA	A	-4 - 362	30 - 396
3	2	3	THR	THR	ARG	ARG	DDD	D	-4 - 362	30 - 396
4	1	4	ALA	ALA	LYS	LYS	BBB	B	-3 - 366	31 - 400
4	2	4	ALA	ALA	LYS	LYS	CCC	C	-3 - 366	31 - 400
5	1	5	THR	THR	GLN	GLN	BBB	B	-4 - 361	30 - 395
5	2	5	THR	THR	GLN	GLN	DDD	D	-4 - 361	30 - 395
6	1	6	ALA	ALA	GLN	GLN	CCC	C	-3 - 361	31 - 395
6	2	6	ALA	ALA	GLN	GLN	DDD	D	-3 - 361	31 - 395

NCS ensembles :

ID
1
2
3
4
5
6

#1: Protein	Formate dehydrogenase / FDH / NAD-dependent formate dehydrogenase Mass: 45630.441 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Chaetomium thermophilum (fungus) / Gene: FDH, CTHT_0067590 / Production host: Escherichia coli BL21 (bacteria) / References: UniProt: G0SGU4, formate dehydrogenase
#2: Chemical	ChemComp-PEG / DI(HYDROXYETHYL)ETHER Mass: 106.120 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C₄H₁₀O₃
#3: Chemical	ChemComp-NAI / 1,4-DIHYDRONICOTINAMIDE ADENINE DINUCLEOTIDE / NADH Mass: 665.441 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C₂₁H₂₉N₇O₁₄P₂ / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical	ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL Mass: 62.068 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C₂H₆O₂
#5: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 1921 / Source method: isolated from a natural source / Formula: H₂O
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: 2.46 Å³/Da / Density % sol: 49.96 %
Crystal grow	Temperature: 291 K / Method: microbatch / pH: 6.5 Details: 0.1 M Sodium cacodylate pH 6.5, 18 % w/v PEG 2000 MME

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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: 1.15→68.9 Å / Num. obs: 536693 / % possible obs: 86.9 % / Redundancy: 1.7 % / CC_1/2: 0.998 / Net I/σ(I): 5.9
Reflection shell	Resolution: 1.15→1.17 Å / Redundancy: 1.5 % / Mean I/σ(I) obs: 0.6 / Num. unique obs: 25189 / CC_1/2: 0.325 / % possible all: 82.3

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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: 1.15→68.9 Å / Cor.coef. F_o:F_c: 0.973 / Cor.coef. F_o:F_c free: 0.966 / Cross valid method: FREE R-VALUE / ESU R: 0.043 / ESU R Free: 0.045
Details: Hydrogens have been added in their riding positions

	R_factor	Num. reflection	% reflection
R_free	0.2179	26885	5.01 %
R_work	0.1964	-	-
all	0.197	-	-
obs	-	536580	86.847 %

Solvent computation

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

Displacement parameters

B_iso mean: 21.743 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	-1.012 Å²	-0.045 Å²	-0.034 Å²
2-	-	1.067 Å²	-0.259 Å²
3-	-	-	-0.152 Å²

Refinement step

Cycle: LAST / Resolution: 1.15→68.9 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	11498	0	243	1921	13662

