[English] 日本語
Yorodumi
- PDB-5xsv: Crystal structure of an archaeal chitinase in the ligand-free form -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 5xsv
TitleCrystal structure of an archaeal chitinase in the ligand-free form
ComponentsChitinase
KeywordsHYDROLASE / chitinase
Function / homology
Function and homology information


chitinase / chitinase activity / polysaccharide binding / carbohydrate metabolic process
Similarity search - Function
Carbohydrate-binding type-2 domain / CBM2 (Carbohydrate-binding type-2) domain profile. / CBD_II / CBM2, carbohydrate-binding domain superfamily / CBM2/CBM3, carbohydrate-binding domain superfamily
Similarity search - Domain/homology
Biological speciesThermococcus chitonophagus (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.723 Å
AuthorsNishitani, Y. / Miki, K.
Funding support Japan, 1items
OrganizationGrant numberCountry
CREST Japan
CitationJournal: Glycobiology / Year: 2018
Title: Crystal structures of an archaeal chitinase ChiD and its ligand complexes.
Authors: Nishitani, Y. / Horiuchi, A. / Aslam, M. / Kanai, T. / Atomi, H. / Miki, K.
History
DepositionJun 15, 2017Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0May 2, 2018Provider: repository / Type: Initial release
Revision 1.1Jun 13, 2018Group: Data collection / Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2Nov 20, 2019Group: Derived calculations / Category: pdbx_struct_conn_angle / struct_conn
Revision 1.3Nov 22, 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_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Chitinase
B: Chitinase
C: Chitinase
D: Chitinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)226,23426
Polymers224,6414
Non-polymers1,59422
Water00
1
A: Chitinase
C: Chitinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)113,11713
Polymers112,3202
Non-polymers79711
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3170 Å2
ΔGint-123 kcal/mol
Surface area39790 Å2
MethodPISA
2
B: Chitinase
D: Chitinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)113,11713
Polymers112,3202
Non-polymers79711
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3260 Å2
ΔGint-125 kcal/mol
Surface area39760 Å2
MethodPISA
Unit cell
Length a, b, c (Å)126.925, 104.730, 156.463
Angle α, β, γ (deg.)90.00, 113.43, 90.00
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-ID
11
21
31
41

NCS domain segments:
Dom-IDComponent-IDEns-IDSelection details
111chain 'A' and (resseq 321:805 )
211chain 'B' and (resseq 321:805 )
311chain 'C' and (resseq 321:805 )
411chain 'D' and (resseq 321:805 )

-
Components

#1: Protein
Chitinase


Mass: 56160.203 Da / Num. of mol.: 4 / Fragment: UNP RESIDUES 321-805
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermococcus chitonophagus (archaea) / Gene: chiD, CHITON_1119 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A161KIT4, chitinase
#2: Chemical
ChemComp-CO / COBALT (II) ION


Mass: 58.933 Da / Num. of mol.: 14 / Source method: obtained synthetically / Formula: Co
#3: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: SO4

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
Sample preparation

CrystalDensity Matthews: 4.25 Å3/Da / Density % sol: 71.04 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.5 / Details: MES monohydrate (pH 6.5), CoCl2, (NH4)2SO4

-
Data collection

DiffractionMean temperature: 95 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-1A / Wavelength: 1.1 Å
DetectorType: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Feb 14, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.1 Å / Relative weight: 1
ReflectionResolution: 3.7→50 Å / Num. obs: 39375 / % possible obs: 99.9 % / Redundancy: 3.3 % / Net I/σ(I): 4.8
Reflection shellResolution: 3.7→3.83 Å

-
Processing

Software
NameVersionClassification
HKL-2000data processing
MOLREPphasing
Cootmodel building
PHENIX1.9_1692refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5XSW

5xsw


Resolution: 3.723→41.803 Å / SU ML: 0.59 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 33.43
RfactorNum. reflection% reflection
Rfree0.2983 1975 5.03 %
Rwork0.2783 --
obs0.2793 39297 98.93 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 3.723→41.803 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms15884 0 54 0 15938
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00216440
X-RAY DIFFRACTIONf_angle_d0.5722452
X-RAY DIFFRACTIONf_dihedral_angle_d11.6095852
X-RAY DIFFRACTIONf_chiral_restr0.0242338
X-RAY DIFFRACTIONf_plane_restr0.0032878
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDTypeRms dev position (Å)
11A3967X-RAY DIFFRACTIONPOSITIONAL
12B3967X-RAY DIFFRACTIONPOSITIONAL0.051
13C3967X-RAY DIFFRACTIONPOSITIONAL0.126
14D3967X-RAY DIFFRACTIONPOSITIONAL0.053
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.7227-3.81570.38631280.37152350X-RAY DIFFRACTION88
3.8157-3.91880.3931350.36192674X-RAY DIFFRACTION100
3.9188-4.03410.39851470.35222679X-RAY DIFFRACTION100
4.0341-4.16420.35821160.33362658X-RAY DIFFRACTION100
4.1642-4.31280.36481260.32312682X-RAY DIFFRACTION100
4.3128-4.48530.33631430.30872699X-RAY DIFFRACTION100
4.4853-4.68920.27841450.2852662X-RAY DIFFRACTION100
4.6892-4.93610.2811700.26542660X-RAY DIFFRACTION100
4.9361-5.24480.28121410.27432701X-RAY DIFFRACTION100
5.2448-5.64880.27911400.2752668X-RAY DIFFRACTION100
5.6488-6.21570.26091470.27492688X-RAY DIFFRACTION100
6.2157-7.11130.31391380.26692720X-RAY DIFFRACTION100
7.1113-8.9450.27071480.2412718X-RAY DIFFRACTION100
8.945-41.80510.23161510.20292763X-RAY DIFFRACTION99

+
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