[English] 日本語
Yorodumi
- PDB-8wk9: Aldo-keto reductase KmAKR - Y28A/K29H/T63M/Q213A/Y296W/W297H -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 8wk9
TitleAldo-keto reductase KmAKR - Y28A/K29H/T63M/Q213A/Y296W/W297H
ComponentsNADPH-dependent alpha-keto amide reductase
KeywordsOXIDOREDUCTASE / apo-form / NADPH-dependent / beta-8/alpha-8-barrel
Function / homology
Function and homology information


oxidoreductase activity, acting on NAD(P)H as acceptor / :
Similarity search - Function
Aldo-keto reductase family 3C2/3 / 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
Similarity search - Domain/homology
NADPH-dependent alpha-keto amide reductase
Similarity search - Component
Biological speciesKluyveromyces marxianus (yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.39 Å
AuthorsXu, S.Y. / Zhou, L. / Xu, Y. / Wang, Y.J. / Zheng, Y.G.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)22178318 China
CitationJournal: To Be Published
Title: Aldo-keto reductase KmAKR - Y28A/K29H/T63M/Q213A/Y296W/W297H from Kluyveromyces marxianus
Authors: Xu, S.Y. / Zhou, L. / Xu, Y. / Wang, Y.J. / Zheng, Y.G.
History
DepositionSep 27, 2023Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Oct 2, 2024Provider: repository / Type: Initial release

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: NADPH-dependent alpha-keto amide reductase
B: NADPH-dependent alpha-keto amide reductase
C: NADPH-dependent alpha-keto amide reductase
D: NADPH-dependent alpha-keto amide reductase


Theoretical massNumber of molelcules
Total (without water)141,1764
Polymers141,1764
Non-polymers00
Water3,801211
1
A: NADPH-dependent alpha-keto amide reductase


Theoretical massNumber of molelcules
Total (without water)35,2941
Polymers35,2941
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: NADPH-dependent alpha-keto amide reductase


Theoretical massNumber of molelcules
Total (without water)35,2941
Polymers35,2941
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: NADPH-dependent alpha-keto amide reductase


Theoretical massNumber of molelcules
Total (without water)35,2941
Polymers35,2941
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: NADPH-dependent alpha-keto amide reductase


Theoretical massNumber of molelcules
Total (without water)35,2941
Polymers35,2941
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)68.276, 114.829, 83.074
Angle α, β, γ (deg.)90.00, 101.32, 90.00
Int Tables number4
Space group name H-MP1211

-
Components

#1: Protein
NADPH-dependent alpha-keto amide reductase


Mass: 35294.090 Da / Num. of mol.: 4 / Mutation: Y28A,K29H,T63M,Q213A,Y296W,W297H
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Kluyveromyces marxianus (yeast) / Gene: KLMA_60481 / Production host: Escherichia coli (E. coli) / References: UniProt: W0TDP7
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 211 / 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: 2.27 Å3/Da / Density % sol: 45.81 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: Sodium acetate trihydrate, TRIS hydrochloride, Polyethylene glycol 4000, glycerol

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL02U1 / Wavelength: 0.97918 Å
DetectorType: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Sep 20, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97918 Å / Relative weight: 1
ReflectionResolution: 2.39→114.83 Å / Num. obs: 49684 / % possible obs: 99.8 % / Redundancy: 6.5 % / CC1/2: 0.952 / Rmerge(I) obs: 0.217 / Rpim(I) all: 0.093 / Rrim(I) all: 0.237 / Χ2: 0.87 / Net I/σ(I): 6.2 / Num. measured all: 323743
Reflection shellResolution: 2.39→2.47 Å / % possible obs: 99.9 % / Redundancy: 6.1 % / Rmerge(I) obs: 0.662 / Num. measured all: 27715 / Num. unique obs: 4574 / CC1/2: 0.843 / Rpim(I) all: 0.293 / Rrim(I) all: 0.726 / Χ2: 0.82 / Net I/σ(I) obs: 3.5

-
Processing

Software
NameVersionClassification
REFMAC5.8.0403refinement
Aimlessdata scaling
DIALSdata reduction
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: AlphaFold

Resolution: 2.39→81.46 Å / Cor.coef. Fo:Fc: 0.896 / Cor.coef. Fo:Fc free: 0.844 / SU B: 9.838 / SU ML: 0.231 / Cross valid method: THROUGHOUT / ESU R: 0.625 / ESU R Free: 0.317 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.28343 2549 5.1 %RANDOM
Rwork0.21963 ---
obs0.22293 47104 99.77 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 27.755 Å2
Baniso -1Baniso -2Baniso -3
1-3.82 Å20 Å20.13 Å2
2---0.32 Å2-0 Å2
3----3.28 Å2
Refinement stepCycle: 1 / Resolution: 2.39→81.46 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9745 0 0 211 9956
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0129959
X-RAY DIFFRACTIONr_bond_other_d0.0010.0169604
X-RAY DIFFRACTIONr_angle_refined_deg0.91.64713496
X-RAY DIFFRACTIONr_angle_other_deg0.3081.57322274
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.63351203
X-RAY DIFFRACTIONr_dihedral_angle_2_deg9.215515
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.348101823
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.0470.21531
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.0211121
X-RAY DIFFRACTIONr_gen_planes_other0.0010.022075
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it2.5742.6584836
X-RAY DIFFRACTIONr_mcbond_other2.5742.6584836
X-RAY DIFFRACTIONr_mcangle_it4.0274.7636031
X-RAY DIFFRACTIONr_mcangle_other4.0274.7636032
X-RAY DIFFRACTIONr_scbond_it3.2262.9715123
X-RAY DIFFRACTIONr_scbond_other3.2262.9715124
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other5.2815.2827466
X-RAY DIFFRACTIONr_long_range_B_refined6.96524.9211502
X-RAY DIFFRACTIONr_long_range_B_other6.9624.8711486
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.39→2.452 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.325 185 -
Rwork0.246 3487 -
obs--99.84 %

+
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