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- PDB-6krt: monodehydroascorbate reductase, MDHAR, from Antarctic hairgrass D... -

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Basic information

Entry
Database: PDB / ID: 6krt
Titlemonodehydroascorbate reductase, MDHAR, from Antarctic hairgrass Deschampsia antarctica
Componentsmonodehydroascorbate reductase
KeywordsOXIDOREDUCTASE / ascorbate / reductase / antioxidant / Antartic hairgrass / Deschampsia antarctica
Function / homologyFLAVIN-ADENINE DINUCLEOTIDE
Function and homology information
Biological speciesDeschampsia antarctica (Antarctic hairgrass)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.2 Å
AuthorsPark, A.K. / Do, H. / Lee, J.H. / Kim, H. / Choi, W. / Kim, I.S. / Kim, H.W.
Funding support Korea, Republic Of, 1items
OrganizationGrant numberCountry
National Research Foundation (Korea)2017M1A5A1013568 Korea, Republic Of
CitationJournal: To Be Published
Title: monodehydroascorbate reductase, MDHAR, from Antarctic hairgrass Deschampsia antarctica
Authors: Park, A.K. / Do, H. / Lee, J.H. / Kim, H. / Choi, W. / Kim, I.S. / Kim, H.W.
History
DepositionAug 22, 2019Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Aug 26, 2020Provider: repository / Type: Initial release
Revision 1.1Nov 22, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: monodehydroascorbate reductase
B: monodehydroascorbate reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)94,7774
Polymers93,2062
Non-polymers1,5712
Water48627
1
A: monodehydroascorbate reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,3882
Polymers46,6031
Non-polymers7861
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1470 Å2
ΔGint-5 kcal/mol
Surface area17820 Å2
MethodPISA
2
B: monodehydroascorbate reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,3882
Polymers46,6031
Non-polymers7861
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1460 Å2
ΔGint-6 kcal/mol
Surface area18130 Å2
MethodPISA
Unit cell
Length a, b, c (Å)74.148, 88.849, 129.352
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 monodehydroascorbate reductase


Mass: 46602.762 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Deschampsia antarctica (Antarctic hairgrass)
Production host: Escherichia coli (E. coli) / References: monodehydroascorbate reductase (NADH)
#2: Chemical ChemComp-FAD / FLAVIN-ADENINE DINUCLEOTIDE / Flavin adenine dinucleotide


Mass: 785.550 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C27H33N9O15P2 / Comment: FAD*YM
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 27 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 2.27 Å3/Da / Density % sol: 45.82 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 8.5 / Details: Tris, Calcium Chloride, PEG 4000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: PAL/PLS / Beamline: 5C (4A) / Wavelength: 0.9796 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Nov 25, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9796 Å / Relative weight: 1
ReflectionResolution: 2.2→30 Å / Num. obs: 43381 / % possible obs: 98.4 % / Redundancy: 4.3 % / Rsym value: 0.087 / Net I/σ(I): 28.5
Reflection shellResolution: 2.2→2.24 Å / Redundancy: 4.5 % / Num. unique obs: 2182 / Rsym value: 0.396 / % possible all: 100

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
HKL-2000data reduction
SCALEPACKdata scaling
MOLREPphasing
REFMAC5.8.0073refinement
PDB_EXTRACT3.25data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5JCI

5jci


Resolution: 2.2→30 Å / Cor.coef. Fo:Fc: 0.944 / Cor.coef. Fo:Fc free: 0.898 / SU B: 7.445 / SU ML: 0.188 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.316 / ESU R Free: 0.252
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2775 2180 5 %RANDOM
Rwork0.2064 ---
obs0.21 41178 98.15 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 107.33 Å2 / Biso mean: 36.015 Å2 / Biso min: 11.12 Å2
Baniso -1Baniso -2Baniso -3
1--0.01 Å2-0 Å20 Å2
2--0.02 Å20 Å2
3----0.02 Å2
Refinement stepCycle: final / Resolution: 2.2→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6547 0 106 27 6680
Biso mean--22.97 22.91 -
Num. residues----866
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.0196803
X-RAY DIFFRACTIONr_bond_other_d0.0010.026450
X-RAY DIFFRACTIONr_angle_refined_deg1.7361.9889234
X-RAY DIFFRACTIONr_angle_other_deg0.837314888
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.6885864
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.824.559272
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.757151092
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.2381526
X-RAY DIFFRACTIONr_chiral_restr0.0940.21015
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0217684
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021472
LS refinement shellResolution: 2.2→2.24 Å / Rfactor Rfree error: 0
RfactorNum. reflection% reflection
Rfree0.346 146 -
Rwork0.262 2948 -
obs--96.03 %

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