[English] 日本語
Yorodumi
- PDB-5zci: Crystal structure of apo form of Xylose reductase from Debaryomyc... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 5zci
TitleCrystal structure of apo form of Xylose reductase from Debaryomyces nepalensis
ComponentsAldose reductase
KeywordsOXIDOREDUCTASE / carbohydrate metabolism / aldo-keto reductase / TIM barrel / NADPH dependent
Function / homology
Function and homology information


D-xylose reductase [NAD(P)H] / D-xylose reductase (NADPH) activity / D-xylose catabolic process / nucleotide binding
Similarity search - Function
Aldo-keto reductase family 2B / Aldo/keto reductase family putative active site signature. / NADP-dependent oxidoreductase domain / Aldo/keto reductase family signature 2. / Aldo/keto reductase, conserved site / Aldo-keto reductase / NADP-dependent oxidoreductase domain / Aldo/keto reductase family / NADP-dependent oxidoreductase domain superfamily / TIM Barrel ...Aldo-keto reductase family 2B / Aldo/keto reductase family putative active site signature. / NADP-dependent oxidoreductase domain / Aldo/keto reductase family signature 2. / 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
D-xylose reductase [NAD(P)H]
Similarity search - Component
Biological speciesDebaryomyces nepalensis (yeast)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsManoj, N.
Citation
Journal: FEBS J. / Year: 2018
Title: Crystal structure of yeast xylose reductase in complex with a novel NADP-DTT adduct provides insights into substrate recognition and catalysis.
Authors: Paidimuddala, B. / Mohapatra, S.B. / Gummadi, S.N. / Manoj, N.
#1: Journal: RSC Adv. / Year: 2017
Title: A halotolerant aldose reductase from Debaryomyces nepalensis: gene isolation, overexpression and biochemical characterization
Authors: Paidimuddala, B. / Aradhyam, G.K. / Gummadi, S.N.
History
DepositionFeb 17, 2018Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Nov 7, 2018Provider: repository / Type: Initial release
Revision 1.1Dec 19, 2018Group: Data collection / Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.2Nov 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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Aldose reductase
B: Aldose reductase


Theoretical massNumber of molelcules
Total (without water)77,8412
Polymers77,8412
Non-polymers00
Water7,188399
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration, Dimeric assembly is consistent with PISA software prediction
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2560 Å2
ΔGint-14 kcal/mol
Surface area25280 Å2
MethodPISA
Unit cell
Length a, b, c (Å)61.760, 69.440, 159.740
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

-
Components

#1: Protein Aldose reductase


Mass: 38920.312 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Debaryomyces nepalensis (yeast) / Gene: AR / Plasmid: pET28a / Production host: Escherichia coli (E. coli) / Variant (production host): Rosetta / References: UniProt: A0A0M4HL56, aldose reductase
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 399 / 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: 2.2 Å3/Da / Density % sol: 44.1 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.2
Details: 24% PEG 3000, 0.1 M sodium citrate (pH 6.2), 0.15 M ammonium acetate

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: BRUKER AXS MICROSTAR / Wavelength: 1.5418 Å
DetectorType: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: Feb 3, 2016
RadiationMonochromator: double mirrors / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2→52.4 Å / Num. obs: 42060 / % possible obs: 89.2 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 10.5 % / Biso Wilson estimate: 25.9 Å2 / CC1/2: 0.997 / Rmerge(I) obs: 0.157 / Rpim(I) all: 0.049 / Rrim(I) all: 0.165 / Net I/σ(I): 12.6
Reflection shellResolution: 2→2.11 Å / Redundancy: 10.7 % / Rmerge(I) obs: 0.745 / Mean I/σ(I) obs: 3.1 / Num. unique obs: 5483 / CC1/2: 0.779 / Rpim(I) all: 0.232 / Rrim(I) all: 0.781 / % possible all: 81.1

-
Processing

Software
NameVersionClassification
PHENIX(1.11.1_2575)refinement
MOSFLMdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1JEZ

1jez


Resolution: 2→48.857 Å / SU ML: 0.22 / SU R Cruickshank DPI: 0.224 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 20.74
RfactorNum. reflection% reflectionSelection details
Rfree0.2184 2093 4.98 %Random
Rwork0.1881 ---
obs0.1896 41998 88.91 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 27.2 Å2
Refine analyzeLuzzati coordinate error obs: 0.238 Å / Luzzati d res low obs: 48.9 Å
Refinement stepCycle: LAST / Resolution: 2→48.857 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5027 0 0 399 5426
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0025168
X-RAY DIFFRACTIONf_angle_d0.4847043
X-RAY DIFFRACTIONf_dihedral_angle_d9.7113057
X-RAY DIFFRACTIONf_chiral_restr0.043771
X-RAY DIFFRACTIONf_plane_restr0.004916
LS refinement shellResolution: 2→2.047 Å
RfactorNum. reflection% reflection
Rfree0.2771 118 -
Rwork0.2579 2299 -
obs--78 %

+
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