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

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Basic information

Entry
Database: PDB / ID: 6t94
TitleNAD+-dependent fungal formate dehydrogenase from Chaetomium thermophilum: A complex of N120C mutant protein with the reduced form of the cofactor NADH.
ComponentsFormate dehydrogenase
KeywordsCYTOSOLIC 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 / cytoplasm
Similarity search - Function
NAD-dependent formate dehydrogenase / D-isomer specific 2-hydroxyacid dehydrogenases signature 2. / D-isomer specific 2-hydroxyacid dehydrogenases NAD-binding signature. / D-isomer specific 2-hydroxyacid dehydrogenase, NAD-binding domain conserved site 1 / D-isomer specific 2-hydroxyacid dehydrogenases signature 3. / D-isomer specific 2-hydroxyacid dehydrogenase, NAD-binding domain conserved site / D-isomer specific 2-hydroxyacid dehydrogenase, catalytic domain / D-isomer specific 2-hydroxyacid dehydrogenase, catalytic domain / D-isomer specific 2-hydroxyacid dehydrogenase, NAD-binding domain / D-isomer specific 2-hydroxyacid dehydrogenase, NAD binding domain / NAD(P)-binding domain superfamily
Similarity search - Domain/homology
1,4-DIHYDRONICOTINAMIDE ADENINE DINUCLEOTIDE / DI(HYDROXYETHYL)ETHER / Formate dehydrogenase
Similarity search - Component
Biological speciesChaetomium thermophilum (fungus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.15 Å
AuthorsIsupov, M.N. / Yelmazer, B. / De Rose, S.A. / Littlechild, J.A.
CitationJournal: 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
DepositionOct 25, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 18, 2020Provider: repository / Type: Initial release
Revision 1.1Jun 2, 2021Group: 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 1.2Jan 24, 2024Group: 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
AAA: Formate dehydrogenase
BBB: Formate dehydrogenase
CCC: Formate dehydrogenase
DDD: Formate dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)186,21121
Polymers182,5224
Non-polymers3,68917
Water34,6071921
1
AAA: Formate dehydrogenase
BBB: Formate dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)93,11411
Polymers91,2612
Non-polymers1,8539
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9770 Å2
ΔGint-29 kcal/mol
Surface area26580 Å2
MethodPISA
2
CCC: Formate dehydrogenase
DDD: Formate dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)93,09610
Polymers91,2612
Non-polymers1,8358
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9130 Å2
ΔGint-42 kcal/mol
Surface area26970 Å2
MethodPISA
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 number1
Space group name H-MP1
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11Chains A B
22Chains A C
33Chains A D
44Chains B C
55Chains B D
66Chains C D

NCS domain segments:
Dom-IDComponent-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
111THRTHRGLNGLNAAAA-4 - 36130 - 395
121THRTHRGLNGLNBBBB-4 - 36130 - 395
212ALAALAGLNGLNAAAA-3 - 36131 - 395
222ALAALAGLNGLNCCCC-3 - 36131 - 395
313THRTHRARGARGAAAA-4 - 36230 - 396
323THRTHRARGARGDDDD-4 - 36230 - 396
414ALAALALYSLYSBBBB-3 - 36631 - 400
424ALAALALYSLYSCCCC-3 - 36631 - 400
515THRTHRGLNGLNBBBB-4 - 36130 - 395
525THRTHRGLNGLNDDDD-4 - 36130 - 395
616ALAALAGLNGLNCCCC-3 - 36131 - 395
626ALAALAGLNGLNDDDD-3 - 36131 - 395

NCS ensembles :
ID
1
2
3
4
5
6

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Components

#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 / 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-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C2H6O2
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 1921 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.46 Å3/Da / Density % sol: 49.96 %
Crystal growTemperature: 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

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.9763 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Feb 26, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9763 Å / Relative weight: 1
ReflectionResolution: 1.15→68.9 Å / Num. obs: 536693 / % possible obs: 86.9 % / Redundancy: 1.7 % / CC1/2: 0.998 / Net I/σ(I): 5.9
Reflection shellResolution: 1.15→1.17 Å / Redundancy: 1.5 % / Mean I/σ(I) obs: 0.6 / Num. unique obs: 25189 / CC1/2: 0.325 / % possible all: 82.3

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Processing

Software
NameVersionClassification
REFMAC5.8.0257refinement
XDSdata reduction
XDSdata scaling
MoRDaphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5dna

