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- PDB-8j83: Crystal structure of formate dehydrogenase from Methylorubrum ext... -

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Basic information

Entry
Database: PDB / ID: 8j83
TitleCrystal structure of formate dehydrogenase from Methylorubrum extorquens AM1
Components(Tungsten-containing formate dehydrogenase ...) x 2
KeywordsOXIDOREDUCTASE / formate dehydrogenase / NAD+ dependent / tungsten-containing / metallopterin guanine dinucleotide
Function / homology
Function and homology information


formate dehydrogenase / formate metabolic process / formate dehydrogenase / oxidoreductase complex / formate dehydrogenase (NAD+) activity / molybdopterin cofactor binding / cellular respiration / NADH dehydrogenase (ubiquinone) activity / 2 iron, 2 sulfur cluster binding / FMN binding ...formate dehydrogenase / formate metabolic process / formate dehydrogenase / oxidoreductase complex / formate dehydrogenase (NAD+) activity / molybdopterin cofactor binding / cellular respiration / NADH dehydrogenase (ubiquinone) activity / 2 iron, 2 sulfur cluster binding / FMN binding / 4 iron, 4 sulfur cluster binding / metal ion binding
Similarity search - Function
Formate dehydrogenase H, molybdopterin-binding domain / Formate dehydrogenase, alpha subunit / Formate dehydrogenase H, N-terminal / Prokaryotic molybdopterin oxidoreductases signature 2. / Molybdopterin oxidoreductase, prokaryotic, conserved site / Molybdopterin oxidoreductase Fe4S4 domain / Molybdopterin oxidoreductase Fe4S4 domain / Molybdopterin dinucleotide-binding domain / Molydopterin dinucleotide binding domain / Soluble ligand binding domain ...Formate dehydrogenase H, molybdopterin-binding domain / Formate dehydrogenase, alpha subunit / Formate dehydrogenase H, N-terminal / Prokaryotic molybdopterin oxidoreductases signature 2. / Molybdopterin oxidoreductase, prokaryotic, conserved site / Molybdopterin oxidoreductase Fe4S4 domain / Molybdopterin oxidoreductase Fe4S4 domain / Molybdopterin dinucleotide-binding domain / Molydopterin dinucleotide binding domain / Soluble ligand binding domain / SLBB domain / Aspartate decarboxylase-like domain superfamily / 2Fe-2S iron-sulfur cluster binding domain / Respiratory-chain NADH dehydrogenase 51 Kd subunit signature 1. / Thioredoxin-like [2Fe-2S] ferredoxin / NADH-quinone oxidoreductase subunit E, N-terminal / NADH:ubiquinone oxidoreductase, 51kDa subunit, conserved site / Respiratory-chain NADH dehydrogenase 51 Kd subunit signature 2. / NADH-ubiquinone oxidoreductase 51kDa subunit, iron-sulphur binding domain / NADH-ubiquinone oxidoreductase 51kDa subunit, iron-sulphur binding domain superfamily / NADH-ubiquinone oxidoreductase-F iron-sulfur binding region / NADH-ubiquinone oxidoreductase-F iron-sulfur binding region / NADH-ubiquinone oxidoreductase 51kDa subunit, FMN-binding domain / NADH-ubiquinone oxidoreductase 51kDa subunit, FMN-binding domain superfamily / Respiratory-chain NADH dehydrogenase 51 Kd subunit / Molybdopterin oxidoreductase, 4Fe-4S domain / Prokaryotic molybdopterin oxidoreductases 4Fe-4S domain profile. / Molybdopterin oxidoreductase / Molybdopterin oxidoreductase / 4Fe-4S dicluster domain / 2Fe-2S ferredoxin-type iron-sulfur binding domain profile. / 2Fe-2S ferredoxin-type iron-sulfur binding domain / 2Fe-2S ferredoxin-like superfamily / 4Fe-4S ferredoxin, iron-sulphur binding, conserved site / 4Fe-4S ferredoxin-type iron-sulfur binding region signature. / 4Fe-4S ferredoxin-type iron-sulfur binding domain profile. / 4Fe-4S ferredoxin-type, iron-sulphur binding domain / Thioredoxin-like superfamily
Similarity search - Domain/homology
FE2/S2 (INORGANIC) CLUSTER / FLAVIN MONONUCLEOTIDE / Chem-MGD / DI(HYDROXYETHYL)ETHER / IRON/SULFUR CLUSTER / : / Tungsten-containing formate dehydrogenase beta subunit / formate dehydrogenase
Similarity search - Component
Biological speciesMethylorubrum extorquens AM1 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.4 Å
AuthorsKobayashi, A. / Taketa, M. / Sowa, K. / Kano, K. / Higuchi, Y. / Ogata, H.
Funding support Japan, 3items
OrganizationGrant numberCountry
Japan Society for the Promotion of Science (JSPS)JP22K14831 Japan
Japan Society for the Promotion of Science (JSPS)19H00984 Japan
Japan Society for the Promotion of Science (JSPS)18H05516 Japan
CitationJournal: Iucrj / Year: 2023
Title: Structure and function relationship of formate dehydrogenases: an overview of recent progress.
Authors: Kobayashi, A. / Taketa, M. / Sowa, K. / Kano, K. / Higuchi, Y. / Ogata, H.
History
DepositionApr 29, 2023Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Oct 11, 2023Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Tungsten-containing formate dehydrogenase alpha subunit
B: Tungsten-containing formate dehydrogenase beta subunit
hetero molecules


