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

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Basic information

Entry
Database: PDB / ID: 5jcn
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 / 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
ASCORBIC ACID / 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: 2.29 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 1.1Feb 19, 2020Group: Data collection / Derived calculations / Category: diffrn_source / pdbx_struct_oper_list
Item: _diffrn_source.pdbx_synchrotron_site / _pdbx_struct_oper_list.symmetry_operation
Revision 1.2Jul 29, 2020Group: Data collection / Derived calculations / Category: chem_comp / struct_site / struct_site_gen / Item: _chem_comp.type / Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.3Nov 8, 2023Group: Data collection / Database references ...Data collection / Database references / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _chem_comp.pdbx_synonyms / _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: Os09g0567300 protein
B: Os09g0567300 protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)100,4888
Polymers97,2382
Non-polymers3,2506
Water1,964109
1
A: Os09g0567300 protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)50,2444
Polymers48,6191
Non-polymers1,6253
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2730 Å2
ΔGint-15 kcal/mol
Surface area17680 Å2
MethodPISA
2
B: Os09g0567300 protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)50,2444
Polymers48,6191
Non-polymers1,6253
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2690 Å2
ΔGint-11 kcal/mol
Surface area17830 Å2
MethodPISA
Unit cell
Length a, b, c (Å)79.635, 85.112, 133.443
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: 48619.055 Da / Num. of mol.: 2 / Fragment: UNP residues 4-435 / Mutation: Y349F
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-NAD / NICOTINAMIDE-ADENINE-DINUCLEOTIDE


Mass: 663.425 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C21H27N7O14P2 / Comment: NAD*YM
#4: Sugar ChemComp-ASC / ASCORBIC ACID / Vitamin C


Type: L-saccharide / Mass: 176.124 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H8O6
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 109 / 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: 2.46 Å3/Da / Density % sol: 49.93 %
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: SPring-8 / Beamline: BL44XU / Wavelength: 0.9 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Jun 18, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9 Å / Relative weight: 1
ReflectionResolution: 2.29→71.76 Å / Num. obs: 41172 / % possible obs: 99.5 % / Redundancy: 13.9 % / Rmerge(I) obs: 0.087 / Rpim(I) all: 0.029 / Rrim(I) all: 0.089 / Χ2: 2.759 / Net I/av σ(I): 56.912 / Net I/σ(I): 13 / Num. measured all: 571023
Reflection shell

Diffraction-ID: 1 / Rejects: _

Resolution (Å)Redundancy (%)Num. unique allCC1/2Rpim(I) allΧ2% possible allRmerge(I) obsRrim(I) all
2.3-2.3414.920450.6990.5021.591100
2.34-2.381520280.760.4311.593100
2.38-2.4314.920450.7810.3721.638100
2.43-2.4814.920410.8590.3111.704100
2.48-2.5314.920100.8770.2621.7221000.982
2.53-2.5914.920680.9250.2131.7851000.7980.826
2.59-2.6614.920460.9440.1671.8611000.6260.648
2.66-2.7314.920220.9620.1312.0371000.4910.508
2.73-2.8114.820440.9810.1022.1271000.3810.395
2.81-2.914.820580.9840.0882.2541000.3290.34
2.9-314.620710.990.072.4621000.2580.267
3-3.1214.320490.9920.0562.7921000.2030.21
3.12-3.2614.220610.9940.0443.0561000.1580.164
3.26-3.4413.820660.9970.0323.42799.90.1140.118
3.44-3.6513.420630.9980.0253.7361000.0880.091
3.65-3.931320810.9970.0224.2271000.0760.079
3.93-4.3311.820820.9980.0214.72899.40.0680.071
4.33-4.9511.420840.9970.0194.84598.90.0610.064
4.95-6.2412.121320.9980.0184.79599.70.060.062
6.24-509.920760.9970.025.22692.20.0610.064

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Processing

Software
NameVersionClassification
HKL-2000data collection
SCALEPACKdata scaling
REFMAC5.8.0103refinement
PDB_EXTRACT3.2data extraction
HKL-2000data reduction
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4H4Q

4h4q


Resolution: 2.29→50 Å / Cor.coef. Fo:Fc: 0.95 / Cor.coef. Fo:Fc free: 0.933 / SU B: 8.799 / SU ML: 0.207 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.361 / ESU R Free: 0.256 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2636 1936 4.7 %RANDOM
Rwork0.2055 ---
obs0.2082 39174 99.22 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 173.23 Å2 / Biso mean: 75.271 Å2 / Biso min: 17.73 Å2
Baniso -1Baniso -2Baniso -3
1-3.6 Å20 Å20 Å2
2---1.34 Å20 Å2
3----2.25 Å2
Refinement stepCycle: final / Resolution: 2.29→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6465 0 218 109 6792
Biso mean--51.71 71.45 -
Num. residues----854
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.0196838
X-RAY DIFFRACTIONr_bond_other_d0.0020.026465
X-RAY DIFFRACTIONr_angle_refined_deg2.0382.0079289
X-RAY DIFFRACTIONr_angle_other_deg1.062314928
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.3245849
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.84824.601263
X-RAY DIFFRACTIONr_dihedral_angle_3_deg19.22151091
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.2021522
X-RAY DIFFRACTIONr_chiral_restr0.1090.21026
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.0217621
X-RAY DIFFRACTIONr_gen_planes_other0.0020.021481
X-RAY DIFFRACTIONr_mcbond_it6.2057.2693411
X-RAY DIFFRACTIONr_mcbond_other6.2047.2673410
X-RAY DIFFRACTIONr_mcangle_it8.21210.8844255
LS refinement shellResolution: 2.292→2.352 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.323 141 -
Rwork0.296 2794 -
all-2935 -
obs--97.06 %

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