5dna


Resolution: 1.15→68.9 Å / Cor.coef. Fo:Fc: 0.973 / Cor.coef. Fo:Fc 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
RfactorNum. reflection% reflection
Rfree0.2179 26885 5.01 %
Rwork0.1964 --
all0.197 --
obs-536580 86.847 %
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 21.743 Å2
Baniso -1Baniso -2Baniso -3
1--1.012 Å2-0.045 Å2-0.034 Å2
2--1.067 Å2-0.259 Å2
3----0.152 Å2
Refinement stepCycle: LAST / Resolution: 1.15→68.9 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11498 0 243 1921 13662
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.01312857
X-RAY DIFFRACTIONr_bond_other_d0.0340.01712317
X-RAY DIFFRACTIONr_angle_refined_deg1.8121.67417523
X-RAY DIFFRACTIONr_angle_other_deg2.3171.59728665
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.75251708
X-RAY DIFFRACTIONr_dihedral_angle_2_deg30.88221.164730
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.182152366
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.5715125
X-RAY DIFFRACTIONr_chiral_restr0.10.21638
X-RAY DIFFRACTIONr_gen_planes_refined0.0140.0214600
X-RAY DIFFRACTIONr_gen_planes_other0.0240.022796
X-RAY DIFFRACTIONr_nbd_refined0.2170.22503
X-RAY DIFFRACTIONr_symmetry_nbd_other0.2140.211503
X-RAY DIFFRACTIONr_nbtor_refined0.1660.26011
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.070.25521
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1510.21389
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_other0.040.23
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.2080.214
X-RAY DIFFRACTIONr_nbd_other0.2310.263
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.2020.247
X-RAY DIFFRACTIONr_mcbond_it3.5315.3796204
X-RAY DIFFRACTIONr_mcbond_other3.5295.3786203
X-RAY DIFFRACTIONr_mcangle_it4.4689.077821
X-RAY DIFFRACTIONr_mcangle_other4.4689.0727822
X-RAY DIFFRACTIONr_scbond_it4.6066.226653
X-RAY DIFFRACTIONr_scbond_other4.6056.226654
X-RAY DIFFRACTIONr_scangle_it5.96210.069591
X-RAY DIFFRACTIONr_scangle_other5.96110.0619592
X-RAY DIFFRACTIONr_lrange_it7.04528.48615127
X-RAY DIFFRACTIONr_lrange_other7.04528.48715128
X-RAY DIFFRACTIONr_ncsr_local_group_10.0740.0512435
X-RAY DIFFRACTIONr_ncsr_local_group_20.0710.0512424
X-RAY DIFFRACTIONr_ncsr_local_group_30.0660.0512639
X-RAY DIFFRACTIONr_ncsr_local_group_40.0720.0512601
X-RAY DIFFRACTIONr_ncsr_local_group_50.0710.0512473
X-RAY DIFFRACTIONr_ncsr_local_group_60.0720.0512365
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.15-1.180.35519890.35535977X-RAY DIFFRACTION82.8536
1.18-1.2120.32918840.33236471X-RAY DIFFRACTION86.2414
1.212-1.2470.33418580.31836091X-RAY DIFFRACTION87.5531
1.247-1.2860.318840.335770X-RAY DIFFRACTION89.5394
1.286-1.3280.29218050.28935051X-RAY DIFFRACTION90.2891
1.328-1.3740.27617900.26734177X-RAY DIFFRACTION91.035
1.374-1.4260.27417440.25732796X-RAY DIFFRACTION91.0313
1.426-1.4850.25117120.23631795X-RAY DIFFRACTION91.357
1.485-1.5510.2516070.22730042X-RAY DIFFRACTION90.0424
1.551-1.6260.23615460.21428315X-RAY DIFFRACTION88.8932
1.626-1.7140.24813880.2126408X-RAY DIFFRACTION87.2853
1.714-1.8180.22513000.19924561X-RAY DIFFRACTION85.3752
1.818-1.9440.22510890.19621887X-RAY DIFFRACTION81.0412
1.944-2.0990.2210610.19120002X-RAY DIFFRACTION79.6996
2.099-2.2990.2099440.17517881X-RAY DIFFRACTION77.5361
2.299-2.5710.198900.15716660X-RAY DIFFRACTION79.8526
2.571-2.9680.1837440.15215276X-RAY DIFFRACTION82.6881
2.968-3.6340.1717100.15313367X-RAY DIFFRACTION86.0295
3.634-5.1360.1655670.14810924X-RAY DIFFRACTION90.8667
5.136-68.90.1973730.1886244X-RAY DIFFRACTION95.8291

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