[English] 日本語
Yorodumi
- PDB-5xzq: Hydroxynitrile lyase from Passiflora edulis (PeHNL) -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 5xzq
TitleHydroxynitrile lyase from Passiflora edulis (PeHNL)
ComponentsHydroxynitrile lyase
KeywordsLYASE / Hydroxynitrile lyase / Cyanohydrins
Function / homology
Function and homology information


Stress-response A/B barrel domain-containing protein HS1/DABB1-like / Stress responsive alpha-beta barrel / Stress responsive A/B Barrel Domain / Stress-response A/B barrel domain profile. / Stress responsive A/B Barrel Domain / Alpha-Beta Plaits - #100 / Dimeric alpha-beta barrel / Alpha-Beta Plaits / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Hydroxynitrile lyase
Similarity search - Component
Biological speciesPassiflora edulis (passion fruit)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.8 Å
AuthorsMotojima, F. / Nuylert, A. / Asano, Y.
Funding support Japan, 1items
OrganizationGrant numberCountry
JSTJPMJER1102 Japan
CitationJournal: FEBS J. / Year: 2018
Title: The crystal structure and catalytic mechanism of hydroxynitrile lyase from passion fruit, Passiflora edulis
Authors: Motojima, F. / Nuylert, A. / Asano, Y.
History
DepositionJul 13, 2017Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Nov 22, 2017Provider: repository / Type: Initial release
Revision 1.1Nov 29, 2017Group: Database references / Category: citation
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.year
Revision 1.2Dec 13, 2017Group: Database references / Category: citation
Item: _citation.journal_abbrev / _citation.journal_id_ISSN ..._citation.journal_abbrev / _citation.journal_id_ISSN / _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.3Feb 7, 2018Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title / _citation.year
Revision 1.4Dec 25, 2019Group: Data collection / Category: reflns_shell / Item: _reflns_shell.pdbx_Rrim_I_all
Revision 1.5Nov 22, 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: Hydroxynitrile lyase
B: Hydroxynitrile lyase
C: Hydroxynitrile lyase
D: Hydroxynitrile lyase
E: Hydroxynitrile lyase
F: Hydroxynitrile lyase
G: Hydroxynitrile lyase
H: Hydroxynitrile lyase
I: Hydroxynitrile lyase
J: Hydroxynitrile lyase
K: Hydroxynitrile lyase
L: Hydroxynitrile lyase


Theoretical massNumber of molelcules
Total (without water)197,86312
Polymers197,86312
Non-polymers00
Water1,13563
1
A: Hydroxynitrile lyase
B: Hydroxynitrile lyase


Theoretical massNumber of molelcules
Total (without water)32,9772
Polymers32,9772
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3950 Å2
ΔGint-27 kcal/mol
Surface area10790 Å2
MethodPISA
2
C: Hydroxynitrile lyase
D: Hydroxynitrile lyase


Theoretical massNumber of molelcules
Total (without water)32,9772
Polymers32,9772
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4180 Å2
ΔGint-30 kcal/mol
Surface area10820 Å2
MethodPISA
3
E: Hydroxynitrile lyase
F: Hydroxynitrile lyase


Theoretical massNumber of molelcules
Total (without water)32,9772
Polymers32,9772
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3680 Å2
ΔGint-23 kcal/mol
Surface area10440 Å2
MethodPISA
4
G: Hydroxynitrile lyase
H: Hydroxynitrile lyase


Theoretical massNumber of molelcules
Total (without water)32,9772
Polymers32,9772
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3870 Å2
ΔGint-27 kcal/mol
Surface area10360 Å2
MethodPISA
5
I: Hydroxynitrile lyase
J: Hydroxynitrile lyase


Theoretical massNumber of molelcules
Total (without water)32,9772
Polymers32,9772
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4060 Å2
ΔGint-30 kcal/mol
Surface area10610 Å2
MethodPISA
6
K: Hydroxynitrile lyase
L: Hydroxynitrile lyase


