[English] 日本語
Yorodumi
- PDB-3sim: Crystallographic structure analysis of family 18 Chitinase from C... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 3sim
TitleCrystallographic structure analysis of family 18 Chitinase from Crocus vernus
ComponentsProtein, Family 18 Chitinase
KeywordsHYDROLASE / Family 18 Plant Chitinase / Tim Barrel / Chitin Binding / Glycosyl Hydrolase
Function / homology
Function and homology information


hydrolase activity, hydrolyzing O-glycosyl compounds / carbohydrate metabolic process
Similarity search - Function
Chitinase-like / Glycosyl hydrolases family 18 (GH18) active site / Glycosyl hydrolases family 18 (GH18) active site signature. / 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
ACETATE ION / Protein, Family 18 Chitinase
Similarity search - Component
Biological speciesCrocus vernus (plant)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å
AuthorsAkrem, A. / Iqbal, S. / Buck, F. / Negm, A. / Perbandt, M. / Betzel, C.
CitationJournal: TO BE PUBLISHED
Title: Crystallographic structure analysis of family 18 Chitinase from Crocus vernus
Authors: Akrem, A. / Iqbal, S. / Buck, F. / Negm, A. / Perbandt, M. / Betzel, C.
History
DepositionJun 19, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 6, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Sep 13, 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 / diffrn_source / pdbx_initial_refinement_model / struct_ncs_dom_lim / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _diffrn_source.pdbx_synchrotron_site / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id / _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: Protein, Family 18 Chitinase
B: Protein, Family 18 Chitinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)60,7175
Polymers60,4732
Non-polymers2433
Water7,314406
1
A: Protein, Family 18 Chitinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,3883
Polymers30,2371
Non-polymers1512
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Protein, Family 18 Chitinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,3292
Polymers30,2371
Non-polymers921
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)172.270, 37.080, 126.370
Angle α, β, γ (deg.)90.00, 127.01, 90.00
Int Tables number5
Space group name H-MC121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B

NCS domain segments:

Component-ID: 1 / Ens-ID: 1 / Beg auth comp-ID: THR / Beg label comp-ID: THR / End auth comp-ID: SER / End label comp-ID: SER / Refine code: 5 / Auth seq-ID: 1 - 275 / Label seq-ID: 1 - 275

Dom-IDAuth asym-IDLabel asym-ID
1AA
2BB

-
Components

#1: Protein Protein, Family 18 Chitinase


Mass: 30236.637 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Crocus vernus (plant) / References: UniProt: G1K3S3*PLUS
#2: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H3O2
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 406 / 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: 2.66 Å3/Da / Density % sol: 53.84 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 9
Details: 0.1M CHES, 20 % (w/v) PEG 8000, pH 9.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: X13 / Wavelength: 0.8123 Å
DetectorType: MAR CCD 165 mm / Detector: CCD / Date: Jun 30, 2010
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.8123 Å / Relative weight: 1
ReflectionResolution: 2.1→30 Å / Num. all: 37995 / Num. obs: 34613 / % possible obs: 96.3 % / Observed criterion σ(F): 2.5 / Observed criterion σ(I): 1 / Redundancy: 3.5 % / Rmerge(I) obs: 0.012 / Rsym value: 0.012 / Net I/σ(I): 2.2
Reflection shellResolution: 2.1→2.2 Å / Rmerge(I) obs: 0.43 / Mean I/σ(I) obs: 1.4 / Rsym value: 0.43 / % possible all: 95.7

-
Processing

Software
NameVersionClassification
DNAdata collection
REFMAC5.5.0109refinement
MOSFLMdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: pdb entry 1NAR

1nar


Resolution: 2.1→30 Å / Cor.coef. Fo:Fc: 0.957 / Cor.coef. Fo:Fc free: 0.922 / SU B: 3.885 / SU ML: 0.106 / Cross valid method: THROUGHOUT / ESU R Free: 0.172 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.21347 1831 5 %RANDOM
Rwork0.15537 ---
obs0.15838 34613 95.97 %-
all-37995 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 15.881 Å2
Baniso -1Baniso -2Baniso -3
1--0.17 Å20 Å2-0.65 Å2
2---0.29 Å20 Å2
3----0.32 Å2
Refinement stepCycle: LAST / Resolution: 2.1→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4288 0 16 406 4710
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0230.0224367
X-RAY DIFFRACTIONr_angle_refined_deg1.6281.9315927
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.7285546
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.3324.603189
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.90115649
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.86159
X-RAY DIFFRACTIONr_chiral_restr0.1260.2655
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.0213350
X-RAY DIFFRACTIONr_mcbond_it0.9461.52729
X-RAY DIFFRACTIONr_mcangle_it1.62624394
X-RAY DIFFRACTIONr_scbond_it2.62731638
X-RAY DIFFRACTIONr_scangle_it3.7094.51532
Refine LS restraints NCS

Dom-ID: 1 / Auth asym-ID: A / Ens-ID: 1 / Refine-ID: X-RAY DIFFRACTION

NumberTypeRms dev position (Å)Weight position
1093MEDIUM POSITIONAL0.140.5
1008LOOSE POSITIONAL0.495
1093MEDIUM THERMAL1.642
1008LOOSE THERMAL2.2610
LS refinement shellResolution: 2.1→2.154 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.214 129 -
Rwork0.155 2522 -
obs--95.63 %

+
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