[English] 日本語
Yorodumi
- PDB-1e8d: MECHANISTIC ASPECTS OF CYANOGENESIS FROM ACTIVE SITE MUTANT SER80... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1e8d
TitleMECHANISTIC ASPECTS OF CYANOGENESIS FROM ACTIVE SITE MUTANT SER80ALA OF HYDROXYNITRILE LYASE FROM MANIHOT ESCULENTA IN COMPLEX WITH ACETONE CYANOHYDRIN
ComponentsHYDROXYNITRILE LYASE
KeywordsLYASE / HYDROXYNITRILE LYASE / ACTIVE SITE MUTANT / ACETONE CYANOHYDRIN 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 jasmonate esterase activity / salicylic acid metabolic process / methyl indole-3-acetate esterase activity
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
2-HYDROXY-2-METHYLPROPANENITRILE / (S)-hydroxynitrile lyase
Similarity search - Component
Biological speciesMANIHOT ESCULENTA (cassava)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 Å
AuthorsLauble, H. / Miehlich, B. / Foerster, S. / Wajant, H. / Effenberger, F.
Citation
Journal: Protein Sci. / Year: 2001
Title: Mechanistic Aspects of Cyanogenesis from Active-Site Mutant Ser80Ala of Hydroxynitrile Lyase from Manihot Esculenta in Complex with Acetone Cyanohydrin.
Authors: Lauble, H. / Miehlich, B. / Forster, S. / Wajant, H. / Effenberger, F.
#1: Journal: Acta Crystallogr.,Sect.D / Year: 2001
Title: Structure of Hydroxynitrile Lyase from Manihot Esculenta in Complex with Substrates Acetone and Chloroacetone: Implications for the Mechanism of Cyanogenesis
Authors: Lauble, H. / Foerster, S. / Miehlich, B. / Wajant, H. / Effenberger, F.
History
DepositionSep 19, 2000Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 17, 2001Provider: repository / Type: Initial release
Revision 1.1Jan 30, 2013Group: Database references / Derived calculations ...Database references / Derived calculations / Non-polymer description / Other / Version format compliance
Revision 1.2Jul 24, 2019Group: Data collection / Category: diffrn_source / Item: _diffrn_source.pdbx_synchrotron_site
Revision 1.3Dec 13, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _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
B: HYDROXYNITRILE LYASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)59,9796
Polymers59,6382
Non-polymers3404
Water4,918273
1
A: HYDROXYNITRILE LYASE
B: HYDROXYNITRILE LYASE
hetero molecules

A: HYDROXYNITRILE LYASE
B: HYDROXYNITRILE LYASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)119,95812
Polymers119,2774
Non-polymers6818
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_556y,x,-z+11
Buried area8150 Å2
ΔGint-53 kcal/mol
Surface area44330 Å2
MethodPISA
Unit cell
Length a, b, c (Å)105.900, 105.900, 187.800
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212

-
Components

#1: Protein HYDROXYNITRILE LYASE / (S)-ACETONE-CYANOHYDRIN LYASE / (S)-HYDROXYNITRILASE


Mass: 29819.209 Da / Num. of mol.: 2 / Mutation: YES
Source method: isolated from a genetically manipulated source
Details: ACETONE CYANOHYDRIN COMPLEX / Source: (gene. exp.) MANIHOT ESCULENTA (cassava) / Production host: ESCHERICHIA COLI (E. coli) / References: UniProt: P52705, EC: 4.2.1.37
#2: Chemical
ChemComp-CNH / 2-HYDROXY-2-METHYLPROPANENITRILE / ACETONE CYANOHYDRIN / Acetone cyanohydrin


Mass: 85.104 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C4H7NO
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 273 / Source method: isolated from a natural source / Formula: H2O
Compound detailsCHAIN A, B: CONTAINS ENGINEERED MUTATION S80A. RESIDUES -4 TO 1 ARE CLONING ARTEFACTS

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 4.5 Å3/Da / Density % sol: 71 %
Crystal growpH: 4.8 / Details: 0.1 M NA CITRATE, PH 4.8, 6% PEG8000, 28% MPD
Crystal grow
*PLUS
Method: vapor diffusion, hanging drop
Details: Lauble, H., (1999) Acta Crystallogr.,Sect.D, 55, 904.
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
15 %PEG80001reservoir
216 %MPD1reservoir
3100 mMsodium citrate1reservoir
430 mg/mlprotein1drop

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: X11 / Wavelength: 0.905
DetectorType: MARRESEARCH / Detector: IMAGE PLATE
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.905 Å / Relative weight: 1
ReflectionResolution: 2.2→15 Å / Num. obs: 52736 / % possible obs: 97.1 % / Redundancy: 3.9 % / Biso Wilson estimate: 22.7 Å2 / Rsym value: 0.068 / Net I/σ(I): 8.1
Reflection shellResolution: 2.2→2.3 Å / Redundancy: 3.8 % / Mean I/σ(I) obs: 3.4 / Rsym value: 0.135 / % possible all: 98.5
Reflection
*PLUS
Num. measured all: 211247 / Rmerge(I) obs: 0.068
Reflection shell
*PLUS
% possible obs: 98.5 % / Rmerge(I) obs: 0.135

-
Processing

Software
NameVersionClassification
X-PLOR3.851refinement
DENZOdata reduction
SCALEPACKdata scaling
X-PLORphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1E89

1e89


Resolution: 2.2→8 Å / Rfactor Rfree error: 0.003 / Data cutoff high absF: 10000000 / Data cutoff low absF: 0.001 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 2
RfactorNum. reflection% reflectionSelection details
Rfree0.238 5079 10.1 %RANDOM
Rwork0.186 ---
obs0.186 50187 93.6 %-
Displacement parametersBiso mean: 25.5 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.28 Å0.22 Å
Luzzati d res low-8 Å
Luzzati sigma a0.16 Å0.19 Å
Refinement stepCycle: LAST / Resolution: 2.2→8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4176 0 24 273 4473
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONx_bond_d0.015
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_deg2.9
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d24.1
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d1.18
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it1.951.5
X-RAY DIFFRACTIONx_mcangle_it2.842
X-RAY DIFFRACTIONx_scbond_it4.112
X-RAY DIFFRACTIONx_scangle_it6.162.5
LS refinement shellResolution: 2.2→2.33 Å / Rfactor Rfree error: 0.009 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.252 799 9.8 %
Rwork0.231 7375 -
obs--93.1 %
Xplor fileSerial no: 1 / Param file: PARAM19X.PRO / Topol file: TOPH19X.PRO
Software
*PLUS
Name: X-PLOR / Version: 3.851 / Classification: refinement
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.02
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_deg24.1
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg1.18

+
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