[English] 日本語
Yorodumi
- PDB-9j0s: CRYSTAL STRUCTURE OF A NOVEL ALDEHYDE DEHYDROGENASE FROM KLEBSIEL... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 9j0s
TitleCRYSTAL STRUCTURE OF A NOVEL ALDEHYDE DEHYDROGENASE FROM KLEBSIELLA PNEUMONIAE WITH LIGAND
ComponentsAldehyde dehydrogenase
KeywordsOXIDOREDUCTASE / catalysis
Function / homology
Function and homology information


benzaldehyde dehydrogenase (NAD+) activity / aldehyde dehydrogenase (NAD+)
Similarity search - Function
Aldehyde dehydrogenase, glutamic acid active site / Aldehyde dehydrogenases glutamic acid active site. / Aldehyde dehydrogenase, cysteine active site / Aldehyde dehydrogenases cysteine active site. / Aldehyde dehydrogenase domain / Aldehyde dehydrogenase family / Aldehyde dehydrogenase, C-terminal / Aldehyde dehydrogenase, N-terminal / Aldehyde/histidinol dehydrogenase
Similarity search - Domain/homology
NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE / Aldehyde dehydrogenase
Similarity search - Component
Biological speciesKlebsiella pneumoniae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.88 Å
AuthorsZhang, J. / Han, Y. / LIu, W.D. / Zhang, W.Y.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC) China
CitationJournal: Adv.Synth.Catal. / Year: 2025
Title: Aldehyde Dehydrogenase from Klebsiella pneumoniae: A Robust Biocatalyst for Preparing Heteroatom-Containing Carboxylic Acids
Authors: Han, Y. / Geng, N. / Sha, J. / Li, H. / You, C. / Liu, W. / Zhang, J. / Shi, J. / Wu, X. / Zhang, W.
History
DepositionAug 2, 2024Deposition site: PDBJ / Processing site: PDBC
Revision 1.0Jul 30, 2025Provider: repository / Type: Initial release

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Aldehyde dehydrogenase
B: Aldehyde dehydrogenase
C: Aldehyde dehydrogenase
D: Aldehyde dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)213,9088
Polymers210,9344
Non-polymers2,9744
Water1,29772
1
A: Aldehyde dehydrogenase
B: Aldehyde dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)106,9544
Polymers105,4672
Non-polymers1,4872
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4510 Å2
ΔGint-21 kcal/mol
Surface area34960 Å2
MethodPISA
2
C: Aldehyde dehydrogenase
D: Aldehyde dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)106,9544
Polymers105,4672
Non-polymers1,4872
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5430 Å2
ΔGint-24 kcal/mol
Surface area35130 Å2
MethodPISA
3


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area14170 Å2
ΔGint-56 kcal/mol
Surface area65860 Å2
MethodPISA
Unit cell
Length a, b, c (Å)102.150, 144.774, 150.239
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

-
Components

#1: Protein
Aldehyde dehydrogenase / Aldehyde dehydrogenase family protein / Putative aldehyde dehydrogenase


Mass: 52733.508 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Details: Sequence reference for Klebsiella pneumoniae (573) is not available in UniProt at the time of biocuration. Current sequence reference is from UniProt ID A0A069Q1D5.
Source: (gene. exp.) Klebsiella pneumoniae (bacteria)
Gene: yfmT, xylC_1, CAZ10_02010, DT376_04100, IPC1295_07430, NCTC13621_03651, PAERUG_P19_London_7_VIM_2_05_10_05035
Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
References: UniProt: A0A069Q1D5, aldehyde dehydrogenase (NAD+), benzaldehyde dehydrogenase (NAD+)
#2: Chemical
ChemComp-NAP / NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE / 2'-MONOPHOSPHOADENOSINE 5'-DIPHOSPHORIBOSE


Mass: 743.405 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Formula: C21H28N7O17P3 / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 72 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationN

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.79 Å3/Da / Density % sol: 55.91 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / Details: 0.1M MMT, 25% PEG1500, 10% Glycerol

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17UM / Wavelength: 0.979176 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jun 16, 2024
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979176 Å / Relative weight: 1
ReflectionResolution: 2.88→48.36 Å / Num. obs: 51167 / % possible obs: 99.9 % / Redundancy: 1.9 % / CC1/2: 0.984 / Net I/σ(I): 5.4
Reflection shellResolution: 2.88→2.97 Å / Redundancy: 1.9 % / Mean I/σ(I) obs: 1 / Num. unique obs: 4372 / CC1/2: 0.475

-
Processing

Software
NameVersionClassification
PHENIX(1.21_5207: ???)refinement
Aimlessdata scaling
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.88→48.36 Å / SU ML: 0.4 / Cross valid method: FREE R-VALUE / σ(F): 1.16 / Phase error: 25.91 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2598 2556 5.01 %
Rwork0.2074 --
obs0.21 51066 99.88 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.88→48.36 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms13470 0 158 72 13700
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00614026
X-RAY DIFFRACTIONf_angle_d1.14219121
X-RAY DIFFRACTIONf_dihedral_angle_d7.8771976
X-RAY DIFFRACTIONf_chiral_restr0.0612163
X-RAY DIFFRACTIONf_plane_restr0.0152508
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.88-2.980.33422500.30754796X-RAY DIFFRACTION100
2.98-3.10.35972610.27754762X-RAY DIFFRACTION100
3.1-3.240.30362490.25354785X-RAY DIFFRACTION100
3.24-3.410.29232520.23384836X-RAY DIFFRACTION100
3.41-3.630.26782530.2174803X-RAY DIFFRACTION100
3.63-3.910.27862450.2094815X-RAY DIFFRACTION100
3.91-4.30.22742600.18664844X-RAY DIFFRACTION100
4.3-4.920.20192560.16394860X-RAY DIFFRACTION100
4.92-6.20.25792620.19584902X-RAY DIFFRACTION100
6.2-48.360.24152680.18715107X-RAY DIFFRACTION100

+
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