[English] 日本語
Yorodumi
- PDB-5z6u: Crystal structure of D-xylose reductase from Scheffersomyces stipitis -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 5z6u
TitleCrystal structure of D-xylose reductase from Scheffersomyces stipitis
ComponentsNAD(P)H-dependent D-xylose reductase
KeywordsOXIDOREDUCTASE / Pontose metabolism / xylose reductase / Scheffersomyces stipitis
Function / homology
Function and homology information


D-xylose reductase [NAD(P)H] / D-xylose:NADP reductase activity / D-xylose catabolic process
Similarity search - Function
Aldo-keto reductase family 2B / Aldo/keto reductase family putative active site signature. / Aldo/keto reductase family signature 1. / Aldo/keto reductase family signature 2. / Aldo/keto reductase, conserved site / NADP-dependent oxidoreductase domain / Aldo-keto reductase / NADP-dependent oxidoreductase domain / Aldo/keto reductase family / NADP-dependent oxidoreductase domain superfamily ...Aldo-keto reductase family 2B / Aldo/keto reductase family putative active site signature. / Aldo/keto reductase family signature 1. / Aldo/keto reductase family signature 2. / Aldo/keto reductase, conserved site / NADP-dependent oxidoreductase domain / 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
NAD(P)H-dependent D-xylose reductase
Similarity search - Component
Biological speciesScheffersomyces stipitis (fungus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.95 Å
AuthorsSon, H.F. / Kim, K.J.
CitationJournal: Sci Rep / Year: 2018
Title: Structural insight intoD-xylose utilization by xylose reductase from Scheffersomyces stipitis.
Authors: Son, H.F. / Lee, S.M. / Kim, K.J.
History
DepositionJan 25, 2018Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Dec 5, 2018Provider: repository / Type: Initial release
Revision 1.1Dec 19, 2018Group: Data collection / Database references / Category: citation
Item: _citation.page_first / _citation.page_last ..._citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2Sep 9, 2020Group: Structure summary / Category: struct / Item: _struct.title

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: NAD(P)H-dependent D-xylose reductase
B: NAD(P)H-dependent D-xylose reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)78,4554
Polymers78,2712
Non-polymers1842
Water7,116395
1
A: NAD(P)H-dependent D-xylose reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,2272
Polymers39,1351
Non-polymers921
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area270 Å2
ΔGint-0 kcal/mol
Surface area14070 Å2
MethodPISA
2
B: NAD(P)H-dependent D-xylose reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,2272
Polymers39,1351
Non-polymers921
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area14230 Å2
MethodPISA
Unit cell
Length a, b, c (Å)69.248, 87.151, 122.623
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

-
Components

#1: Protein NAD(P)H-dependent D-xylose reductase / XR


Mass: 39135.328 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Scheffersomyces stipitis (strain ATCC 58785 / CBS 6054 / NBRC 10063 / NRRL Y-11545) (fungus)
Strain: ATCC 58785 / CBS 6054 / NBRC 10063 / NRRL Y-11545 / Gene: XYL1, PICST_89614 / Plasmid: pProEX-HTa / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / Variant (production host): T1R / References: UniProt: P31867, D-xylose reductase [NAD(P)H]
#2: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 395 / 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: 2.57 Å3/Da / Density % sol: 52.18 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / Details: PEG 3350, Ammonium citrate tribasic

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: PAL/PLS / Beamline: 7A (6B, 6C1) / Wavelength: 0.97934 Å
DetectorType: ADSC QUANTUM 270 / Detector: CCD / Date: May 10, 2017
RadiationMonochromator: Double Crystal Monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97934 Å / Relative weight: 1
ReflectionResolution: 1.95→71.04 Å / Num. obs: 51177 / % possible obs: 98.8 % / Redundancy: 6.7 % / Rsym value: 0.208 / Net I/σ(I): 55.2
Reflection shellResolution: 1.95→1.98 Å / Num. unique obs: 2698 / Rsym value: 0.208

-
Processing

Software
NameVersionClassification
HKL-2000data collection
REFMAC5.8.0135refinement
PDB_EXTRACT3.22data extraction
HKL-2000data reduction
HKL-2000data scaling
REFMACphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1Z9A
Resolution: 1.95→71.04 Å / Cor.coef. Fo:Fc: 0.956 / Cor.coef. Fo:Fc free: 0.935 / SU B: 3.595 / SU ML: 0.104 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.163 / ESU R Free: 0.154
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2358 2725 5.1 %RANDOM
Rwork0.189 ---
obs0.1914 51177 98.43 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 93.79 Å2 / Biso mean: 36.514 Å2 / Biso min: 19.97 Å2
Baniso -1Baniso -2Baniso -3
1--2.68 Å2-0 Å2-0 Å2
2---1 Å20 Å2
3---3.67 Å2
Refinement stepCycle: final / Resolution: 1.95→71.04 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5084 0 12 395 5491
Biso mean--37.89 42.37 -
Num. residues----636
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0180.0195224
X-RAY DIFFRACTIONr_bond_other_d0.0020.024996
X-RAY DIFFRACTIONr_angle_refined_deg1.761.9627086
X-RAY DIFFRACTIONr_angle_other_deg1.042311520
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.0215634
X-RAY DIFFRACTIONr_dihedral_angle_2_deg39.62124.553246
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.39915884
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.691526
X-RAY DIFFRACTIONr_chiral_restr0.1180.2772
X-RAY DIFFRACTIONr_gen_planes_refined0.010.0215878
X-RAY DIFFRACTIONr_gen_planes_other0.0020.021196
LS refinement shellResolution: 1.951→2.001 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.297 177 -
Rwork0.228 3661 -
all-3838 -
obs--96.58 %

+
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