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- PDB-6t8y: NAD+-dependent fungal formate dehydrogenase from Chaetomium therm... -

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Basic information

Entry
Database: PDB / ID: 6t8y
TitleNAD+-dependent fungal formate dehydrogenase from Chaetomium thermophilum: A complex with the reduced form of the cofactor NADH and the substrate formate at a secondary site.
ComponentsFormate dehydrogenase
KeywordsCYTOSOLIC 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 / mitochondrion / cytosol
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 dehydrogenases signature 3. / D-isomer specific 2-hydroxyacid dehydrogenase, NAD-binding domain conserved site 1 / 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
FORMIC ACID / 1,4-DIHYDRONICOTINAMIDE ADENINE DINUCLEOTIDE / DI(HYDROXYETHYL)ETHER / Formate dehydrogenase
Similarity search - Component
Biological speciesChaetomium thermophilum (fungus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.26 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 / 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 1.2Jan 24, 2024Group: 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

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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)186,52725
Polymers182,5664
Non-polymers3,96121
Water34,1021893
1
AAA: Formate dehydrogenase
BBB: Formate dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)93,33414
Polymers91,2832
Non-polymers2,05212
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area10410 Å2
ΔGint-23 kcal/mol
Surface area26920 Å2
MethodPISA
2
CCC: Formate dehydrogenase
DDD: Formate dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)93,19211
Polymers91,2832
Non-polymers1,9099
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9580 Å2
ΔGint-37 kcal/mol
Surface area27170 Å2
MethodPISA
Unit cell
Length a, b, c (Å)50.568, 94.756, 94.604
Angle α, β, γ (deg.)85.592, 89.932, 81.614
Int Tables number1
Space group name H-MP1
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11Chains A B
21Chains A C
31Chains A D
41Chains B C
51Chains B D
61Chains C D

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Components

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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

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Non-polymers , 5 types, 1914 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-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-FMT / FORMIC ACID


Mass: 46.025 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: CH2O2 / Feature type: SUBJECT OF INVESTIGATION
#5: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C2H6O2
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1893 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 2.45 Å3/Da / Density % sol: 49.78 %
Crystal growTemperature: 291 K / Method: microbatch
Details: 0.1 M Bis-Tris, pH 6.5, 20% w/v PEG 5000 MME, 2.5 mM NAD+

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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: 1.26→47.06 Å / Num. obs: 407315 / % possible obs: 87 % / Redundancy: 1.7 % / Biso Wilson estimate: 22.1 Å2 / CC1/2: 0.999 / Net I/σ(I): 7.6
Reflection shellResolution: 1.26→1.28 Å / Redundancy: 1.5 % / Num. unique obs: 11117 / CC1/2: 0.215 / % possible all: 48.1

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Processing

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

5dna


Resolution: 1.26→46.774 Å / Cor.coef. Fo:Fc: 0.978 / Cor.coef. Fo:Fc free: 0.972 / Cross valid method: FREE R-VALUE / ESU R: 0.048 / ESU R Free: 0.05
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.1931 20297 4.983 %
Rwork0.1692 --
all0.17 --
obs-407312 86.99 %
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 23.935 Å2
Baniso -1Baniso -2Baniso -3
1-0.088 Å20.304 Å2-0.244 Å2
2--0.444 Å2-0.21 Å2
3----0.484 Å2
Refinement stepCycle: LAST / Resolution: 1.26→46.774 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11614 0 261 1893 13768
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.01312983
X-RAY DIFFRACTIONr_bond_other_d0.0340.01712474
X-RAY DIFFRACTIONr_angle_refined_deg1.7661.67517678
X-RAY DIFFRACTIONr_angle_other_deg2.2971.59829038
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.61151720
X-RAY DIFFRACTIONr_dihedral_angle_2_deg30.66221.26738
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.879152398
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.68515125
X-RAY DIFFRACTIONr_chiral_restr0.0940.21648
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.0214710
X-RAY DIFFRACTIONr_gen_planes_other0.020.022805
X-RAY DIFFRACTIONr_nbd_refined0.2150.22460
X-RAY DIFFRACTIONr_symmetry_nbd_other0.2120.211099
X-RAY DIFFRACTIONr_nbtor_refined0.1650.26049
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.070.25428
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1770.21442
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_other0.1280.25
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.1940.213
X-RAY DIFFRACTIONr_nbd_other0.1730.256
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.2040.250
X-RAY DIFFRACTIONr_mcbond_it4.255.8956247
X-RAY DIFFRACTIONr_mcbond_other4.255.8956248
X-RAY DIFFRACTIONr_mcangle_it4.969.9217870
X-RAY DIFFRACTIONr_mcangle_other4.9569.9227870
X-RAY DIFFRACTIONr_scbond_it5.6376.8856736
X-RAY DIFFRACTIONr_scbond_other5.6366.8856737
X-RAY DIFFRACTIONr_scangle_it6.92311.0859696
X-RAY DIFFRACTIONr_scangle_other6.92311.0869697
X-RAY DIFFRACTIONr_lrange_it7.89631.35815237
X-RAY DIFFRACTIONr_lrange_other7.89631.35815238
X-RAY DIFFRACTIONr_ncsr_local_group_10.070.0512576
X-RAY DIFFRACTIONr_ncsr_local_group_20.0770.0512531
X-RAY DIFFRACTIONr_ncsr_local_group_30.0650.0512701
X-RAY DIFFRACTIONr_ncsr_local_group_40.0710.0512501
X-RAY DIFFRACTIONr_ncsr_local_group_50.0720.0512493
X-RAY DIFFRACTIONr_ncsr_local_group_60.0730.0512538
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.26-1.2930.3598710.35816626X-RAY DIFFRACTION50.4556
1.293-1.3280.3611000.34122239X-RAY DIFFRACTION69.2737
1.328-1.3670.32314630.32727583X-RAY DIFFRACTION88.509
1.367-1.4090.31414880.30727720X-RAY DIFFRACTION91.5382
1.409-1.4550.29514020.28627066X-RAY DIFFRACTION92.1832
1.455-1.5060.26814300.25526263X-RAY DIFFRACTION92.628
1.506-1.5630.24513860.22825329X-RAY DIFFRACTION92.6768
1.563-1.6270.22913270.20224602X-RAY DIFFRACTION93.0956
1.627-1.6990.21712270.18523407X-RAY DIFFRACTION92.8814
1.699-1.7820.19911990.1722525X-RAY DIFFRACTION93.1924
1.782-1.8780.18410790.16221449X-RAY DIFFRACTION92.9987
1.878-1.9920.19710110.16420057X-RAY DIFFRACTION92.3873
1.992-2.1290.1899630.1618811X-RAY DIFFRACTION91.9379
2.129-2.30.1719060.14517482X-RAY DIFFRACTION91.4826
2.3-2.5190.1628860.13215767X-RAY DIFFRACTION90.5497
2.519-2.8160.1636880.12914296X-RAY DIFFRACTION89.994
2.816-3.2520.1726360.14312394X-RAY DIFFRACTION88.8813
3.252-3.9810.1695120.13810523X-RAY DIFFRACTION89.0638
3.981-5.6250.1554500.148252X-RAY DIFFRACTION90.712
5.625-46.7740.1792730.1774625X-RAY DIFFRACTION93.3842

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