Theoretical massNumber of molelcules
Total (without water)32,9772
Polymers32,9772
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3790 Å2
ΔGint-26 kcal/mol
Surface area10510 Å2
MethodPISA
Unit cell
Length a, b, c (Å)85.446, 88.567, 104.574
Angle α, β, γ (deg.)90.00, 105.99, 90.00
Int Tables number4
Space group name H-MP1211

-
Components

#1: Protein
Hydroxynitrile lyase


Mass: 16488.611 Da / Num. of mol.: 12 / Fragment: UNP residues 27-147
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Passiflora edulis (passion fruit) / Tissue: leave / Gene: PeHNL / Plasmid: pCold-I / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: A0A1L7NZN4
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 63 / 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: 1.93 Å3/Da / Density % sol: 35.58 % / Description: Rod
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 20% (w/v) PEG6000 200 mM lithium acetate 100 mM Bis-Tris-HCl, pH 6.5
PH range: 6.5-7.5

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-1A / Wavelength: 1.1 Å
DetectorType: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Jun 20, 2015
RadiationMonochromator: SI(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.1 Å / Relative weight: 1
ReflectionResolution: 2.8→100.53 Å / Num. obs: 196401 / % possible obs: 99.3 % / Redundancy: 5.3 % / CC1/2: 0.999 / Rmerge(I) obs: 0.044 / Rpim(I) all: 0.021 / Rsym value: 0.048 / Net I/σ(I): 19.2
Reflection shellResolution: 2.8→2.95 Å / Redundancy: 5.6 % / Rmerge(I) obs: 0.197 / Mean I/σ(I) obs: 7.7 / Num. unique obs: 5327 / CC1/2: 0.986 / Rpim(I) all: 0.089 / Rsym value: 0.217 / % possible all: 99

-
Processing

Software
NameVersionClassification
REFMAC5.8.0158refinement
XDSdata reduction
SCALA3.3.22data scaling
MOLREP11.2.08phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1SI9

1si9


Resolution: 2.8→100.53 Å / Cor.coef. Fo:Fc: 0.94 / Cor.coef. Fo:Fc free: 0.884 / SU B: 18.218 / SU ML: 0.354 / Cross valid method: THROUGHOUT / ESU R Free: 0.439 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.27877 1892 5.1 %RANDOM
Rwork0.20748 ---
obs0.21127 34927 99.11 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 63.358 Å2
Baniso -1Baniso -2Baniso -3
1-2.61 Å2-0 Å21.39 Å2
2--3.67 Å2-0 Å2
3----6.08 Å2
Refinement stepCycle: 1 / Resolution: 2.8→100.53 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10523 0 0 63 10586
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.01910871
X-RAY DIFFRACTIONr_bond_other_d0.0020.029577
X-RAY DIFFRACTIONr_angle_refined_deg1.5811.92514772
X-RAY DIFFRACTIONr_angle_other_deg1.023322290
X-RAY DIFFRACTIONr_dihedral_angle_1_deg8.26451270
X-RAY DIFFRACTIONr_dihedral_angle_2_deg40.37224.711588
X-RAY DIFFRACTIONr_dihedral_angle_3_deg19.482151703
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.0091536
X-RAY DIFFRACTIONr_chiral_restr0.1040.21530
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.02112148
X-RAY DIFFRACTIONr_gen_planes_other0.0020.022388
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_it4.2166.3335104
X-RAY DIFFRACTIONr_mcbond_other4.2136.3325103
X-RAY DIFFRACTIONr_mcangle_it6.699.4766360
X-RAY DIFFRACTIONr_mcangle_other6.6899.4766361
X-RAY DIFFRACTIONr_scbond_it3.7046.5915767
X-RAY DIFFRACTIONr_scbond_other3.7046.5925768
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other5.9729.7978411
X-RAY DIFFRACTIONr_long_range_B_refined9.11972.70312153
X-RAY DIFFRACTIONr_long_range_B_other9.11972.7112153
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.8→2.873 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.368 133 -
Rwork0.296 2567 -
obs--98.83 %

+
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