[English] 日本語
Yorodumi
- PDB-5jcm: Structure and catalytic mechanism of monodehydroascorbate reducta... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 5jcm
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
FLAVIN-ADENINE DINUCLEOTIDE / ISOASCORBIC ACID / NICOTINAMIDE-ADENINE-DINUCLEOTIDE / Monodehydroascorbate reductase 3, cytosolic
Similarity search - Component
Biological speciesOryza sativa subsp. japonica (Japanese rice)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 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 2.0Jul 29, 2020Group: Advisory / Atomic model ...Advisory / Atomic model / Derived calculations / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / entity / pdbx_entity_nonpoly / pdbx_struct_oper_list / pdbx_validate_symm_contact / struct_site / struct_site_gen
Item: _atom_site.auth_atom_id / _atom_site.label_atom_id ..._atom_site.auth_atom_id / _atom_site.label_atom_id / _chem_comp.name / _chem_comp.type / _entity.pdbx_description / _pdbx_entity_nonpoly.name / _pdbx_struct_oper_list.symmetry_operation / _pdbx_validate_symm_contact.auth_atom_id_2
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Nov 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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
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
Water10,557586
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-8 kcal/mol
Surface area17240 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 area2710 Å2
ΔGint-11 kcal/mol
Surface area17550 Å2
MethodPISA
Unit cell
Length a, b, c (Å)78.391, 85.137, 131.806
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

-
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-ISD / ISOASCORBIC ACID / (5R)-5-[(1R)-1,2-DIHYDROXYETHYL]-3,4-DIHYDROXYFURAN-2(5H)-ONE


Type: D-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.: 586 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
Sample preparation

CrystalDensity Matthews: 2.38 Å3/Da / Density % sol: 48.41 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / Details: Tris, ammonium acetate, PEG 3350

-
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: Nov 17, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97954 Å / Relative weight: 1
ReflectionResolution: 1.9→71.52 Å / Num. obs: 69512 / % possible obs: 99.3 % / Redundancy: 14.1 % / Rmerge(I) obs: 0.103 / Rpim(I) all: 0.03 / Rrim(I) all: 0.107 / Χ2: 2.568 / Net I/av σ(I): 52.35 / Net I/σ(I): 10.8 / Num. measured all: 982181
Reflection shell

Diffraction-ID: 1 / Rejects: _

Resolution (Å)Redundancy (%)Num. unique allCC1/2Rpim(I) allΧ2% possible allRmerge(I) obsRrim(I) all
1.9-1.9314.934070.8250.2691.43998.8
1.93-1.9714.934140.8790.2271.46798.80.8580.888
1.97-2.0114.934310.9010.1951.52999.10.7360.762
2.01-2.0514.933870.9330.1641.5698.90.620.641
2.05-2.0914.934160.9430.1411.58898.80.5330.551
2.09-2.1414.934570.9580.1221.64599.40.4570.473
2.14-2.1914.934390.9730.0981.742990.3670.38
2.19-2.2514.934230.9790.0811.82199.50.3050.316
2.25-2.3214.834430.9840.0721.90999.20.2720.281
2.32-2.3914.834590.9890.0622.01999.30.2330.241
2.39-2.4814.834530.9910.0522.13199.60.1960.203
2.48-2.5814.734760.9940.0442.30999.50.1660.172
2.58-2.714.634940.9950.0382.55199.60.140.145
2.7-2.8414.434680.9960.0322.85599.70.1180.122
2.84-3.0214.134970.9960.0293.34499.70.1050.109
3.02-3.2513.535040.9970.0253.89799.70.090.093
3.25-3.5812.735410.9980.0234.49699.90.0770.08
3.58-4.0912.435310.9980.0214.7499.70.070.073
4.09-5.1611.835630.9970.024.84999.60.0660.069
5.16-5011.337090.9960.0215.13698.20.0680.071

-
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: 1.9→50 Å / Cor.coef. Fo:Fc: 0.968 / Cor.coef. Fo:Fc free: 0.949 / SU B: 3.387 / SU ML: 0.099 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.15 / ESU R Free: 0.144 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2239 3409 4.9 %RANDOM
Rwork0.1744 ---
obs0.1768 66047 99.25 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 122.3 Å2 / Biso mean: 39.303 Å2 / Biso min: 6.52 Å2
Baniso -1Baniso -2Baniso -3
1-0.12 Å2-0 Å2-0 Å2
2---0.39 Å20 Å2
3---0.27 Å2
Refinement stepCycle: final / Resolution: 1.9→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6479 0 218 586 7283
Biso mean--30.51 44.69 -
Num. residues----854
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0210.026852
X-RAY DIFFRACTIONr_bond_other_d0.0030.026469
X-RAY DIFFRACTIONr_angle_refined_deg2.2252.0099303
X-RAY DIFFRACTIONr_angle_other_deg1.1933.00814944
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.2355849
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.82324.682267
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.731151099
X-RAY DIFFRACTIONr_dihedral_angle_4_deg22.4891522
X-RAY DIFFRACTIONr_chiral_restr0.2540.21032
X-RAY DIFFRACTIONr_gen_planes_refined0.0120.0217625
X-RAY DIFFRACTIONr_gen_planes_other0.0020.021473
X-RAY DIFFRACTIONr_mcbond_it3.7293.6293411
X-RAY DIFFRACTIONr_mcbond_other3.733.6283410
X-RAY DIFFRACTIONr_mcangle_it4.8385.4234255
LS refinement shellResolution: 1.902→1.951 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.27 258 -
Rwork0.229 4748 -
all-5006 -
obs--98.43 %

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more