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.012	0.013	12857
X-RAY DIFFRACTION	r_bond_other_d	0.034	0.017	12317
X-RAY DIFFRACTION	r_angle_refined_deg	1.812	1.674	17523
X-RAY DIFFRACTION	r_angle_other_deg	2.317	1.597	28665
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	6.752	5	1708
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	30.882	21.164	730
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	13.182	15	2366
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	14.57	15	125
X-RAY DIFFRACTION	r_chiral_restr	0.1	0.2	1638
X-RAY DIFFRACTION	r_gen_planes_refined	0.014	0.02	14600
X-RAY DIFFRACTION	r_gen_planes_other	0.024	0.02	2796
X-RAY DIFFRACTION	r_nbd_refined	0.217	0.2	2503
X-RAY DIFFRACTION	r_symmetry_nbd_other	0.214	0.2	11503
X-RAY DIFFRACTION	r_nbtor_refined	0.166	0.2	6011
X-RAY DIFFRACTION	r_symmetry_nbtor_other	0.07	0.2	5521
X-RAY DIFFRACTION	r_xyhbond_nbd_refined	0.151	0.2	1389
X-RAY DIFFRACTION	r_symmetry_xyhbond_nbd_other	0.04	0.2	3
X-RAY DIFFRACTION	r_symmetry_nbd_refined	0.208	0.2	14
X-RAY DIFFRACTION	r_nbd_other	0.231	0.2	63
X-RAY DIFFRACTION	r_symmetry_xyhbond_nbd_refined	0.202	0.2	47
X-RAY DIFFRACTION	r_mcbond_it	3.531	5.379	6204
X-RAY DIFFRACTION	r_mcbond_other	3.529	5.378	6203
X-RAY DIFFRACTION	r_mcangle_it	4.468	9.07	7821
X-RAY DIFFRACTION	r_mcangle_other	4.468	9.072	7822
X-RAY DIFFRACTION	r_scbond_it	4.606	6.22	6653
X-RAY DIFFRACTION	r_scbond_other	4.605	6.22	6654
X-RAY DIFFRACTION	r_scangle_it	5.962	10.06	9591
X-RAY DIFFRACTION	r_scangle_other	5.961	10.061	9592
X-RAY DIFFRACTION	r_lrange_it	7.045	28.486	15127
X-RAY DIFFRACTION	r_lrange_other	7.045	28.487	15128
X-RAY DIFFRACTION	r_ncsr_local_group_1	0.074	0.05	12435
X-RAY DIFFRACTION	r_ncsr_local_group_2	0.071	0.05	12424
X-RAY DIFFRACTION	r_ncsr_local_group_3	0.066	0.05	12639
X-RAY DIFFRACTION	r_ncsr_local_group_4	0.072	0.05	12601
X-RAY DIFFRACTION	r_ncsr_local_group_5	0.071	0.05	12473
X-RAY DIFFRACTION	r_ncsr_local_group_6	0.072	0.05	12365

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 (%)
1.15-1.18	0.355	1989	0.355	35977	X-RAY DIFFRACTION	82.8536
1.18-1.212	0.329	1884	0.332	36471	X-RAY DIFFRACTION	86.2414
1.212-1.247	0.334	1858	0.318	36091	X-RAY DIFFRACTION	87.5531
1.247-1.286	0.3	1884	0.3	35770	X-RAY DIFFRACTION	89.5394
1.286-1.328	0.292	1805	0.289	35051	X-RAY DIFFRACTION	90.2891
1.328-1.374	0.276	1790	0.267	34177	X-RAY DIFFRACTION	91.035
1.374-1.426	0.274	1744	0.257	32796	X-RAY DIFFRACTION	91.0313
1.426-1.485	0.251	1712	0.236	31795	X-RAY DIFFRACTION	91.357
1.485-1.551	0.25	1607	0.227	30042	X-RAY DIFFRACTION	90.0424
1.551-1.626	0.236	1546	0.214	28315	X-RAY DIFFRACTION	88.8932
1.626-1.714	0.248	1388	0.21	26408	X-RAY DIFFRACTION	87.2853
1.714-1.818	0.225	1300	0.199	24561	X-RAY DIFFRACTION	85.3752
1.818-1.944	0.225	1089	0.196	21887	X-RAY DIFFRACTION	81.0412
1.944-2.099	0.22	1061	0.191	20002	X-RAY DIFFRACTION	79.6996
2.099-2.299	0.209	944	0.175	17881	X-RAY DIFFRACTION	77.5361
2.299-2.571	0.19	890	0.157	16660	X-RAY DIFFRACTION	79.8526
2.571-2.968	0.183	744	0.152	15276	X-RAY DIFFRACTION	82.6881
2.968-3.634	0.171	710	0.153	13367	X-RAY DIFFRACTION	86.0295
3.634-5.136	0.165	567	0.148	10924	X-RAY DIFFRACTION	90.8667
5.136-68.9	0.197	373	0.188	6244	X-RAY DIFFRACTION	95.8291

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