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- PDB-7ezi: Rice L-galactose dehydrogenase (apo form) -

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Basic information

Entry
Database: PDB / ID: 7ezi
TitleRice L-galactose dehydrogenase (apo form)
ComponentsL-galactose dehydrogenase
KeywordsOXIDOREDUCTASE / dehydrogenase
Function / homology
Function and homology information


L-galactose dehydrogenase activity / L-ascorbic acid biosynthetic process / nucleotide binding / metal ion binding
Similarity search - Function
L-galactose dehydrogenase-like / Aldo-keto reductase / NADP-dependent oxidoreductase domain / Aldo/keto reductase family / NADP-dependent oxidoreductase domain superfamily
Similarity search - Domain/homology
Os12g0482700 protein
Similarity search - Component
Biological speciesOryza sativa subsp. japonica (Japanese rice)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.2 Å
AuthorsMomma, M. / Fujimoto, Z.
Citation
Journal: To Be Published
Title: Crystal structure of rice L-galactose dehydrogenase
Authors: Momma, M. / Fujimoto, Z.
#1: Journal: Acta Crystallogr Sect F Struct Biol Cryst Commun / Year: 2013
Title: Expression, crystallization and preliminary X-ray analysis of rice L-galactose dehydrogenase.
Authors: Momma, M. / Fujimoto, Z.
History
DepositionJun 1, 2021Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jun 23, 2021Provider: repository / Type: Initial release
Revision 1.1Nov 29, 2023Group: 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
A: L-galactose dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,3242
Polymers35,2991
Non-polymers241
Water5,332296
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area130 Å2
ΔGint-9 kcal/mol
Surface area14360 Å2
MethodPISA
Unit cell
Length a, b, c (Å)46.745, 54.877, 56.753
Angle α, β, γ (deg.)90.000, 102.268, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein L-galactose dehydrogenase


Mass: 35299.324 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Oryza sativa subsp. japonica (Japanese rice)
Plasmid: pET-45b / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q2QQV2
#2: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 296 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 2.02 Å3/Da / Density % sol: 39 % / Description: rod
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 0.1M bis-tris pH 6.5, 0.2M MgCl2, 25% poly- ethylene glycol 3350

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Data collection

DiffractionMean temperature: 95 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-1A / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 270 / Detector: CCD / Date: Jan 23, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.2→100 Å / Num. obs: 87015 / % possible obs: 99.1 % / Redundancy: 7 % / Rmerge(I) obs: 0.077 / Χ2: 1.096 / Net I/σ(I): 17.4
Reflection shellResolution: 1.2→1.22 Å / Rmerge(I) obs: 0.611 / Mean I/σ(I) obs: 4.1 / Num. unique obs: 3919 / Χ2: 1.163

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Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
HKL-2000data reduction
SCALEPACKdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3LUT

3lut


Resolution: 1.2→32.092 Å / Cor.coef. Fo:Fc: 0.968 / Cor.coef. Fo:Fc free: 0.959 / SU B: 1.25 / SU ML: 0.026 / Cross valid method: THROUGHOUT / ESU R: 0.041 / ESU R Free: 0.042
Details: Hydrogens have been used if present in the input file
RfactorNum. reflection% reflection
Rfree0.1872 4348 4.999 %
Rwork0.1516 82622 -
all0.153 --
obs-86970 99.245 %
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT
Displacement parametersBiso mean: 18.964 Å2
Baniso -1Baniso -2Baniso -3
1-1.537 Å2-0 Å2-0.028 Å2
2---0.563 Å20 Å2
3----0.879 Å2
Refinement stepCycle: LAST / Resolution: 1.2→32.092 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2470 0 1 296 2767
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0170.0122525
X-RAY DIFFRACTIONr_angle_refined_deg2.1451.6293431
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.975322
X-RAY DIFFRACTIONr_dihedral_angle_2_deg29.50921.967122
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.05515419
X-RAY DIFFRACTIONr_dihedral_angle_4_deg211516
X-RAY DIFFRACTIONr_chiral_restr0.1340.2330
X-RAY DIFFRACTIONr_gen_planes_refined0.0150.021909
X-RAY DIFFRACTIONr_nbd_refined0.2130.21243
X-RAY DIFFRACTIONr_nbtor_refined0.3140.21773
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1780.2217
X-RAY DIFFRACTIONr_metal_ion_refined0.0240.21
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.1920.275
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.2360.224
X-RAY DIFFRACTIONr_mcbond_it2.0511.4981291
X-RAY DIFFRACTIONr_mcangle_it2.3732.2581612
X-RAY DIFFRACTIONr_scbond_it3.7061.9091234
X-RAY DIFFRACTIONr_scangle_it3.8742.7251819
X-RAY DIFFRACTIONr_lrange_it3.33422.9783968
X-RAY DIFFRACTIONr_rigid_bond_restr7.3832525
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.2-1.2310.2123460.185842X-RAY DIFFRACTION95.7598
1.231-1.2650.23120.1585951X-RAY DIFFRACTION99.9202
1.265-1.3020.1732930.1485797X-RAY DIFFRACTION100
1.302-1.3420.1882710.1395693X-RAY DIFFRACTION100
1.342-1.3860.1652860.1225474X-RAY DIFFRACTION100
1.386-1.4340.1612820.1185290X-RAY DIFFRACTION100
1.434-1.4880.1652400.1135159X-RAY DIFFRACTION99.963
1.488-1.5490.1652540.1084905X-RAY DIFFRACTION99.9806
1.549-1.6180.1512680.1024718X-RAY DIFFRACTION99.9799
1.618-1.6970.1642320.1114474X-RAY DIFFRACTION99.9788
1.697-1.7880.1772300.1164313X-RAY DIFFRACTION99.978
1.788-1.8970.162280.1214079X-RAY DIFFRACTION100
1.897-2.0270.181930.1273851X-RAY DIFFRACTION100
2.027-2.190.1571790.1423562X-RAY DIFFRACTION99.9733
2.19-2.3980.1722000.1553242X-RAY DIFFRACTION100
2.398-2.6810.2241470.1742989X-RAY DIFFRACTION100
2.681-3.0940.21300.1822645X-RAY DIFFRACTION100
3.094-3.7870.1911160.1742219X-RAY DIFFRACTION98.7733
3.787-5.3430.209850.1831603X-RAY DIFFRACTION92.0393
5.343-32.0920.29560.239811X-RAY DIFFRACTION82.4145

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