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

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Basic information

Entry
Database: PDB / ID: 5jcl
TitleStructure and catalytic mechanism of monodehydroascorbate reductase, MDHAR, from Oryza sativa L. japonica
ComponentsOs09g0567300 protein
KeywordsOXIDOREDUCTASE
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 ...: / 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 / Chem-NDP / Monodehydroascorbate reductase 3, cytosolic
Similarity search - Component
Biological speciesOryza sativa subsp. japonica (Japanese rice)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsPark, A.K. / Kim, H.W.
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 1.1Nov 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
B: Os09g0567300 protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)100,2166
Polymers97,1542
Non-polymers3,0624
Water15,853880
1
A: Os09g0567300 protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)50,1083
Polymers48,5771
Non-polymers1,5312
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2700 Å2
ΔGint-8 kcal/mol
Surface area17500 Å2
MethodPISA
2
B: Os09g0567300 protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)50,1083
Polymers48,5771
Non-polymers1,5312
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2720 Å2
ΔGint-8 kcal/mol
Surface area17830 Å2
MethodPISA
Unit cell
Length a, b, c (Å)78.249, 85.518, 131.263
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Os09g0567300 protein / Putative monodehydroascorbate reductase


Mass: 48577.020 Da / Num. of mol.: 2 / Fragment: UNP residues 4-435 / Mutation: E196A
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.: 2 / Source method: obtained synthetically / Formula: C27H33N9O15P2 / Comment: FAD*YM
#3: Chemical ChemComp-NDP / NADPH DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE


Mass: 745.421 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C21H30N7O17P3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 880 / 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: 2.38 Å3/Da / Density % sol: 48.38 %
Description: THE ENTRY CONTAINS FRIEDEL PAIRS IN F_PLUS/MINUS COLUMNS.
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / Details: Tris, ammonium acetate, PEG 3350

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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: May 14, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97954 Å / Relative weight: 1
ReflectionResolution: 1.8→50 Å / Num. obs: 82522 / % possible obs: 99.7 % / Redundancy: 13.2 % / Rmerge(I) obs: 0.08 / Rpim(I) all: 0.023 / Rrim(I) all: 0.083 / Χ2: 2.11 / Net I/av σ(I): 56.645 / Net I/σ(I): 10.3 / Num. measured all: 1090531
Reflection shell

Diffraction-ID: 1 / Rejects: _

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allCC1/2Rpim(I) allRrim(I) allΧ2% possible all
1.8-1.8313.40.78441160.890.2220.8161.364100
1.83-1.8613.40.64940960.920.1830.6751.419100
1.86-1.913.40.59240580.9380.1670.6161.511100
1.9-1.94130.51440940.9510.1480.5352.343100
1.94-1.9813.50.38340960.9710.1080.3991.627100
1.98-2.0313.50.3140660.9790.0870.3221.657100
2.03-2.0813.50.26941160.9820.0760.281.789100
2.08-2.1313.50.2340970.9880.0650.2391.763100
2.13-2.213.50.18341150.9910.0520.1911.817100
2.2-2.27130.18841000.9860.0550.1962.514100
2.27-2.3513.50.14441110.9950.0410.151.98100
2.35-2.4413.50.12241200.9960.0340.1261.975100
2.44-2.5513.50.10441250.9970.0290.1082.025100
2.55-2.6913.50.09341350.9970.0260.0972.122100
2.69-2.8613.50.08141440.9980.0230.0842.237100
2.86-3.0813.40.07141580.9980.020.0742.341100
3.08-3.3913.30.06241650.9980.0180.0652.575100
3.39-3.8812.80.05941760.9980.0170.0622.90899.5
3.88-4.8812.50.05842080.9980.0170.0613.19299.1
4.88-5011.40.06242260.9960.0190.0653.29495.3

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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: 1.8→50 Å / Cor.coef. Fo:Fc: 0.968 / Cor.coef. Fo:Fc free: 0.945 / SU B: 3.402 / SU ML: 0.102 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.133 / ESU R Free: 0.134 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES. SF FILE CONTAINS FRIEDEL PAIRS UNDER I/F_MINUS AND I/F_PLUS COLUMNS.
RfactorNum. reflection% reflectionSelection details
Rfree0.2335 4089 5 %RANDOM
Rwork0.1821 ---
obs0.1846 77728 99.46 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 127.54 Å2 / Biso mean: 37.903 Å2 / Biso min: 17.53 Å2
Baniso -1Baniso -2Baniso -3
1--0.06 Å2-0 Å2-0 Å2
2---0.64 Å20 Å2
3---0.71 Å2
Refinement stepCycle: final / Resolution: 1.8→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6493 0 202 880 7575
Biso mean--27.82 45.29 -
Num. residues----857
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0180.0196851
X-RAY DIFFRACTIONr_bond_other_d0.0020.026482
X-RAY DIFFRACTIONr_angle_refined_deg2.0482.0049307
X-RAY DIFFRACTIONr_angle_other_deg1.082314969
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.3845853
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.76224.642265
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.865151099
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.5781522
X-RAY DIFFRACTIONr_chiral_restr0.1260.21024
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.0217629
X-RAY DIFFRACTIONr_gen_planes_other0.0020.021483
X-RAY DIFFRACTIONr_mcbond_it3.3853.5283424
X-RAY DIFFRACTIONr_mcbond_other3.3823.5273423
X-RAY DIFFRACTIONr_mcangle_it4.5075.2754273
LS refinement shellResolution: 1.8→1.847 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.312 308 -
Rwork0.239 5686 -
all-5994 -
obs--100 %

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