[English] 日本語
Yorodumi
- PDB-8jm6: Endo-deglycosylated hydroxynitrile lyase isozyme 5 mutant L331A/S... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 8jm6
TitleEndo-deglycosylated hydroxynitrile lyase isozyme 5 mutant L331A/S333V/P340L from Prunus communis complexed with 2,2-dimethyl-4H-benzo[d][1,3]dioxine-6-carbaldehyde (catalytic conformation)
Components(R)-mandelonitrile lyase
KeywordsLYASE / Hydroxynitrile lyase / FAD / hydrocynanation
Function / homologyFLAVIN-ADENINE DINUCLEOTIDE / : / PHOSPHATE ION
Function and homology information
Biological speciesPrunus dulcis (almond)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.91 Å
AuthorsZheng, Y.-C. / Li, F.-L. / Yu, H.-L. / Xu, J.-H.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC) China
CitationJournal: To Be Published
Title: Endo-deglycosylated hydroxynitrile lyase isozyme 5 mutant L331A/S333V/P340L from Prunus communis complexed with 2,2-dimethyl-4H-benzo[d][1,3]dioxine-6-carbaldehyde (catalytic conformation)
Authors: Zheng, Y.-C. / Li, F.-L. / Yu, H.-L. / Xu, J.-H.
History
DepositionJun 4, 2023Deposition site: PDBJ / Processing site: PDBC
Revision 1.0Jun 5, 2024Provider: repository / Type: Initial release
Revision 1.1Oct 9, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: (R)-mandelonitrile lyase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)61,40010
Polymers59,0001
Non-polymers2,4009
Water8,647480
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3130 Å2
ΔGint13 kcal/mol
Surface area18700 Å2
MethodPISA
Unit cell
Length a, b, c (Å)49.596, 90.682, 130.512
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

-
Components

-
Protein / Sugars , 2 types, 7 molecules A

#1: Protein (R)-mandelonitrile lyase


Mass: 59000.449 Da / Num. of mol.: 1 / Mutation: L331A,S333V,P340L
Source method: isolated from a genetically manipulated source
Details: Author stated the sequence reference is Genbank AAP84580.1, and the initial signal peptide (Met1 to Ser27) was exchanged into yeast alpha-factor subjected to cleavage during extracellular expression.
Source: (gene. exp.) Prunus dulcis (almond) / Gene: ALMOND_2B028509 / Production host: Komagataella pastoris (fungus) / References: (R)-mandelonitrile lyase
#4: Sugar
ChemComp-NAG / 2-acetamido-2-deoxy-beta-D-glucopyranose / N-acetyl-beta-D-glucosamine / 2-acetamido-2-deoxy-beta-D-glucose / 2-acetamido-2-deoxy-D-glucose / 2-acetamido-2-deoxy-glucose / N-ACETYL-D-GLUCOSAMINE


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C8H15NO6
IdentifierTypeProgram
DGlcpNAcbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
N-acetyl-b-D-glucopyranosamineCOMMON NAMEGMML 1.0
b-D-GlcpNAcIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcNAcSNFG CARBOHYDRATE SYMBOLGMML 1.0

-
Non-polymers , 4 types, 483 molecules

#2: Chemical ChemComp-FQ3 / 2,2-dimethyl-4H-1,3-benzodioxine-6-carbaldehyde / 2,2-dimethyl-4H-benzo[d][1,3]dioxine-6-carbaldehyde


Mass: 192.211 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C11H12O3 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-FAD / FLAVIN-ADENINE DINUCLEOTIDE


Mass: 785.550 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C27H33N9O15P2 / Comment: FAD*YM
#5: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: PO4
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 480 / Source method: isolated from a natural source / Formula: H2O

-
Details

Has ligand of interestY
Has protein modificationY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.52 Å3/Da / Density % sol: 51.2 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: tris-bicine, 100 mM, pH 8.5; CaCl2, 60 mM; MgCl2, 60 mM; PEG 500MME, 20%, v/v; PEG 20000, 10%, w/v
PH range: 8.5

