[English] 日本語
Yorodumi
- PDB-3aqu: Crystal structure of a class V chitinase from Arabidopsis thaliana -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 3aqu
TitleCrystal structure of a class V chitinase from Arabidopsis thaliana
ComponentsAt4g19810
KeywordsHYDROLASE / stress response / TIM barrel / chitin
Function / homology
Function and homology information


exochitinase activity / secretory vesicle / endochitinase activity / response to jasmonic acid / response to abscisic acid / chitinase / cell wall / chitinase activity / chitin catabolic process / chitin binding ...exochitinase activity / secretory vesicle / endochitinase activity / response to jasmonic acid / response to abscisic acid / chitinase / cell wall / chitinase activity / chitin catabolic process / chitin binding / polysaccharide catabolic process / response to salt stress / extracellular region
Similarity search - Function
Chitinase A; domain 3 - #10 / Chitinase insertion domain superfamily / Chitinase II / Glyco_18 / Glycosyl hydrolases family 18 (GH18) domain profile. / Glycoside hydrolase family 18, catalytic domain / Glycosyl hydrolases family 18 / Chitinase A; domain 3 / Glycosidases / Glycoside hydrolase superfamily ...Chitinase A; domain 3 - #10 / Chitinase insertion domain superfamily / Chitinase II / Glyco_18 / Glycosyl hydrolases family 18 (GH18) domain profile. / Glycoside hydrolase family 18, catalytic domain / Glycosyl hydrolases family 18 / Chitinase A; domain 3 / Glycosidases / Glycoside hydrolase superfamily / TIM Barrel / Roll / Alpha-Beta Barrel / Alpha Beta
Similarity search - Domain/homology
CITRATE ANION / Class V chitinase
Similarity search - Component
Biological speciesArabidopsis thaliana (thale cress)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.01 Å
AuthorsNumata, T. / Ohnuma, T. / Osawa, T. / Fukamizo, T.
CitationJournal: Planta / Year: 2011
Title: A class V chitinase from Arabidopsis thaliana: gene responses, enzymatic properties, and crystallographic analysis
Authors: Ohnuma, T. / Numata, T. / Osawa, T. / Mizuhara, M. / Lampela, O. / Juffer, A.H. / Skriver, K. / Fukamizo, T.
History
DepositionNov 19, 2010Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jul 20, 2011Provider: repository / Type: Initial release
Revision 1.1Nov 1, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _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: At4g19810
B: At4g19810
C: At4g19810
D: At4g19810
hetero molecules


Theoretical massNumber of molelcules
Total (without water)155,2637
Polymers154,6954
Non-polymers5673
Water10,467581
1
A: At4g19810
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,0523
Polymers38,6741
Non-polymers3782
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: At4g19810
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,8632
Polymers38,6741
Non-polymers1891
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: At4g19810


Theoretical massNumber of molelcules
Total (without water)38,6741
Polymers38,6741
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
4
D: At4g19810


Theoretical massNumber of molelcules
Total (without water)38,6741
Polymers38,6741
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)74.574, 75.079, 97.347
Angle α, β, γ (deg.)73.63, 73.34, 68.47
Int Tables number1
Space group name H-MP1

-
Components

#1: Protein
At4g19810 / A class V chitinase from Arabidopsis thaliana / AtChiC / Putative chitinase


Mass: 38673.824 Da / Num. of mol.: 4 / Fragment: residues in UNP 25-379
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Arabidopsis thaliana (thale cress) / Gene: AT4g19810 / Plasmid: pET11a / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta2 (DE3) / References: UniProt: O81862, chitinase
#2: Chemical ChemComp-FLC / CITRATE ANION


Mass: 189.100 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C6H5O7
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 581 / 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: 3.08 Å3/Da / Density % sol: 60.03 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 5.6
Details: 100mM trisodium citrate, 20% PEG10000, pH 5.6, VAPOR DIFFUSION, SITTING DROP, temperature 293K

-
Data collection

DiffractionMean temperature: 95 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-17A / Wavelength: 0.98 Å
DetectorType: ADSC QUANTUM 270 / Detector: CCD / Date: Mar 17, 2010 / Details: mirrors
RadiationMonochromator: Numerical link type Si(111) double crystal monochromator, liquid nitrogen cooling
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 2→50 Å / Num. obs: 116512 / % possible obs: 94.5 % / Redundancy: 2.9 % / Rsym value: 0.102 / Net I/σ(I): 7.6
Reflection shellResolution: 2→2.03 Å / Redundancy: 2.3 % / Rmerge(I) obs: 0.336 / Mean I/σ(I) obs: 1.9 / % possible all: 88.7

-
Processing

Software
NameVersionClassification
HKL-2000data collection
PHASERphasing
REFMAC5.5.0102refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3ALF

3alf


Resolution: 2.01→50 Å / Cor.coef. Fo:Fc: 0.923 / Cor.coef. Fo:Fc free: 0.898 / SU B: 3.869 / SU ML: 0.106 / Cross valid method: THROUGHOUT / ESU R Free: 0.15 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.22715 5800 5 %RANDOM
Rwork0.19626 ---
obs0.1978 110709 94.21 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 12.842 Å2
Baniso -1Baniso -2Baniso -3
1-0.63 Å2-0.28 Å20.66 Å2
2---0.25 Å20.11 Å2
3----0.6 Å2
Refinement stepCycle: LAST / Resolution: 2.01→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10564 0 39 581 11184
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.02210912
X-RAY DIFFRACTIONr_angle_refined_deg1.1551.92714915
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.63551372
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.66723.051472
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.318151508
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.1171560
X-RAY DIFFRACTIONr_chiral_restr0.0770.21599
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0218560
X-RAY DIFFRACTIONr_mcbond_it0.5321.56838
X-RAY DIFFRACTIONr_mcangle_it1210963
X-RAY DIFFRACTIONr_scbond_it1.42534074
X-RAY DIFFRACTIONr_scangle_it2.3294.53952
LS refinement shellResolution: 2.005→2.057 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.329 361 -
Rwork0.271 7421 -
obs--85.62 %

+
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://pdbjlvh1.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