[English] 日本語
Yorodumi
- PDB-9jj4: NADP-dependent oxidoreductase complexed with NADP and substrate 1a -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 9jj4
TitleNADP-dependent oxidoreductase complexed with NADP and substrate 1a
ComponentsNADP-dependent oxidoreductase
KeywordsBIOSYNTHETIC PROTEIN / alcohol dehydrogenase
Function / homology
Function and homology information


oxidoreductase activity, acting on the CH-CH group of donors, NAD or NADP as acceptor
Similarity search - Function
Oxidoreductase, N-terminal domain / Medium-chain dehydrogenase/reductase / N-terminal domain of oxidoreductase / Alcohol dehydrogenase-like, C-terminal / Zinc-binding dehydrogenase / Polyketide synthase, enoylreductase domain / Enoylreductase / GroES-like superfamily / NAD(P)-binding domain superfamily
Similarity search - Domain/homology
Chem-E8T / NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE / Ox4
Similarity search - Component
Biological speciesLysobacter enzymogenes (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.6 Å
AuthorsLi, Y. / Zhu, D. / Xie, X. / Li, F. / Lu, M.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)82173702 China
CitationJournal: J.Am.Chem.Soc. / Year: 2025
Title: Structural Basis for Medium-Chain Dehydrogenase/Reductase-Catalyzed Reductive Cyclization in Polycyclic Tetramate Macrolactam Biosynthesis.
Authors: Xie, X. / Li, F. / Mu, Y. / Lu, M. / Luo, J. / Wang, H. / Shen, Y. / Du, L. / Zhu, D. / Li, Y.
History
DepositionSep 12, 2024Deposition site: PDBJ / Processing site: PDBC
Revision 1.0Jun 18, 2025Provider: repository / Type: Initial release

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: NADP-dependent oxidoreductase
B: NADP-dependent oxidoreductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)80,3676
Polymers77,8872
Non-polymers2,4804
Water2,540141
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6910 Å2
ΔGint-36 kcal/mol
Surface area27320 Å2
MethodPISA
Unit cell
Length a, b, c (Å)87.719, 87.719, 226.086
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212

-
Components

#1: Protein NADP-dependent oxidoreductase / Oxidoreductase / zinc-binding dehydrogenase family protein


Mass: 38943.332 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Lysobacter enzymogenes (bacteria) / Gene: GLE_3219 / Production host: Escherichia coli (E. coli) / References: UniProt: C3PTT2
#2: Chemical ChemComp-NAP / NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE / 2'-MONOPHOSPHOADENOSINE 5'-DIPHOSPHORIBOSE


Mass: 743.405 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C21H28N7O17P3 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-E8T / (1Z,3E,5S,7S,8R,9S,10S,11R,13R,15R,16S,18Z,25S)-11-ethyl-2,7-dihydroxy-10-methyl-21,26-diazapentacyclo[23.2.1.09,13.08,15.05,16]octacosa-1(2),3,18-triene-20,27,28-trione / 10-epi-deOH-HSAF


Mass: 496.638 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C29H40N2O5 / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 141 / 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: 55.94 %
Crystal growTemperature: 277.15 K / Method: vapor diffusion, sitting drop / Details: PEG3350,sodium chloride,bis-tris hydrochloride / PH range: 8.5-9.0

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL18U1 / Wavelength: 0.97915 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Jul 17, 2021
RadiationMonochromator: Si111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97915 Å / Relative weight: 1
ReflectionResolution: 2.597→81.78 Å / Num. obs: 28235 / % possible obs: 100 % / Redundancy: 12.8 % / CC1/2: 0.998 / Net I/σ(I): 14.6
Reflection shellResolution: 2.6→2.74 Å / Num. unique obs: 4021 / CC1/2: 0.789

-
Processing

Software
NameVersionClassification
PHENIX(???)refinement
PDB_EXTRACTdata extraction
HKL-3000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.6→43.86 Å / SU ML: 0.41 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 28.27 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2635 1407 5 %
Rwork0.1989 --
obs0.2021 28137 99.95 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.6→43.86 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5640 0 0 141 5781
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0085784
X-RAY DIFFRACTIONf_angle_d1.0157874
X-RAY DIFFRACTIONf_dihedral_angle_d18.7782234
X-RAY DIFFRACTIONf_chiral_restr0.054862
X-RAY DIFFRACTIONf_plane_restr0.011004
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.6-2.690.39971380.28572616X-RAY DIFFRACTION100
2.69-2.80.36261380.2662610X-RAY DIFFRACTION100
2.8-2.920.33461380.25092629X-RAY DIFFRACTION100
2.93-3.080.37181370.27562607X-RAY DIFFRACTION100
3.08-3.270.35581400.24232657X-RAY DIFFRACTION100
3.27-3.520.28481380.2212638X-RAY DIFFRACTION100
3.52-3.880.27131410.20842665X-RAY DIFFRACTION100
3.88-4.440.23581420.16422697X-RAY DIFFRACTION100
4.44-5.590.18471430.15432716X-RAY DIFFRACTION100
5.59-43.860.19251520.15792895X-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