Theoretical massNumber of molelcules
Total (without water)174,30818
Polymers169,8622
Non-polymers4,44616
Water181
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area13040 Å2
ΔGint-191 kcal/mol
Surface area48780 Å2
MethodPISA
Unit cell
Length a, b, c (Å)232.860, 73.950, 95.740
Angle α, β, γ (deg.)90.00, 106.72, 90.00
Int Tables number5
Space group name H-MC121

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Components

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Tungsten-containing formate dehydrogenase ... , 2 types, 2 molecules AB

#1: Protein Tungsten-containing formate dehydrogenase alpha subunit


Mass: 107464.000 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Methylorubrum extorquens AM1 (bacteria) / References: UniProt: C5ATT7, formate dehydrogenase
#2: Protein Tungsten-containing formate dehydrogenase beta subunit


Mass: 62397.508 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Methylorubrum extorquens AM1 (bacteria) / References: UniProt: C5ATT6, formate dehydrogenase

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Non-polymers , 8 types, 17 molecules

#3: Chemical ChemComp-MGD / 2-AMINO-5,6-DIMERCAPTO-7-METHYL-3,7,8A,9-TETRAHYDRO-8-OXA-1,3,9,10-TETRAAZA-ANTHRACEN-4-ONE GUANOSINE DINUCLEOTIDE / MOLYBDOPTERIN GUANOSINE DINUCLEOTIDE


Mass: 740.557 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C20H26N10O13P2S2
#4: Chemical ChemComp-W / TUNGSTEN ION


Mass: 183.840 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: W
#5: Chemical ChemComp-FES / FE2/S2 (INORGANIC) CLUSTER


Mass: 175.820 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Formula: Fe2S2
#6: Chemical
ChemComp-SF4 / IRON/SULFUR CLUSTER


Mass: 351.640 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Fe4S4
#7: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C3H8O3
#8: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O3
#9: Chemical ChemComp-FMN / FLAVIN MONONUCLEOTIDE / RIBOFLAVIN MONOPHOSPHATE


Mass: 456.344 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C17H21N4O9P / Feature type: SUBJECT OF INVESTIGATION
#10: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1 / 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: 49.9 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop
Details: Trisodium citrate dihydrate, Tris-HCl, PEG 400, NAD

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL44XU / Wavelength: 0.9 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jul 27, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9 Å / Relative weight: 1
ReflectionResolution: 2.4→47.5 Å / Num. obs: 57343 / % possible obs: 93.6 % / Redundancy: 2.8 % / CC1/2: 0.994 / Net I/σ(I): 8.5
Reflection shellResolution: 2.4→2.46 Å / Num. unique obs: 4364 / CC1/2: 0.635

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Processing

Software
NameVersionClassification
PHENIX(1.20.1_4487: ???)refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.4→47.48 Å / SU ML: 0.37 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 29.61 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2589 2866 5 %
Rwork0.2192 --
obs0.2212 57323 93.61 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.4→47.48 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11285 0 203 1 11489
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00411761
X-RAY DIFFRACTIONf_angle_d0.86916014
X-RAY DIFFRACTIONf_dihedral_angle_d15.6064363
X-RAY DIFFRACTIONf_chiral_restr0.0481755
X-RAY DIFFRACTIONf_plane_restr0.0072092
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.4-2.440.34281460.31022770X-RAY DIFFRACTION96
2.44-2.490.36591470.30682789X-RAY DIFFRACTION97
2.49-2.530.35251480.30572800X-RAY DIFFRACTION97
2.53-2.590.3531450.30022770X-RAY DIFFRACTION96
2.59-2.640.35951450.30412772X-RAY DIFFRACTION96
2.64-2.70.35451450.30552770X-RAY DIFFRACTION96
2.7-2.770.31711470.29462790X-RAY DIFFRACTION96
2.77-2.850.35451450.28492756X-RAY DIFFRACTION95
2.85-2.930.32671440.28192734X-RAY DIFFRACTION95
2.93-3.020.3351450.28252741X-RAY DIFFRACTION94
3.02-3.130.28431430.2652716X-RAY DIFFRACTION94
3.13-3.260.30251400.25552674X-RAY DIFFRACTION92
3.26-3.410.28131440.23842721X-RAY DIFFRACTION93
3.41-3.580.26461410.23882692X-RAY DIFFRACTION93
3.58-3.810.28871420.21142695X-RAY DIFFRACTION93
3.81-4.10.2521410.19292684X-RAY DIFFRACTION92
4.1-4.520.20171400.17712651X-RAY DIFFRACTION91
4.52-5.170.19631400.17292666X-RAY DIFFRACTION91
5.17-6.510.23571370.17972604X-RAY DIFFRACTION88
6.51-47.480.16761410.1472662X-RAY DIFFRACTION88

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