[English] 日本語
Yorodumi
- PDB-6coi: AtHNL enantioselectivity mutant At-A9-H7 Apo, Y13C,Y121L,P126F,L1... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6coi
TitleAtHNL enantioselectivity mutant At-A9-H7 Apo, Y13C,Y121L,P126F,L128W,C131T,A209I with CYANIDE, benzaldehyde, MANDELIC ACID NITRILE
ComponentsAlpha-hydroxynitrile lyase
KeywordsLYASE / alpha beta hydrolase globular hydroxynitrile lyase
Function / homology
Function and homology information


mandelonitrile lyase activity / (R)-mandelonitrile lyase / glycoside catabolic process / response to wounding
Similarity search - Function
Methylesterase/Alpha-hydroxynitrile lyase / Alpha/beta hydrolase family / 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
CYANIDE ION / benzaldehyde / (S)-MANDELIC ACID NITRILE / (2R)-hydroxy(phenyl)ethanenitrile / Alpha-hydroxynitrile lyase
Similarity search - Component
Biological speciesArabidopsis thaliana (thale cress)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.024 Å
AuthorsJones, B.J. / Kazlauskas, R.J. / Desrouleaux, R.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)5R01GM102205 United States
CitationJournal: To be published
Title: AtHNL enantioselectivity mutants
Authors: Jones, B.J. / Desrouleaux, R. / Kazlauskas, R.J.
History
DepositionMar 12, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 20, 2019Provider: repository / Type: Initial release
Revision 1.1Apr 10, 2019Group: Author supporting evidence / Data collection / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.2Jan 1, 2020Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.3Oct 4, 2023Group: 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: Alpha-hydroxynitrile lyase
B: Alpha-hydroxynitrile lyase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)59,6579
Polymers58,9542
Non-polymers7037
Water2,846158
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: homology
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2290 Å2
ΔGint-19 kcal/mol
Surface area19530 Å2
MethodPISA
Unit cell
Length a, b, c (Å)49.917, 86.943, 122.982
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

-
Components

-
Protein , 1 types, 2 molecules AB

#1: Protein Alpha-hydroxynitrile lyase / AtHNL / (R)-hydroxynitrile lyase / (R)-oxynitrilase / Methylesterase 5 / AtMES5


Mass: 29476.996 Da / Num. of mol.: 2 / Fragment: AtHNL / Mutation: Y13C,Y121L,P126F,L128W,C131T,A209I
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Arabidopsis thaliana (thale cress) / Gene: HNL, MES5, At5g10300, F18D22_70 / Plasmid: pET21a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q9LFT6, (R)-mandelonitrile lyase

-
Non-polymers , 6 types, 165 molecules

#2: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#3: Chemical ChemComp-CYN / CYANIDE ION


Mass: 26.017 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: CN
#4: Chemical ChemComp-HBX / benzaldehyde


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


Mass: 133.147 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H7NO
#6: Chemical ChemComp-MNN / (S)-MANDELIC ACID NITRILE / (S)-HYDROXY(PHENYL)ACETONITRILE


Mass: 133.147 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H7NO
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 158 / 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: 2.26 Å3/Da / Density % sol: 45.66 % / Mosaicity: 1.57 ° / Mosaicity esd: 0.016 °
Crystal growTemperature: 292 K / Method: vapor diffusion, hanging drop / pH: 6.2 / Details: 0.1 M bis-tris, 18% PEG 3350

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.54178 Å
DetectorType: RIGAKU SATURN 944 / Detector: CCD / Date: Sep 8, 2016
RadiationMonochromator: Rigaku VariMax Confocal Max-Flux / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54178 Å / Relative weight: 1
ReflectionResolution: 2.024→50 Å / Num. obs: 35084 / % possible obs: 98.4 % / Redundancy: 4.4 % / Rmerge(I) obs: 0.084 / Rpim(I) all: 0.043 / Rrim(I) all: 0.095 / Χ2: 0.926 / Net I/σ(I): 7.5
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
2.03-2.074.10.65717520.690.3630.7550.722100
2.07-2.14.20.52617440.7360.290.6040.85799.9
2.1-2.144.20.52617520.8170.290.6030.72899.8
2.14-2.194.10.44517590.850.2470.5110.78399.7
2.19-2.234.10.39517420.8810.2210.4550.81399.7
2.23-2.2940.36717630.8950.2060.4231.04399.3
2.29-2.344.10.35417150.9340.1950.4060.76899.3
2.34-2.414.10.27717400.9410.1520.3170.81798.4
2.41-2.484.10.25417460.9550.1410.2920.89198.6
2.48-2.564.10.21917270.9610.1190.250.92898
2.56-2.654.20.19217280.9730.1040.2190.93597.5
2.65-2.764.20.17817170.9750.0960.2030.99498.3
2.76-2.884.20.1417510.9850.0750.160.99797.5
2.88-3.034.20.1217150.9910.0640.1371.00597.2
3.03-3.224.30.08417420.9940.0440.096197.2
3.22-3.474.40.06317270.9960.0320.0711.0396.5
3.47-3.824.40.0617200.9960.030.0681.00695.4
3.82-4.374.70.05317640.9970.0260.0591.0196.7
4.37-5.515.50.05218340.9970.0240.0570.99199.5
5.51-506.50.04519460.9990.0190.0491.02899.1

-
Processing

Software
NameVersionClassification
REFMAC5.8.0155refinement
DENZOdata reduction
HKL-2000data scaling
PDB_EXTRACT3.24data extraction
REFMACphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: pdbid 3DQZ

3dqz


Resolution: 2.024→50 Å / Cor.coef. Fo:Fc: 0.96 / Cor.coef. Fo:Fc free: 0.929 / SU B: 11.205 / SU ML: 0.149 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.209 / ESU R Free: 0.195
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.2577 1696 4.9 %RANDOM
Rwork0.1898 ---
obs0.193 33202 97.75 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 115.65 Å2 / Biso mean: 34.112 Å2 / Biso min: 14.65 Å2
Baniso -1Baniso -2Baniso -3
1--0.46 Å2-0 Å20 Å2
2--0.24 Å2-0 Å2
3---0.22 Å2
Refinement stepCycle: final / Resolution: 2.024→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4126 0 52 158 4336
Biso mean--34.79 32.3 -
Num. residues----518
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0230.0194357
X-RAY DIFFRACTIONr_bond_other_d0.0020.024135
X-RAY DIFFRACTIONr_angle_refined_deg2.1951.975890
X-RAY DIFFRACTIONr_angle_other_deg1.11839579
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.765538
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.21924.49196
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.40815777
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.7091517
X-RAY DIFFRACTIONr_chiral_restr0.1290.2636
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.0214852
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02996
LS refinement shellResolution: 2.024→2.077 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.325 136 -
Rwork0.268 2385 -
all-2521 -
obs--96.55 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.90960.0771-0.11030.2011-0.23640.6578-0.08890.1598-0.0863-0.04670.0111-0.00250.04550.03490.07770.0792-0.01580.01580.037-0.00690.02448.263589.5719126.0529
20.97460.0318-0.10990.5010.11820.19410.022-0.1481-0.01040.0348-0.00560.02110.0037-0.0032-0.01630.0723-0.00340.01920.03360.01640.0258-9.372794.0197155.9752
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 260
2X-RAY DIFFRACTION2B1 - 258

+
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