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- PDB-7ezl: Rice L-galactose dehydrogenase (holo form) -

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Basic information

Entry
Database: PDB / ID: 7ezl
TitleRice L-galactose dehydrogenase (holo 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
NICOTINAMIDE-ADENINE-DINUCLEOTIDE / Os12g0482700 protein
Similarity search - Component
Biological speciesOryza sativa subsp. japonica (Japanese rice)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 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 / refine_hist
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 / _refine_hist.d_res_high

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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)35,9873
Polymers35,2991
Non-polymers6882
Water1,60389
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1320 Å2
ΔGint-16 kcal/mol
Surface area12970 Å2
MethodPISA
Unit cell
Length a, b, c (Å)47.838, 55.170, 56.911
Angle α, β, γ (deg.)90.000, 101.529, 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-NAD / 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-MG / MAGNESIUM ION


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


Mass: 18.015 Da / Num. of mol.: 89 / 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: 2.09 Å3/Da / Density % sol: 41.6 % / 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: AR-NW12A / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Apr 19, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.8→50 Å / Num. obs: 27173 / % possible obs: 99.6 % / Redundancy: 7 % / Rmerge(I) obs: 0.104 / Χ2: 2.765 / Net I/σ(I): 35.3
Reflection shellResolution: 1.8→1.83 Å / Rmerge(I) obs: 0.878 / Mean I/σ(I) obs: 2.7 / Num. unique obs: 1342 / Χ2: 1.547

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Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
HKL-2000data reduction
SCALEPACKdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 7EZI

7ezi


Resolution: 1.8→32.797 Å / Cor.coef. Fo:Fc: 0.959 / Cor.coef. Fo:Fc free: 0.936 / SU B: 4.892 / SU ML: 0.138 / Cross valid method: THROUGHOUT / ESU R: 0.156 / ESU R Free: 0.149
Details: Hydrogens have been used if present in the input file
RfactorNum. reflection% reflection
Rfree0.2573 1359 5.038 %
Rwork0.2089 25615 -
all0.211 --
obs-26974 99.587 %
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: 37.347 Å2
Baniso -1Baniso -2Baniso -3
1--0.171 Å20 Å20.367 Å2
2--0.212 Å20 Å2
3----0.176 Å2
Refinement stepCycle: LAST / Resolution: 1.8→32.797 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2425 0 45 89 2559
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0122521
X-RAY DIFFRACTIONr_angle_refined_deg1.5131.6353432
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.3765317
X-RAY DIFFRACTIONr_dihedral_angle_2_deg28.43622.034118
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.84515414
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.6841516
X-RAY DIFFRACTIONr_chiral_restr0.1080.2334
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.021894
X-RAY DIFFRACTIONr_nbd_refined0.2210.21248
X-RAY DIFFRACTIONr_nbtor_refined0.3090.21769
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1580.2118
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.1720.234
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.1650.22
X-RAY DIFFRACTIONr_mcbond_it3.1163.531271
X-RAY DIFFRACTIONr_mcangle_it4.4595.2721587
X-RAY DIFFRACTIONr_scbond_it3.8473.891250
X-RAY DIFFRACTIONr_scangle_it5.7825.681845
X-RAY DIFFRACTIONr_lrange_it7.78749.3233878
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRfactor allNum. reflection allFsc freeFsc work% reflection obs (%)WRfactor Rwork
1.8-1.8470.4611020.42318690.42519950.20.21598.7970.312
1.847-1.8970.379870.36318410.36419330.4850.52999.74130.275
1.897-1.9520.346790.31917740.3218630.7320.75399.46320.236
1.952-2.0120.306920.26817490.2718460.840.84799.72910.198
2.012-2.0770.3141120.26616620.26917770.8340.85599.83120.209
2.077-2.150.31830.25816300.26117160.8430.86599.82520.211
2.15-2.2310.338860.24915500.25416360.8320.8741000.215
2.231-2.3210.32680.22715030.2315720.860.90399.93640.192
2.321-2.4240.265930.21914470.22215410.8870.91299.93510.189
2.424-2.5420.287740.22514110.22814860.8960.91699.93270.199
2.542-2.6780.272690.22513220.22713940.9150.9299.78480.193
2.678-2.840.261720.21912480.22113200.9290.9271000.193
2.84-3.0340.222600.19911860.212490.9330.93699.75980.182
3.034-3.2750.275550.19111070.19411620.9080.9381000.188
3.275-3.5840.212550.17710180.17910740.930.95199.90690.183
3.584-4.0010.206410.1689320.179740.9520.9699.89730.176
4.001-4.6080.202460.158080.1538630.9520.96898.95710.164
4.608-5.6160.181420.166890.1627350.9630.96699.45580.183
5.616-7.8290.26280.1975570.25880.9210.95199.48980.224
7.829-32.7970.244150.1533000.1573450.9450.97391.30440.201

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