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- PDB-3n7u: NAD-dependent formate dehydrogenase from higher-plant Arabidopsis... -

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Basic information

Entry
Database: PDB / ID: 3n7u
TitleNAD-dependent formate dehydrogenase from higher-plant Arabidopsis thaliana in complex with NAD and azide
ComponentsFormate dehydrogenase
KeywordsOXIDOREDUCTASE / homodimer / Holo-form
Function / homology
Function and homology information


formate catabolic process / formate dehydrogenase / formate dehydrogenase (NAD+) activity / thylakoid / oxidoreductase activity, acting on the CH-OH group of donors, NAD or NADP as acceptor / plastid / chloroplast / 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 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-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 Rossmann-like Domain / NAD(P)-binding domain superfamily / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
AZIDE ION / NICOTINAMIDE-ADENINE-DINUCLEOTIDE / Formate dehydrogenase, chloroplastic/mitochondrial
Similarity search - Component
Biological speciesArabidopsis thaliana (thale cress)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2 Å
AuthorsShabalin, I.G. / Polyakov, K.M. / Serov, A.E. / Skirgello, O.E. / Sadykhov, E.G. / Dorovatovskiy, P.V. / Tishkov, V.I. / Popov, V.O.
CitationJournal: To be Published
Title: Structures of the apo and holo forms of NAD-dependent formate dehydrogenase from the higher-plant Arabidopsis Thaliana
Authors: Shabalin, I.G. / Polyakov, K.M. / Skirgello, O.E. / Tishkov, V.I. / Popov, V.O.
History
DepositionMay 27, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 9, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Feb 21, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Formate dehydrogenase
B: Formate dehydrogenase
C: Formate dehydrogenase
D: Formate dehydrogenase
E: Formate dehydrogenase
F: Formate dehydrogenase
G: Formate dehydrogenase
H: Formate dehydrogenase
I: Formate dehydrogenase
J: Formate dehydrogenase
K: Formate dehydrogenase
L: Formate dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)478,96764
Polymers467,88712
Non-polymers11,08052
Water67,4663745
1
A: Formate dehydrogenase
B: Formate dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)79,6769
Polymers77,9812
Non-polymers1,6957
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9560 Å2
ΔGint-71 kcal/mol
Surface area26360 Å2
MethodPISA
2
C: Formate dehydrogenase
D: Formate dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)80,13714
Polymers77,9812
Non-polymers2,15612
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area10230 Å2
ΔGint-71 kcal/mol
Surface area26470 Å2
MethodPISA
3
E: Formate dehydrogenase
F: Formate dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)79,6729
Polymers77,9812
Non-polymers1,6917
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9740 Å2
ΔGint-65 kcal/mol
Surface area26430 Å2
MethodPISA
4
G: Formate dehydrogenase
H: Formate dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)79,86111
Polymers77,9812
Non-polymers1,8799
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area10080 Å2
ΔGint-87 kcal/mol
Surface area26190 Å2
MethodPISA
5
I: Formate dehydrogenase
J: Formate dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)79,76410
Polymers77,9812
Non-polymers1,7838
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area10170 Å2
ΔGint-74 kcal/mol
Surface area26070 Å2
MethodPISA
6
K: Formate dehydrogenase
L: Formate dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)79,85711
Polymers77,9812
Non-polymers1,8759
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area10290 Å2
ΔGint-78 kcal/mol
Surface area26180 Å2
MethodPISA
Unit cell
Length a, b, c (Å)229.620, 217.680, 139.110
Angle α, β, γ (deg.)90.000, 92.620, 90.000
Int Tables number5
Space group name H-MC121

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Components

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Protein , 1 types, 12 molecules ABCDEFGHIJKL

#1: Protein
Formate dehydrogenase / / NAD-dependent formate dehydrogenase / FDH


Mass: 38990.621 Da / Num. of mol.: 12
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Arabidopsis thaliana (thale cress) / Gene: At5g14780, FDH, FDH1, T9L3_80 / Plasmid: p1AraFDH / Production host: Escherichia coli (E. coli) / Strain (production host): Bl21(DE3) / References: UniProt: Q9S7E4, formate dehydrogenase

