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- PDB-5jci: Structure and catalytic mechanism of monodehydroascorbate reducta... -

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Basic information

Entry
Database: PDB / ID: 5jci
TitleStructure and catalytic mechanism of monodehydroascorbate reductase, MDHAR, from Oryza sativa L. japonica
ComponentsOs09g0567300 protein
KeywordsHYDROLASE
Function / homology
Function and homology information


monodehydroascorbate reductase (NADH) / monodehydroascorbate reductase (NADH) activity / oxidoreductase activity, acting on NAD(P)H / cellular oxidant detoxification / peroxisomal matrix / flavin adenine dinucleotide binding / mRNA binding / cytoplasm
Similarity search - Function
: / Monodehydroascorbate reductase 3-like, C-terminal domain / FAD/NAD-linked reductase, C-terminal dimerisation domain / FAD/NAD-linked reductase, dimerisation domain superfamily / FAD/NAD(P)-binding domain / Pyridine nucleotide-disulphide oxidoreductase / Enolase-like; domain 1 / FAD/NAD(P)-binding domain / FAD/NAD(P)-binding domain / 3-Layer(bba) Sandwich ...: / Monodehydroascorbate reductase 3-like, C-terminal domain / FAD/NAD-linked reductase, C-terminal dimerisation domain / FAD/NAD-linked reductase, dimerisation domain superfamily / FAD/NAD(P)-binding domain / Pyridine nucleotide-disulphide oxidoreductase / Enolase-like; domain 1 / FAD/NAD(P)-binding domain / FAD/NAD(P)-binding domain / 3-Layer(bba) Sandwich / FAD/NAD(P)-binding domain superfamily / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
FLAVIN-ADENINE DINUCLEOTIDE / Monodehydroascorbate reductase 3, cytosolic
Similarity search - Component
Biological speciesOryza sativa subsp. japonica (Japanese rice)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.7 Å
AuthorsPark, A.K. / Kim, H.W.
Funding support Korea, Republic Of, 1items
OrganizationGrant numberCountry
Korea Polar Research InstitutePE16070 Korea, Republic Of
CitationJournal: Sci Rep / Year: 2016
Title: Structure and catalytic mechanism of monodehydroascorbate reductase, MDHAR, from Oryza sativa L. japonica
Authors: Park, A.K. / Kim, I.S. / Do, H. / Jeon, B.W. / Lee, C.W. / Roh, S.J. / Shin, S.C. / Park, H. / Kim, Y.S. / Kim, Y.H. / Yoon, H.S. / Lee, J.H. / Kim, H.W.
History
DepositionApr 15, 2016Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Oct 12, 2016Provider: repository / Type: Initial release
Revision 1.1Mar 20, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_oper_list
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_oper_list.symmetry_operation

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Os09g0567300 protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)49,6512
Polymers48,8651
Non-polymers7861
Water8,665481
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1430 Å2
ΔGint-6 kcal/mol
Surface area17940 Å2
MethodPISA
Unit cell
Length a, b, c (Å)81.270, 81.270, 120.665
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number92
Space group name H-MP41212
Components on special symmetry positions
IDModelComponents
11A-740-

HOH

21A-837-

HOH

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Components

#1: Protein Os09g0567300 protein / Putative monodehydroascorbate reductase


Mass: 48865.379 Da / Num. of mol.: 1 / Fragment: UNP residues 4-435
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Oryza sativa subsp. japonica (Japanese rice)
Gene: Os09g0567300, Os09g0567300, OJ1155_H10.27, OSNPB_090567300
Production host: Escherichia coli (E. coli) / References: UniProt: Q652L6
#2: Chemical ChemComp-FAD / FLAVIN-ADENINE DINUCLEOTIDE / Flavin adenine dinucleotide


Mass: 785.550 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Formula: C27H33N9O15P2 / Comment: FAD*YM
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 481 / 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: 2.24 Å3/Da / Density % sol: 39.67 %
Description: THE ENTRY CONTAINS FRIEDEL PAIRS IN F_PLUS/MINUS COLUMNS.
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / Details: Tris, lithium sulfate, PEG 5000 MME

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: PAL/PLS / Beamline: 5C (4A) / Wavelength: 0.97954 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Oct 10, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97954 Å / Relative weight: 1
ReflectionResolution: 1.7→67.5 Å / Num. obs: 85440 / % possible obs: 99.2 % / Redundancy: 4.8 % / Rmerge(I) obs: 0.063 / Χ2: 2.707 / Net I/av σ(I): 41.391 / Net I/σ(I): 17.3 / Num. measured all: 410067
Reflection shell

Diffraction-ID: 1 / Rejects: 0

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2% possible all
1.7-1.734.70.29542911.854100
1.73-1.764.80.26342671.991100
1.76-1.794.80.22842862.049100
1.79-1.834.80.19943082.154100
1.83-1.874.90.17642582.261100
1.87-1.914.90.15443572.367100
1.91-1.964.90.13442442.474100
1.96-2.024.90.11743132.536100
2.02-2.074.90.10342812.734100
2.07-2.144.90.09643302.785100
2.14-2.224.90.08442712.837100
2.22-2.314.90.07742992.963100
2.31-2.414.90.07442882.941100
2.41-2.544.90.06943212.909100
2.54-2.74.90.06543133.089100
2.7-2.914.90.05843033.164100
2.91-3.24.80.05143003.163100
3.2-3.664.70.04642913.32399.5
3.66-4.614.30.04541973.38696.7
4.61-504.10.04739223.38289.1

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Processing

Software
NameVersionClassification
REFMAC5.8.0103refinement
HKL-2000data collection
SCALEPACKdata scaling
PDB_EXTRACT3.2data extraction
HKL-2000data reduction
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.7→50 Å / Cor.coef. Fo:Fc: 0.973 / Cor.coef. Fo:Fc free: 0.958 / SU B: 1.759 / SU ML: 0.058 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.092 / ESU R Free: 0.093 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.1798 2140 4.8 %RANDOM
Rwork0.1433 ---
obs0.145 42704 98.99 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 92.42 Å2 / Biso mean: 22.765 Å2 / Biso min: 11 Å2
Baniso -1Baniso -2Baniso -3
1--0.02 Å2-0 Å20 Å2
2---0.02 Å20 Å2
3---0.03 Å2
Refinement stepCycle: final / Resolution: 1.7→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3278 0 53 481 3812
Biso mean--13.92 33.83 -
Num. residues----432
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.030.0193406
X-RAY DIFFRACTIONr_bond_other_d0.0020.023247
X-RAY DIFFRACTIONr_angle_refined_deg2.6571.9874619
X-RAY DIFFRACTIONr_angle_other_deg1.24637499
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.0055431
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.6824.741135
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.19315557
X-RAY DIFFRACTIONr_dihedral_angle_4_deg12.8671511
X-RAY DIFFRACTIONr_chiral_restr0.1830.2509
X-RAY DIFFRACTIONr_gen_planes_refined0.0150.0213830
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02734
X-RAY DIFFRACTIONr_mcbond_it2.41.9141727
X-RAY DIFFRACTIONr_mcbond_other2.3931.9121726
X-RAY DIFFRACTIONr_mcangle_it3.1932.8672157
LS refinement shellResolution: 1.698→1.742 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.226 158 -
Rwork0.191 3108 -
all-3266 -
obs--99.39 %

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