[English] 日本語
Yorodumi
- PDB-5e4b: Hydroxynitrile lyase from the fern Davallia tyermanii in complex ... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 5e4b
TitleHydroxynitrile lyase from the fern Davallia tyermanii in complex with (R)-mandelonitrile / benzaldehyde
ComponentsHydroxynitrile lyase
KeywordsLYASE / hydroxynitrile lyase / fern / (R)-mandelonitrile / benzaldehyde
Function / homologySTART domain / Alpha-D-Glucose-1,6-Bisphosphate; Chain A, domain 4 / START-like domain superfamily / lyase activity / 2-Layer Sandwich / Alpha Beta / benzaldehyde / (2R)-hydroxy(phenyl)ethanenitrile / Hydroxynitrile lyase
Function and homology information
Biological speciesDavallia tyermannii (plant)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.5 Å
AuthorsPavkov-Keller, T. / Diepold, M. / Gruber, K.
Funding support Austria, 1items
OrganizationGrant numberCountry
Austria
CitationJournal: Sci Rep / Year: 2017
Title: Enzyme discovery beyond homology: a unique hydroxynitrile lyase in the Bet v1 superfamily.
Authors: Lanfranchi, E. / Pavkov-Keller, T. / Koehler, E.M. / Diepold, M. / Steiner, K. / Darnhofer, B. / Hartler, J. / Van Den Bergh, T. / Joosten, H.J. / Gruber-Khadjawi, M. / Thallinger, G.G. / ...Authors: Lanfranchi, E. / Pavkov-Keller, T. / Koehler, E.M. / Diepold, M. / Steiner, K. / Darnhofer, B. / Hartler, J. / Van Den Bergh, T. / Joosten, H.J. / Gruber-Khadjawi, M. / Thallinger, G.G. / Birner-Gruenberger, R. / Gruber, K. / Winkler, M. / Glieder, A.
History
DepositionOct 5, 2015Deposition site: RCSB / Processing site: PDBE
Revision 1.0Oct 5, 2016Provider: repository / Type: Initial release
Revision 1.1Dec 23, 2020Group: Database references / Category: citation / citation_author
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
Revision 1.2Jan 10, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Hydroxynitrile lyase
B: Hydroxynitrile lyase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,9986
Polymers46,5202
Non-polymers4794
Water9,728540
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3810 Å2
ΔGint-17 kcal/mol
Surface area15160 Å2
MethodPISA
Unit cell
Length a, b, c (Å)73.362, 94.135, 116.143
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number23
Space group name H-MI222

-
Components

#1: Protein Hydroxynitrile lyase


Mass: 23259.975 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: GenBank asseccion number KT804569 / Source: (gene. exp.) Davallia tyermannii (plant) / Production host: Escherichia coli (E. coli) / References: UniProt: A0A1C9V3S9*PLUS
#2: Chemical ChemComp-HBX / benzaldehyde


Mass: 106.122 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C7H6O
#3: Chemical ChemComp-MXN / (2R)-hydroxy(phenyl)ethanenitrile / (R)-mandelonitrile


Mass: 133.147 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C8H7NO
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 540 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION

-
Sample preparation

CrystalDensity Matthews: 2.16 Å3/Da / Density % sol: 42.93 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 8
Details: Native crystals of DtHNL1 were obtained by mixing 0.5ul 4 mg/mL protein sample (in 10 mM Tris-HCl pH 8.0) with 1 ul reservoir solution (0.9 M NaNO3; Na2HPO4; (NH4)2SO4 mix, 0.1 M Tris-Bicine ...Details: Native crystals of DtHNL1 were obtained by mixing 0.5ul 4 mg/mL protein sample (in 10 mM Tris-HCl pH 8.0) with 1 ul reservoir solution (0.9 M NaNO3; Na2HPO4; (NH4)2SO4 mix, 0.1 M Tris-Bicine Buffer pH 8.5 and 30% (w/v) polyethylene glycol monomethyl ether 550 & polyethylene glycol 20k; Morpheus condition C9). Additionally, native crystals were also grown by mixing 1 ul 4 mg/mL protein sample (in 10 mM Tris-HCl pH 8.0) with 0.5ul reservoir solution (0.1 M 2-(4-(2-hydroxyethyl)-1-piperazinyl) ethanesulfonic acid pH 7.5 and 10% (w/v) polyethylene glycol; JSCG condition B4).

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: BM14 / Wavelength: 0.9184 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Jun 22, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9184 Å / Relative weight: 1
ReflectionResolution: 1.5→35.8 Å / Num. obs: 63070 / % possible obs: 97.48 % / Redundancy: 4.1 % / Rmerge(I) obs: 0.066 / Net I/σ(I): 13.74
Reflection shellResolution: 1.5→1.55 Å / Redundancy: 3 % / Rmerge(I) obs: 0.611 / Mean I/σ(I) obs: 1.86 / % possible all: 80.88

-
Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Starting model: 5.0E+46 / Resolution: 1.5→35.8 Å / SU ML: 0.14 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 18.24 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.179 3154 5 %
Rwork0.1562 --
obs0.1573 63062 97.47 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.5→35.8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2750 0 36 540 3326
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0073050
X-RAY DIFFRACTIONf_angle_d1.0334177
X-RAY DIFFRACTIONf_dihedral_angle_d12.5141075
X-RAY DIFFRACTIONf_chiral_restr0.047461
X-RAY DIFFRACTIONf_plane_restr0.005538
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.4988-1.52110.31030.29061965X-RAY DIFFRACTION75
1.5211-1.54490.2811200.26182262X-RAY DIFFRACTION85
1.5449-1.57020.24081270.23912411X-RAY DIFFRACTION91
1.5702-1.59730.2391310.22282499X-RAY DIFFRACTION95
1.5973-1.62640.20791380.2012619X-RAY DIFFRACTION100
1.6264-1.65760.20641390.19252638X-RAY DIFFRACTION100
1.6576-1.69150.22861390.1922635X-RAY DIFFRACTION100
1.6915-1.72830.23991400.18912663X-RAY DIFFRACTION100
1.7283-1.76850.22171390.18662637X-RAY DIFFRACTION100
1.7685-1.81270.20631390.17922654X-RAY DIFFRACTION100
1.8127-1.86170.20051390.17042631X-RAY DIFFRACTION100
1.8617-1.91650.21291400.1592654X-RAY DIFFRACTION100
1.9165-1.97830.18381410.15222686X-RAY DIFFRACTION100
1.9783-2.0490.16021390.15122641X-RAY DIFFRACTION100
2.049-2.1310.18741400.14812663X-RAY DIFFRACTION100
2.131-2.2280.16241410.14252670X-RAY DIFFRACTION100
2.228-2.34550.17571390.14742656X-RAY DIFFRACTION100
2.3455-2.49240.16371420.15422694X-RAY DIFFRACTION100
2.4924-2.68480.17681410.15192686X-RAY DIFFRACTION100
2.6848-2.95480.16111420.15842682X-RAY DIFFRACTION100
2.9548-3.38210.17961410.14482690X-RAY DIFFRACTION100
3.3821-4.260.14581440.12812734X-RAY DIFFRACTION100
4.26-35.81480.15841500.13572838X-RAY DIFFRACTION99

+
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://pdbjlvh1.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