[English] 日本語
Yorodumi
- PDB-1yas: HYDROXYNITRILE LYASE COMPLEXED WITH HISTIDINE -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1yas
TitleHYDROXYNITRILE LYASE COMPLEXED WITH HISTIDINE
ComponentsHYDROXYNITRILE LYASE
KeywordsCOMPLEX (LYASE/PEPTIDE) / OXYNITRILASE / CYANOGENESIS / CYANHYDRIN FORMATION / LYASE / COMPLEX (LYASE-PEPTIDE) / COMPLEX (LYASE-PEPTIDE) complex
Function / homology
Function and homology information


(S)-hydroxynitrile lyase / aliphatic (S)-hydroxynitrile lyase activity / aromatic (S)-hydroxynitrile lyase activity / jasmonic acid metabolic process / methyl salicylate esterase activity / methyl indole-3-acetate esterase activity / methyl jasmonate esterase activity / salicylic acid metabolic process
Similarity search - Function
Methylesterase/Alpha-hydroxynitrile lyase / alpha/beta hydrolase fold / Alpha/beta hydrolase fold-1 / Alpha/Beta hydrolase fold, catalytic domain / Alpha/Beta hydrolase fold / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
HISTIDINE / (S)-hydroxynitrile lyase
Similarity search - Component
Biological speciesHevea brasiliensis (rubber tree)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MIR / Resolution: 1.9 Å
AuthorsWagner, U.G. / Kratky, C.
Citation
Journal: Structure / Year: 1996
Title: Mechanism of cyanogenesis: the crystal structure of hydroxynitrile lyase from Hevea brasiliensis.
Authors: Wagner, U.G. / Hasslacher, M. / Griengl, H. / Schwab, H. / Kratky, C.
#1: Journal: Proteins / Year: 1997
Title: Hydroxynitrile Lyase from Hevea Brasiliensis: Molecular Characterization and Mechanism of Enzyme Catalysis
Authors: Hasslacher, M. / Kratky, C. / Griengl, H. / Schwab, H. / Kohlwein, S.D.
#2: Journal: Acta Crystallogr.,Sect.D / Year: 1996
Title: Crystallization of a Hydroxynitrile Lyase
Authors: Wagner, U.G. / Schall, M. / Hayn, M. / Hasslacher, M. / Schwab, H. / Griengl, H.S. / Kratky, C.
#3: Journal: J.Biol.Chem. / Year: 1996
Title: Molecular Cloning of the Full-Length Cdna of (S)-Hydroxynitrile Lyase from Hevea Brasiliensis. Functional Expression in Escherichia Coli and Saccharomyces Cerevisiae and Identification of an Active Site Residue
Authors: Hasslacher, M. / Schall, M. / Hayn, M. / Griengl, H. / Kohlwein, S.D. / Schwab, H.
History
DepositionMay 15, 1996Processing site: BNL
Revision 1.0Jun 16, 1997Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 14, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / diffrn_source / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _diffrn_source.pdbx_synchrotron_site / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: HYDROXYNITRILE LYASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,5153
Polymers29,2631
Non-polymers2522
Water1,38777
1
A: HYDROXYNITRILE LYASE
hetero molecules

A: HYDROXYNITRILE LYASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)59,0306
Polymers58,5252
Non-polymers5044
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_565x,-y+1,-z1
Unit cell
Length a, b, c (Å)47.703, 109.010, 128.226
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221

-
Components

#1: Protein HYDROXYNITRILE LYASE / OXYNITRILE LYASE


Mass: 29262.598 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Hevea brasiliensis (rubber tree) / Gene: HNL / Organ: LEAF / Plasmid: BHIL-D2 / Gene (production host): HNL / Production host: Pichia pastoris (fungus) / References: UniProt: P52704, EC: 4.1.2.39
#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-HIS / HISTIDINE


Type: L-peptide linking / Mass: 156.162 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H10N3O2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 77 / 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: 2.8 Å3/Da / Density % sol: 56 %
Crystal growTemperature: 293 K / pH: 7.5
Details: 0.1 M NATRIUM HEPES BUFFER PH=7.5 2 % PEG 400, 2.0 M AMMONIUM SULFATE, 20 DEGREES., temperature 293K
Crystal grow
*PLUS
Method: vapor diffusion, hanging drop / Details: used to seeding
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
12 %PEG4001reservoir
22.0 Mammonium sulfate1reservoir
30.1 MNa HEPES1reservoir

-
Data collection

DiffractionMean temperature: 120 K
Diffraction sourceSource: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: X31 / Wavelength: 0.92
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: May 12, 1995
RadiationMonochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.92 Å / Relative weight: 1
ReflectionResolution: 1.9→15 Å / Num. obs: 24031 / % possible obs: 90.4 % / Observed criterion σ(I): 0 / Redundancy: 5 % / Biso Wilson estimate: 15.29 Å2 / Rmerge(I) obs: 0.073
Reflection shellResolution: 1.9→1.93 Å / Redundancy: 2.5 % / Rmerge(I) obs: 0.355 / % possible all: 67.8
Reflection
*PLUS
Num. measured all: 137615

-
Processing

Software
NameVersionClassification
DENZOdata reduction
SCALEPACKdata scaling
X-PLOR3.1model building
X-PLOR3.1refinement
X-PLOR3.1phasing
RefinementMethod to determine structure: MIR / Resolution: 1.9→15 Å / Cross valid method: FREE-R / σ(F): 3
RfactorNum. reflection% reflection
Rfree0.241 2030 10 %
Rwork0.199 --
obs0.199 20547 76.7 %
Displacement parametersBiso mean: 8.75 Å2
Baniso -1Baniso -2Baniso -3
1--2.856 Å20 Å20 Å2
2--1.298 Å20 Å2
3---1.558 Å2
Refine analyzeLuzzati d res low obs: 15 Å
Refinement stepCycle: LAST / Resolution: 1.9→15 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2057 0 16 77 2150
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.018
X-RAY DIFFRACTIONx_bond_d_na
X-RAY DIFFRACTIONx_bond_d_prot
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_angle_d_na
X-RAY DIFFRACTIONx_angle_d_prot
X-RAY DIFFRACTIONx_angle_deg2.99
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d24.47
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d1.388
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it
X-RAY DIFFRACTIONx_mcangle_it
X-RAY DIFFRACTIONx_scbond_it
X-RAY DIFFRACTIONx_scangle_it
LS refinement shellResolution: 1.9→1.99 Å
RfactorNum. reflection% reflection
Rfree0.381 139 7.58 %
Rwork0.338 1230 -
obs--76.68 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PARAM19X.PROTOPH19X.PRO
X-RAY DIFFRACTION2PARAM19X.SOLTOPH19X.SOL
Software
*PLUS
Name: X-PLOR / Version: 3.1 / Classification: refinement
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_deg24.471
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg1.388

+
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