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Non-polymers , 5 types, 3797 molecules

#2: Chemical
ChemComp-NAD / NICOTINAMIDE-ADENINE-DINUCLEOTIDE / Nicotinamide adenine dinucleotide


Mass: 663.425 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: C21H27N7O14P2 / Comment: NAD*YM
#3: Chemical
ChemComp-AZI / AZIDE ION / Azide


Mass: 42.020 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: N3
#4: Chemical
ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: SO4
#5: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 19 / Source method: obtained synthetically / Formula: C3H8O3
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 3745 / Source method: isolated from a natural source / Formula: H2O

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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: 3.71 Å3/Da / Density % sol: 66.86 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: Protein solution (2ml): 14 mg/ml FDH, 0.1M Na2HPO4, pH 7.0, 10 mM EDTA, 5mM sodium azide, 5mM NAD. Reservoir solution (2ml): 0.1M Bis-Tris, pH 5.5, 2.1M Ammonium Sulfate, VAPOR DIFFUSION, ...Details: Protein solution (2ml): 14 mg/ml FDH, 0.1M Na2HPO4, pH 7.0, 10 mM EDTA, 5mM sodium azide, 5mM NAD. Reservoir solution (2ml): 0.1M Bis-Tris, pH 5.5, 2.1M Ammonium Sulfate, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: KURCHATOV SNC / Beamline: K4.4 / Wavelength: 0.99 Å
DetectorType: MAR CCD 165 mm / Detector: CCD
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.99 Å / Relative weight: 1
ReflectionResolution: 2→19.99 Å / Num. all: 457766 / Num. obs: 428654 / % possible obs: 93.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 2.1 % / Biso Wilson estimate: 25.095 Å2 / Rmerge(I) obs: 0.075 / Net I/σ(I): 8.93
Reflection shellResolution: 2→2.07 Å / Redundancy: 1.8 % / Rmerge(I) obs: 0.328 / Mean I/σ(I) obs: 2.6 / Num. measured obs: 75579 / Num. unique all: 39349 / Num. unique obs: 42823 / % possible all: 87.9

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
XSCALEdata scaling
MOLREPphasing
REFMACrefinement
PDB_EXTRACT3.1data extraction
AUTOMARdata collection
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2→19.99 Å / Cor.coef. Fo:Fc: 0.953 / Cor.coef. Fo:Fc free: 0.928 / WRfactor Rfree: 0.206 / WRfactor Rwork: 0.168 / Occupancy max: 1 / Occupancy min: 0.5 / FOM work R set: 0.839 / SU B: 3.551 / SU ML: 0.097 / SU R Cruickshank DPI: 0.144 / SU Rfree: 0.141 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.141 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: U VALUES REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.231 22264 5 %RANDOM
Rwork0.189 ---
obs0.191 421051 96.95 %-
all-434297 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso max: 62.55 Å2 / Biso mean: 24.463 Å2 / Biso min: 6.15 Å2
Baniso -1Baniso -2Baniso -3
1-0.61 Å20 Å20 Å2
2---1.28 Å20 Å2
3---0.67 Å2
Refine analyzeLuzzati coordinate error obs: 0.226 Å
Refinement stepCycle: LAST / Resolution: 2→19.99 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms32868 0 723 3745 37336
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0190.02234285
X-RAY DIFFRACTIONr_angle_refined_deg1.6391.99346483
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.45754200
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.46524.721500
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.434155882
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.01415180
X-RAY DIFFRACTIONr_chiral_restr0.1130.25112
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.02125668
X-RAY DIFFRACTIONr_mcbond_it0.8071.520904
X-RAY DIFFRACTIONr_mcangle_it1.419233636
X-RAY DIFFRACTIONr_scbond_it2.415313381
X-RAY DIFFRACTIONr_scangle_it3.7424.512847
LS refinement shellResolution: 2→2.051 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.349 1518 -
Rwork0.3 30332 -
all-31850 -
obs--94.98 %

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