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- PDB-3jtm: Structure of recombinant formate dehydrogenase from Arabidopsis t... -

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Basic information

Entry
Database: PDB / ID: 3jtm
TitleStructure of recombinant formate dehydrogenase from Arabidopsis thaliana
ComponentsFormate dehydrogenase, mitochondrial
KeywordsOXIDOREDUCTASE / formate dehydrogenase / Mitochondrion / NAD / Transit peptide
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 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-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 Rossmann-like Domain / NAD(P)-binding domain superfamily / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
AZIDE ION / Formate dehydrogenase, chloroplastic/mitochondrial
Similarity search - Component
Biological speciesArabidopsis thaliana (thale cress)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.3 Å
AuthorsTimofeev, V.I. / Shabalin, I.G. / Serov, A.E. / Polyakov, K.M. / Popov, V.O. / Tishkov, V.I. / Kuranova, I.P. / Samigina, V.R.
CitationJournal: to be published
Title: Structure of recombinant formate dehydrogenase from Arabidopsis thaliana
Authors: Timofeev, V.I. / Shabalin, I.G. / Serov, A.E. / Polyakov, K.M. / Popov, V.O. / Tishkov, V.I. / Kuranova, I.P. / Samigina, V.R.
History
DepositionSep 13, 2009Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Sep 15, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Mar 20, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / diffrn_source / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _diffrn_source.pdbx_synchrotron_site / _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

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Assembly

Deposited unit
A: Formate dehydrogenase, mitochondrial
hetero molecules


Theoretical massNumber of molelcules
Total (without water)40,37217
Polymers38,9911
Non-polymers1,38116
Water7,080393
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: Formate dehydrogenase, mitochondrial
hetero molecules

A: Formate dehydrogenase, mitochondrial
hetero molecules


Theoretical massNumber of molelcules
Total (without water)80,74434
Polymers77,9812
Non-polymers2,76332
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_555y,x,-z1
Buried area11780 Å2
ΔGint-93 kcal/mol
Surface area29400 Å2
MethodPISA
Unit cell
Length a, b, c (Å)107.865, 107.865, 71.180
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212
Components on special symmetry positions
IDModelComponents
11A-450-

HOH

21A-591-

HOH

31A-735-

HOH

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Components

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


Mass: 38990.621 Da / Num. of mol.: 1 / Fragment: UNP residues 34-384
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Arabidopsis thaliana (thale cress) / Strain: ecotype Columbia / Gene: formate dehydrogenase AF217195 / Plasmid: modified pET23a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 / References: UniProt: Q9S7E4, formate dehydrogenase
#2: Chemical ChemComp-SO4 / SULFATE ION


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


Mass: 92.094 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: C3H8O3
#4: Chemical ChemComp-AZI / AZIDE ION


Mass: 42.020 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: N3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 393 / 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: 2.66 Å3/Da / Density % sol: 53.67 %

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: X11 / Wavelength: 0.97 Å
DetectorType: MARRESEARCH / Detector: CCD
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97 Å / Relative weight: 1
ReflectionResolution: 1.294→76.249 Å / Num. obs: 101134 / Biso Wilson estimate: 15.12 Å2

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Processing

SoftwareName: PHENIX / Version: (phenix.refine) / Classification: refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.3→5.996 Å / Occupancy max: 1 / Occupancy min: 0.3 / FOM work R set: 0.929 / SU ML: 0.14 / σ(F): 4.45 / Phase error: 14.23 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.178 4097 4.98 %
Rwork0.1526 78178 -
obs0.1538 82275 80.78 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 94.657 Å2 / ksol: 0.6 e/Å3
Displacement parametersBiso max: 56.67 Å2 / Biso mean: 24.178 Å2 / Biso min: 10.18 Å2
Baniso -1Baniso -2Baniso -3
1-2.406 Å20 Å2-0 Å2
2--2.406 Å20 Å2
3----4.812 Å2
Refinement stepCycle: LAST / Resolution: 1.3→5.996 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2703 0 88 393 3184
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0062903
X-RAY DIFFRACTIONf_angle_d1.1363928
X-RAY DIFFRACTIONf_dihedral_angle_d15.8121065
X-RAY DIFFRACTIONf_chiral_restr0.079423
X-RAY DIFFRACTIONf_plane_restr0.006498
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.3-1.31520.1581220.10872026X-RAY DIFFRACTION61
1.3152-1.3310.15341060.11032030X-RAY DIFFRACTION62
1.331-1.34770.15771170.11532177X-RAY DIFFRACTION66
1.3477-1.36520.1942910.11612273X-RAY DIFFRACTION68
1.3652-1.38370.1551150.12032281X-RAY DIFFRACTION69
1.3837-1.40320.17071060.11662320X-RAY DIFFRACTION70
1.4032-1.42390.15321110.11142424X-RAY DIFFRACTION73
1.4239-1.44580.17661320.1162408X-RAY DIFFRACTION74
1.4458-1.46920.13921490.11092434X-RAY DIFFRACTION74
1.4692-1.49410.15871340.10772533X-RAY DIFFRACTION77
1.4941-1.52090.1381300.11112576X-RAY DIFFRACTION77
1.5209-1.54960.14581320.11022622X-RAY DIFFRACTION79
1.5496-1.58070.14971390.11472726X-RAY DIFFRACTION81
1.5807-1.61440.13881510.1142719X-RAY DIFFRACTION83
1.6144-1.65120.14831420.12252717X-RAY DIFFRACTION82
1.6512-1.69160.1661280.12952709X-RAY DIFFRACTION81
1.6916-1.73630.20111220.13692861X-RAY DIFFRACTION85
1.7363-1.7860.18131550.13922737X-RAY DIFFRACTION83
1.786-1.84210.16751510.13822710X-RAY DIFFRACTION82
1.8421-1.90590.15151500.14712751X-RAY DIFFRACTION82
1.9059-1.97950.14491530.14322873X-RAY DIFFRACTION86
1.9795-2.06610.16651660.14153100X-RAY DIFFRACTION93
2.0661-2.17010.16731470.14863137X-RAY DIFFRACTION93
2.1701-2.29890.18321680.14743062X-RAY DIFFRACTION91
2.2989-2.46480.19141800.15523056X-RAY DIFFRACTION91
2.4648-2.69230.21271750.16823064X-RAY DIFFRACTION91
2.6923-3.03670.20151730.17673197X-RAY DIFFRACTION94
3.0367-3.67340.17691740.16063308X-RAY DIFFRACTION96
3.6734-5.99560.16621780.15953347X-RAY DIFFRACTION95

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