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.97854 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Jun 19, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97854 Å / Relative weight: 1
ReflectionResolution: 1.9→50 Å / Num. obs: 45993 / % possible obs: 100 % / Redundancy: 13 % / CC1/2: 0.993 / CC star: 0.998 / Rmerge(I) obs: 0.189 / Rpim(I) all: 0.054 / Rrim(I) all: 0.196 / Χ2: 0.907 / Net I/σ(I): 3.4 / Num. measured all: 598873
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2CC starRpim(I) allRrim(I) allΧ2% possible all
1.9-1.9312.70.97722690.880.9680.2821.0170.88100
1.93-1.9712.80.78922440.9550.9880.2280.8220.6100
1.97-2.0112.40.69422650.9310.9820.2030.7230.605100
2.01-2.05120.74922880.9150.9770.2220.7820.937100
2.05-2.0913.60.67622480.8860.9690.1920.7041.07100
2.09-2.1413.60.5122560.9620.990.1420.530.68100
2.14-2.1913.60.45222750.9710.9930.1260.4690.677100
2.19-2.2513.40.57422620.9280.9810.1620.5971.261100
2.25-2.3213.20.36723070.9730.9930.1040.3820.694100
2.32-2.39130.32122610.9790.9950.0920.3340.733100
2.39-2.48120.29922660.9760.9940.090.3130.76100
2.48-2.5813.60.26623200.9860.9970.0740.2770.775100
2.58-2.713.60.26722700.9830.9960.0750.2780.972100
2.7-2.8413.50.2122960.9880.9970.0590.2190.858100
2.84-3.0213.30.18123110.9890.9970.0510.1880.86699.9
3.02-3.2512.20.16123150.990.9980.0480.1680.956100
3.25-3.5813.70.15723090.9910.9980.0430.1631.222100
3.58-4.0913.40.13923530.9910.9980.0390.1441.211100
4.09-5.1612.40.11923610.9920.9980.0350.1241.0499.9
5.16-5012.40.11625170.9920.9980.0340.1211.26799.9

-
Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
HKL-3000data scaling
HKL-3000data reduction
REFMACphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.91→46.4 Å / Cor.coef. Fo:Fc: 0.967 / Cor.coef. Fo:Fc free: 0.954 / WRfactor Rfree: 0.185 / WRfactor Rwork: 0.148 / SU B: 2.809 / SU ML: 0.08 / Average fsc free: 0.9474 / Average fsc work: 0.9569 / Cross valid method: THROUGHOUT / ESU R: 0.126 / ESU R Free: 0.118 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.18367 2213 4.9 %RANDOM
Rwork0.14735 42732 --
all0.149 ---
obs0.1491 42732 97.06 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 20.958 Å2
Baniso -1Baniso -2Baniso -3
1-0.16 Å20 Å2-0 Å2
2---0.2 Å20 Å2
3---0.05 Å2
Refinement stepCycle: 1 / Resolution: 1.91→46.4 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3960 0 156 480 4596
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0134222
X-RAY DIFFRACTIONr_bond_other_d0.0010.0173808
X-RAY DIFFRACTIONr_angle_refined_deg1.7251.6735783
X-RAY DIFFRACTIONr_angle_other_deg1.4421.5988785
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.7765512
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.65723.383201
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.17515612
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.5331517
X-RAY DIFFRACTIONr_chiral_restr0.090.2563
X-RAY DIFFRACTIONr_gen_planes_refined0.010.024805
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02943
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.7671.9922057
X-RAY DIFFRACTIONr_mcbond_other1.7641.9912056
X-RAY DIFFRACTIONr_mcangle_it2.492.9722566
X-RAY DIFFRACTIONr_mcangle_other2.492.9732567
X-RAY DIFFRACTIONr_scbond_it2.712.3032165
X-RAY DIFFRACTIONr_scbond_other2.6852.2962162
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other4.0623.3553212
X-RAY DIFFRACTIONr_long_range_B_refined5.63825.5374908
X-RAY DIFFRACTIONr_long_range_B_other5.32824.754764
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.913→1.962 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.266 143 -
Rwork0.22 2292 -
obs--72.97 %

+
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