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

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Basic information

Entry
Database: PDB / ID: 5jck
TitleStructure and catalytic mechanism of monodehydroascorbate reductase, MDHAR, from Oryza sativa L. japonica
ComponentsOs09g0567300 protein
KeywordsHYDROLASE / hydrorase
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 / nucleotide 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 ...: / 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 / NICOTINAMIDE-ADENINE-DINUCLEOTIDE / Monodehydroascorbate reductase 3, cytosolic
Similarity search - Component
Biological speciesOryza sativa subsp. japonica (Japanese rice)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsPark, A.K. / Kim, H.W.
CitationJournal: Sci Rep
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 1.1Nov 8, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / 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)50,3143
Polymers48,8651
Non-polymers1,4492
Water7,098394
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2750 Å2
ΔGint-10 kcal/mol
Surface area17590 Å2
MethodPISA
Unit cell
Length a, b, c (Å)81.473, 81.473, 121.357
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-746-

HOH

21A-912-

HOH

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Components

#1: Protein Os09g0567300 protein / Putative monodehydroascorbate reductase


Mass: 48865.379 Da / Num. of mol.: 1
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


Mass: 785.550 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C27H33N9O15P2 / Comment: FAD*YM
#3: Chemical ChemComp-NAD / NICOTINAMIDE-ADENINE-DINUCLEOTIDE


Mass: 663.425 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C21H27N7O14P2 / Comment: NAD*YM
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 394 / 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: 2.17 Å3/Da / Density % sol: 43.28 %
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, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97954 Å / Relative weight: 1
ReflectionResolution: 2→50 Å / Num. obs: 53422 / % possible obs: 99.7 % / Redundancy: 14.1 % / Rmerge(I) obs: 0.145 / Χ2: 1.433 / Net I/av σ(I): 25.701 / Net I/σ(I): 5.7 / Num. measured all: 751594
Reflection shell

Diffraction-ID: 1 / Rejects: _

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2% possible all
2-2.0314.40.35526730.746100
2.03-2.0714.50.31826590.837100
2.07-2.1114.50.29926710.869100
2.11-2.1514.40.28426630.951100
2.15-2.214.50.2626841.047100
2.2-2.2514.60.24226761.163100
2.25-2.3114.60.23926501.202100
2.31-2.3714.70.22226711.203100
2.37-2.4414.70.20726761.27100
2.44-2.5214.80.19826711.3100
2.52-2.6114.80.18427101.406100
2.61-2.7114.80.1726571.551100
2.71-2.8414.80.15726691.665100
2.84-2.9914.70.14626861.811100
2.99-3.1714.40.12926781.907100
3.17-3.4213.20.11726922.22499.9
3.42-3.7612.40.10826592.20399.4
3.76-4.3111.70.10226802.14999.1
4.31-5.4312.40.09526681.95899.1
5.43-5012.30.08926291.65295.7

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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
Starting model: 4H4Q

4h4q


Resolution: 2→50 Å / Cor.coef. Fo:Fc: 0.962 / Cor.coef. Fo:Fc free: 0.929 / SU B: 3.399 / SU ML: 0.097 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.166 / ESU R Free: 0.159 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2087 1360 4.8 %RANDOM
Rwork0.1444 ---
obs0.1474 26925 99.45 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 88.9 Å2 / Biso mean: 20.488 Å2 / Biso min: 8.3 Å2
Baniso -1Baniso -2Baniso -3
1--0.21 Å20 Å20 Å2
2---0.21 Å20 Å2
3---0.41 Å2
Refinement stepCycle: final / Resolution: 2→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3278 0 97 394 3769
Biso mean--12.02 29.87 -
Num. residues----432
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0240.023454
X-RAY DIFFRACTIONr_bond_other_d0.0030.023271
X-RAY DIFFRACTIONr_angle_refined_deg2.2252.0064693
X-RAY DIFFRACTIONr_angle_other_deg1.3983.0087555
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.5195431
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.96324.741135
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.46515557
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.6851511
X-RAY DIFFRACTIONr_chiral_restr0.2340.2521
X-RAY DIFFRACTIONr_gen_planes_refined0.0130.0213859
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02744
X-RAY DIFFRACTIONr_mcbond_it2.1681.7721727
X-RAY DIFFRACTIONr_mcbond_other2.1661.771726
X-RAY DIFFRACTIONr_mcangle_it3.0552.6492157
LS refinement shellResolution: 1.997→2.049 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.231 107 -
Rwork0.159 1927 -
all-2034 -
obs--99.07 %

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