[English] 日本語
Yorodumi
- PDB-4toq: Crystal structure of class III chitinase from pomegranate provide... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 4toq
TitleCrystal structure of class III chitinase from pomegranate provides the insight into its metal storage capacity
ComponentsClass III chitinase
KeywordsHYDROLASE / chitinase / metal binding / a / b-barrel / pomegranate seed
Function / homology
Function and homology information


amyloplast / seedling development / seed germination / chitinase / chitinase activity / chitin catabolic process / polysaccharide catabolic process / calcium ion binding
Similarity search - Function
Glycosyl hydrolases family 18 (GH18) active site / Glycosyl hydrolases family 18 (GH18) active site signature. / Glycosyl hydrolases family 18 (GH18) domain profile. / Glycoside hydrolase family 18, catalytic domain / Glycosyl hydrolases family 18 / Glycosidases / Glycoside hydrolase superfamily / TIM Barrel / Alpha-Beta Barrel / Alpha Beta
Similarity search - Domain/homology
Acidic endochitinase Pun g 14, amyloplastic
Similarity search - Component
Biological speciesPunica granatum (pomegranate)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.6 Å
AuthorsMasuda, T. / Zhao, G. / Mikami, B.
Funding support Japan, 1items
OrganizationGrant numberCountry
Japan
CitationJournal: Biosci.Biotechnol.Biochem. / Year: 2015
Title: Crystal structure of class III chitinase from pomegranate provides the insight into its metal storage capacity.
Authors: Masuda, T. / Zhao, G. / Mikami, B.
History
DepositionJun 6, 2014Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Sep 10, 2014Provider: repository / Type: Initial release
Revision 1.1Oct 15, 2014Group: Database references
Revision 1.2Feb 4, 2015Group: Database references
Revision 1.3Nov 4, 2015Group: Data collection
Revision 1.4Jan 29, 2020Group: Data collection / Derived calculations / Category: diffrn_source / pdbx_struct_oper_list
Item: _diffrn_source.pdbx_synchrotron_site / _pdbx_struct_oper_list.symmetry_operation

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Class III chitinase
B: Class III chitinase
C: Class III chitinase
D: Class III chitinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)116,62923
Polymers116,1004
Non-polymers52919
Water22,9151272
1
A: Class III chitinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,2178
Polymers29,0251
Non-polymers1927
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Class III chitinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,1806
Polymers29,0251
Non-polymers1555
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Class III chitinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,1586
Polymers29,0251
Non-polymers1335
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: Class III chitinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,0743
Polymers29,0251
Non-polymers492
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)58.462, 79.969, 97.532
Angle α, β, γ (deg.)90.000, 102.970, 90.000
Int Tables number4
Space group name H-MP1211

-
Components

#1: Protein
Class III chitinase


Mass: 29025.045 Da / Num. of mol.: 4 / Fragment: UNP residues 27-299
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Punica granatum (pomegranate) / Gene: PSC / Production host: Escherichia coli (E. coli) / References: UniProt: G1UH28, chitinase
#2: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 13 / Source method: obtained synthetically / Formula: Mg
#3: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Cl
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1272 / 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: 1.91 Å3/Da / Density % sol: 35.72 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8.5 / Details: PEG3350, Tris-HCl, magnesium chloride

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL38B1 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jan 28, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.6→50 Å / Num. obs: 111603 / % possible obs: 96.5 % / Redundancy: 5 % / Biso Wilson estimate: 13.13 Å2 / Rmerge(I) obs: 0.072 / Χ2: 1.939 / Net I/av σ(I): 30.725 / Net I/σ(I): 12.1 / Num. measured all: 558123
Reflection shell

Diffraction-ID: 1 / Rejects: _

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2% possible all
1.6-1.664.60.412107081.7693.4
1.66-1.724.70.335108221.77593.7
1.72-1.84.70.262108831.79294.6
1.8-1.94.80.194108711.83194.5
1.9-2.024.90.136110261.85695.7
2.02-2.175.10.1112551.84497.3
2.17-2.395.20.077113481.78698.5
2.39-2.745.30.061114611.69398.9
2.74-3.455.40.046115421.85299.3
3.45-505.20.049116873.06299.4

-
Phasing

PhasingMethod: molecular replacement

-
Processing

Software
NameVersionClassification
HKL-2000data processing
MOLREPphasing
PDB_EXTRACT3.14data extraction
Cootmodel building
PHENIX(phenix.refine: 1.8.1_1168)refinement
MOLREPmodel building
HKLdata reduction
HKLdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.6→30.595 Å / FOM work R set: 0.8777 / SU ML: 0.15 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 19.54 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1917 5612 5.03 %
Rwork0.1547 105932 -
obs0.1566 111544 96.44 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 58.57 Å2 / Biso mean: 14.7 Å2 / Biso min: 4.18 Å2
Refinement stepCycle: final / Resolution: 1.6→30.595 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8159 0 19 1272 9450
Biso mean--22.24 23.38 -
Num. residues----1089
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.018741
X-RAY DIFFRACTIONf_angle_d1.14612039
X-RAY DIFFRACTIONf_chiral_restr0.0841342
X-RAY DIFFRACTIONf_plane_restr0.0051573
X-RAY DIFFRACTIONf_dihedral_angle_d12.3533093
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 30

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.5982-1.61630.2351790.19683323350292
1.6163-1.63540.28031730.19093407358094
1.6354-1.65530.22061630.18633397356093
1.6553-1.67630.23131950.17793389358493
1.6763-1.69830.22931620.17993454361694
1.6983-1.72160.23731650.17633456362193
1.7216-1.74620.22051890.17553414360395
1.7462-1.77220.22321700.17593473364393
1.7722-1.79990.23082130.17013428364196
1.7999-1.82940.23031720.1753441361394
1.8294-1.8610.23011850.16343476366196
1.861-1.89480.21161760.16283418359494
1.8948-1.93120.23691980.15973497369596
1.9312-1.97070.18651640.15513503366795
1.9707-2.01350.19462100.16323454366495
2.0135-2.06030.20782050.16073550375597
2.0603-2.11180.21261880.1513568375697
2.1118-2.16890.18961760.14693563373997
2.1689-2.23270.1862060.14633589379599
2.2327-2.30480.17451900.15643599378998
2.3048-2.38710.22292040.15643571377599
2.3871-2.48260.19161810.16253672385399
2.4826-2.59560.22021970.16663594379199
2.5956-2.73230.20981920.17513627381999
2.7323-2.90340.20051810.17293655383699
2.9034-3.12740.20491850.163655384099
3.1274-3.44170.15842090.13983652386199
3.4417-3.93890.13662000.125636673867100
3.9389-4.95910.1431870.120636903877100
4.9591-30.60080.17511970.15083750394799

+
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