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- PDB-7arz: Ternary complex of NAD-dependent formate dehydrogenase from Physc... -

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Basic information

Entry
Database: PDB / ID: 7arz
TitleTernary complex of NAD-dependent formate dehydrogenase from Physcomitrium patens
ComponentsFormate dehydrogenase, mitochondrial
KeywordsOXIDOREDUCTASE / formate dehydrogenase / biocatalyst / cofactor / NAD / nicotinamide mononucleotide
Function / homology
Function and homology information


formate dehydrogenase complex / formate catabolic process / formate dehydrogenase / formate dehydrogenase (NAD+) activity / oxidoreductase activity, acting on the CH-OH group of donors, NAD or NADP as acceptor / chloroplast / NAD binding / mitochondrion
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 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
AZIDE ION / NICOTINAMIDE-ADENINE-DINUCLEOTIDE / Formate dehydrogenase, mitochondrial
Similarity search - Component
Biological speciesPhyscomitrium patens (plant)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.15 Å
AuthorsGoryaynova, D.A. / Nikolaeva, A.Y. / Pometun, A.A. / Savin, S.S. / Parshin, P.D. / Popov, V.O. / Tishkov, V.I. / Boyko, K.M.
Funding support Russian Federation, 1items
OrganizationGrant numberCountry
Russian Foundation for Basic Research18-34-20098 Russian Federation
CitationJournal: To Be Published
Title: Ternary complex of NAD-dependent formate dehydrogenase from Physcomitrium patens
Authors: Boyko, K.M. / Pometun, A.A. / Goryaynova, D.A. / Nikolaeva, A.Y. / Parshin, P.D. / Popov, V.O. / Tishkov, V.I.
History
DepositionOct 26, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 3, 2021Provider: repository / Type: Initial release
Revision 1.1Jan 31, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Formate dehydrogenase, mitochondrial
hetero molecules


Theoretical massNumber of molelcules
Total (without water)40,4654
Polymers39,7181
Non-polymers7473
Water2,216123
1
A: Formate dehydrogenase, mitochondrial
hetero molecules

A: Formate dehydrogenase, mitochondrial
hetero molecules


Theoretical massNumber of molelcules
Total (without water)80,9318
Polymers79,4362
Non-polymers1,4956
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation5_555x-y,-y,-z+1/31
Buried area9180 Å2
ΔGint-50 kcal/mol
Surface area26940 Å2
MethodPISA
Unit cell
Length a, b, c (Å)68.360, 68.360, 203.440
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number154
Space group name H-MP3221

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Components

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


Mass: 39717.973 Da / Num. of mol.: 1
Fragment: We used plasmid with gene of maturated enzyme without signal peptide. We also added extra Ala residue at N-terminus because according to Warshasly rule presence of Ala or Gly residues ...Fragment: We used plasmid with gene of maturated enzyme without signal peptide. We also added extra Ala residue at N-terminus because according to Warshasly rule presence of Ala or Gly residues exactly at N-terminus provides higher protein resistance and stability during expression in E.coli. Expression in E.coli of full length pro-peptide resulted in inactive inclusion bodies.
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Physcomitrium patens (plant) / Gene: PHYPA_020821, PHYPADRAFT_214795 / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): CodonPlus-RP / References: UniProt: A9SQZ2, formate dehydrogenase
#2: Chemical ChemComp-NAD / NICOTINAMIDE-ADENINE-DINUCLEOTIDE / Nicotinamide adenine dinucleotide


Mass: 663.425 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C21H27N7O14P2 / Feature type: SUBJECT OF INVESTIGATION / Comment: NAD*YM
#3: Chemical ChemComp-AZI / AZIDE ION / Azide


Mass: 42.020 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: N3 / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 123 / 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: 3.44 Å3/Da / Density % sol: 64.28 %
Crystal growTemperature: 288 K / Method: vapor diffusion, hanging drop / pH: 8 / Details: Tris 0.1M pH 8.0 + Ammonium sulfate 2.0M

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.969 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Dec 9, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.969 Å / Relative weight: 1
ReflectionResolution: 2.15→56.91 Å / Num. obs: 30481 / % possible obs: 98.5 % / Redundancy: 2.71 % / Biso Wilson estimate: 51.52 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.056 / Rrim(I) all: 0.07 / Χ2: 1.044 / Net I/σ(I): 11.08 / Num. measured all: 82602 / Scaling rejects: 8
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. possibleNum. unique obsCC1/2Rrim(I) all% possible all
2.15-2.32.6710.7541.2414490554154250.5170.93197.9
2.3-2.42.8240.4482.218294296929370.7440.54998.9
2.4-2.52.8340.3312.977113253425100.8320.40699.1
2.5-2.632.7730.2414.067605277027430.9050.29699
2.63-2.812.6440.1645.727727298829230.9590.20397.8
2.81-3.032.8020.1148.647750279327660.9790.14199
3.03-3.322.7570.07213.317212264626160.9910.08898.9
3.32-3.712.6070.04419.996164240123640.9960.05598.5
3.71-4.272.7790.03227.115769210720760.9980.0498.5
4.27-5.22.6010.02830.024646180617860.9980.03598.9
5.2-7.242.5930.02729.173736145314410.9980.03499.2
7.24-56.912.3450.0235.1320969328940.9990.02695.9

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
HKL-2000data reduction
XSCALEdata scaling
MOLREPphasing
REFMAC5.8.0267refinement
PDB_EXTRACT3.25data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3N7U

3n7u


Resolution: 2.15→56.91 Å / Cor.coef. Fo:Fc: 0.959 / Cor.coef. Fo:Fc free: 0.936 / SU B: 7.534 / SU ML: 0.177 / SU R Cruickshank DPI: 0.1887 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.189 / ESU R Free: 0.181 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2573 1516 5 %RANDOM
Rwork0.2056 ---
obs0.2082 28965 98.52 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 105.87 Å2 / Biso mean: 47.625 Å2 / Biso min: 19.86 Å2
Baniso -1Baniso -2Baniso -3
1-0.49 Å20.25 Å2-0 Å2
2--0.49 Å2-0 Å2
3----1.59 Å2
Refinement stepCycle: final / Resolution: 2.15→56.91 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2785 0 50 123 2958
Biso mean--46.5 46.15 -
Num. residues----361
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0132912
X-RAY DIFFRACTIONr_bond_other_d0.0010.0172728
X-RAY DIFFRACTIONr_angle_refined_deg1.6081.6433940
X-RAY DIFFRACTIONr_angle_other_deg1.2791.5876295
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.5195362
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.74622.483145
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.86315497
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.1751517
X-RAY DIFFRACTIONr_chiral_restr0.0740.2371
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.023307
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02646
LS refinement shellResolution: 2.15→2.206 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.426 96 -
Rwork0.351 2104 -
all-2200 -
obs--97.56 %

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