[English] 日本語
Yorodumi
- PDB-1a80: Native 2,5-DIKETO-D-GLUCONIC acid reductase a from CORYNBACTERIUM... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1a80
TitleNative 2,5-DIKETO-D-GLUCONIC acid reductase a from CORYNBACTERIUM SP. complexed with nadph
Components2,5-DIKETO-D-GLUCONIC ACID REDUCTASE A
KeywordsOXIDOREDUCTASE / ALPHA8/BETA8 BARREL / 2 / 5-DIKETO-D-GLUCONIC ACID / COMMERCIAL VITAMIN C SYNTHESIS
Function / homology
Function and homology information


2,5-didehydrogluconate reductase (2-dehydro-L-gulonate-forming) / L-ascorbic acid biosynthetic process / oxidoreductase activity / cytoplasm
Similarity search - Function
Aldo-keto reductase family 5C1 / Aldo/keto reductase family signature 1. / NADP-dependent oxidoreductase domain / Aldo/keto reductase, conserved site / Aldo-keto reductase / NADP-dependent oxidoreductase domain / Aldo/keto reductase family / NADP-dependent oxidoreductase domain superfamily / TIM Barrel / Alpha-Beta Barrel / Alpha Beta
Similarity search - Domain/homology
Chem-NDP / 2,5-diketo-D-gluconic acid reductase A
Similarity search - Component
Biological speciesCorynebacterium sp. (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.1 Å
AuthorsKhurana, S. / Powers, D.B. / Anderson, S. / Blaber, M.
Citation
Journal: Proc.Natl.Acad.Sci.USA / Year: 1998
Title: Crystal structure of 2,5-diketo-D-gluconic acid reductase A complexed with NADPH at 2.1-A resolution.
Authors: Khurana, S. / Powers, D.B. / Anderson, S. / Blaber, M.
#1: Journal: Biochem.J. / Year: 1997
Title: Comparative Anatomy of the Aldo-Keto Reductase Superfamily
Authors: Jez, J.M. / Bennett, M.J. / Schlegel, B.P. / Lewis, M. / Penning, T.M.
#2: Journal: Science / Year: 1985
Title: Production of 2-Keto-L-Gulonate, an Intermediate in L-Ascorbate Synthesis, by a Genetically Modified Erwinia Herbicola
Authors: Anderson, S. / Marks, C.B. / Lazarus, R. / Miller, J. / Stafford, K. / Seymour, J. / Light, D. / Rastetter, W.
History
DepositionMar 31, 1998Processing site: BNL
Revision 1.0Mar 30, 1999Provider: repository / Type: Initial release
Revision 1.1Mar 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Aug 2, 2023Group: Database references / Derived calculations / Refinement description
Category: database_2 / pdbx_initial_refinement_model ...database_2 / pdbx_initial_refinement_model / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: 2,5-DIKETO-D-GLUCONIC ACID REDUCTASE A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,7662
Polymers30,0201
Non-polymers7451
Water1,892105
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)35.700, 55.800, 74.700
Angle α, β, γ (deg.)90.00, 92.20, 90.00
Int Tables number4
Space group name H-MP1211

-
Components

#1: Protein 2,5-DIKETO-D-GLUCONIC ACID REDUCTASE A / 2 / 5-DKG REDUCTASE A


Mass: 30020.473 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Corynebacterium sp. (bacteria) / Gene: 2 5-DIKETO-D-GLUCONIC ACID / Variant: A / Plasmid: PTRP1-35 / Gene (production host): 2 5-DIKETO-D-GLUCONIC ACID / Production host: Pantoea citrea (bacteria) / Strain (production host): IFO3263 / References: UniProt: P06632
#2: Chemical ChemComp-NDP / NADPH DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE


Mass: 745.421 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C21H30N7O17P3
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 105 / 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: 2.16 Å3/Da / Density % sol: 50.31 %
Crystal growpH: 7.1 / Details: pH 7.1
Crystal grow
*PLUS
Method: vapor diffusion, hanging drop / Details: and 4 degrees centigrade
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
118.3 mg/mlenzyme1drop
21.0 Msodium phosphate1reservoir
31.0 Mpotassium phosphate1reservoir
4100 mMHEPES1reservoir

-
Data collection

DiffractionMean temperature: 295 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RUH2R / Wavelength: 1.5418
DetectorType: RIGAKU RAXIS II / Detector: IMAGE PLATE / Date: Jul 7, 1996
RadiationMonochromator: GRAPHITE(002) / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.1→100 Å / Num. obs: 14803 / % possible obs: 85 % / Observed criterion σ(I): 0 / Redundancy: 2.6 % / Biso Wilson estimate: 14.6 Å2 / Rsym value: 0.116 / Net I/σ(I): 10
Reflection shellResolution: 2.1→2.18 Å / Redundancy: 2.6 % / Mean I/σ(I) obs: 2.5 / Rsym value: 0.421 / % possible all: 75.2
Reflection
*PLUS
Rmerge(I) obs: 0.116
Reflection shell
*PLUS
% possible obs: 75.2 % / Rmerge(I) obs: 0.421

-
Processing

Software
NameVersionClassification
AMoREphasing
TNT5Erefinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1ADS

1ads


Resolution: 2.1→60 Å / Isotropic thermal model: TRONRUD, 1996 / σ(F): 0 / Stereochemistry target values: TRONRUD, 1987 /
Num. reflection% reflection
all14803 -
obs12891 85 %
Solvent computationSolvent model: TRONRUD, 1987 / Bsol: 365.4 Å2 / ksol: 0.972 e/Å3
Refinement stepCycle: LAST / Resolution: 2.1→60 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2122 0 48 105 2275
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONt_bond_d0.01
X-RAY DIFFRACTIONt_angle_deg1.9
X-RAY DIFFRACTIONt_dihedral_angle_d
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes
X-RAY DIFFRACTIONt_gen_planes
X-RAY DIFFRACTIONt_it
X-RAY DIFFRACTIONt_nbd
Software
*PLUS
Name: TNT / Version: 5E / Classification: refinement
Refinement
*PLUS
Rfactor obs: 0.191 / Rfactor Rfree: 0.288
Solvent computation
*PLUS
Displacement parameters
*PLUS

+
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