[English] 日本語
Yorodumi
- PDB-8hwy: Ancestral imine reductase mutant N559_M6 -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 8hwy
TitleAncestral imine reductase mutant N559_M6
Componentsancestral imine reductase mutant N559_M6
KeywordsOXIDOREDUCTASE / ancestral enzyme / NADP+
Function / homologyNADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE
Function and homology information
Biological speciesEscherichia (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.32 Å
AuthorsZhu, X.X.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)21878085 China
CitationJournal: Nat Commun / Year: 2024
Title: Evolutionary insights into the stereoselectivity of imine reductases based on ancestral sequence reconstruction.
Authors: Zhu, X.X. / Zheng, W.Q. / Xia, Z.W. / Chen, X.R. / Jin, T. / Ding, X.W. / Chen, F.F. / Chen, Q. / Xu, J.H. / Kong, X.D. / Zheng, G.W.
History
DepositionJan 3, 2023Deposition site: PDBJ / Processing site: PDBC
Revision 1.0Jan 10, 2024Provider: repository / Type: Initial release
Revision 1.1Dec 11, 2024Group: Database references / Structure summary / Category: citation / citation_author / pdbx_entry_details
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _pdbx_entry_details.has_protein_modification

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: ancestral imine reductase mutant N559_M6
B: ancestral imine reductase mutant N559_M6
hetero molecules


Theoretical massNumber of molelcules
Total (without water)63,2244
Polymers61,7382
Non-polymers1,4872
Water2,648147
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area10430 Å2
ΔGint-92 kcal/mol
Surface area21110 Å2
MethodPISA
Unit cell
Length a, b, c (Å)60.336, 71.762, 65.108
Angle α, β, γ (deg.)90.00, 113.20, 90.00
Int Tables number4
Space group name H-MP1211

-
Components

#1: Protein ancestral imine reductase mutant N559_M6


Mass: 30868.789 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: Sequence reference for this entry is not available in UniProt at the time of biocuration.
Source: (gene. exp.) Escherichia (bacteria) / Production host: Escherichia coli (E. coli)
#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: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 147 / 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: 2.1 Å3/Da / Density % sol: 41.39 %
Crystal growTemperature: 277.15 K / Method: vapor diffusion, sitting drop / Details: 25% PEG3350, 0.1M Bis-Tris (pH = 6.5), 0.2 M NaCl

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.97853 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Nov 28, 2022
RadiationMonochromator: Si11 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97853 Å / Relative weight: 1
ReflectionResolution: 2.32→59.84 Å / Num. obs: 22088 / % possible obs: 99.3 % / Redundancy: 5.9 % / CC1/2: 0.997 / Net I/σ(I): 15.5
Reflection shellResolution: 2.32→2.38 Å / Redundancy: 3.9 % / Num. unique obs: 5668 / CC1/2: 0.957

-
Processing

Software
NameVersionClassification
PHENIX(1.20.1_4487: ???)refinement
PDB_EXTRACTV4.0data extraction
Aimless0.7.7data scaling
PHENIX1.20.1phasing
DIALS3.14.1data reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.32→52.2 Å / SU ML: 0.24 / Cross valid method: FREE R-VALUE / σ(F): 1.39 / Phase error: 23.3 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2246 1177 5.33 %
Rwork0.1696 --
obs0.1727 22065 99.25 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.32→52.2 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4168 0 96 147 4411
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_dihedral_angle_d8.852624
X-RAY DIFFRACTIONf_chiral_restr0.052691
X-RAY DIFFRACTIONf_plane_restr0.008775
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.32-2.430.30841250.19152462X-RAY DIFFRACTION94
2.43-2.550.28381490.19412626X-RAY DIFFRACTION100
2.55-2.710.29871210.20532624X-RAY DIFFRACTION100
2.71-2.920.26631240.20152649X-RAY DIFFRACTION100
2.92-3.220.26431550.19192613X-RAY DIFFRACTION100
3.22-3.680.19571890.16732586X-RAY DIFFRACTION100
3.68-4.640.20121550.13872653X-RAY DIFFRACTION100
4.64-52.20.18461590.14962675X-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