[English] 日本語
Yorodumi
- PDB-3ebv: Crystal structure of putative Chitinase A from Streptomyces coeli... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 3ebv
TitleCrystal structure of putative Chitinase A from Streptomyces coelicolor.
ComponentsChinitase A
Keywordsstructural genomics / unknown function / Chitinase A / ChiA / Glycosidase / Hydrolase / PSI-2 / Protein Structure Initiative / New York SGX Research Center for Structural Genomics / NYSGXRC
Function / homology
Function and homology information


chitinase / chitin binding / polysaccharide catabolic process / hydrolase activity, hydrolyzing O-glycosyl compounds
Similarity search - Function
: / Carbohydrate-binding, CenC-like / Carbohydrate binding domain / Glycosyl hydrolases family 18 (GH18) active site / Glycosyl hydrolases family 18 (GH18) active site signature. / Chitinase II / Glyco_18 / Glycosyl hydrolases family 18 (GH18) domain profile. / Glycosyl hydrolases family 18 / Glycoside hydrolase family 18, catalytic domain ...: / Carbohydrate-binding, CenC-like / Carbohydrate binding domain / Glycosyl hydrolases family 18 (GH18) active site / Glycosyl hydrolases family 18 (GH18) active site signature. / Chitinase II / Glyco_18 / Glycosyl hydrolases family 18 (GH18) domain profile. / Glycosyl hydrolases family 18 / Glycoside hydrolase family 18, catalytic domain / Fibronectin type III domain / Fibronectin type 3 domain / Fibronectin type-III domain profile. / Galactose-binding-like domain superfamily / Fibronectin type III / Fibronectin type III superfamily / Glycosidases / Glycoside hydrolase superfamily / TIM Barrel / Alpha-Beta Barrel / Immunoglobulin-like fold / Alpha Beta
Similarity search - Domain/homology
chitinase / chitinase
Similarity search - Component
Biological speciesStreptomyces coelicolor (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 1.5 Å
AuthorsVigdorovich, V. / Ramagopal, U.A. / Toro, R. / Burley, S.K. / Almo, S.C. / New York SGX Research Center for Structural Genomics (NYSGXRC)
CitationJournal: To be Published
Title: Crystal structure of putative Chitinase A from Streptomyces coelicolor
Authors: Vigdorovich, V. / Ramagopal, U.A. / Toro, R. / Burley, S.K. / Almo, S.C.
History
DepositionAug 28, 2008Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 30, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Oct 25, 2017Group: Refinement description / Category: software
Revision 1.3Feb 10, 2021Group: Database references / Derived calculations / Structure summary
Category: audit_author / citation_author ...audit_author / citation_author / struct_conn / struct_site
Item: _audit_author.identifier_ORCID / _citation_author.identifier_ORCID ..._audit_author.identifier_ORCID / _citation_author.identifier_ORCID / _struct_conn.pdbx_leaving_atom_flag / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Nov 20, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Chinitase A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,1892
Polymers32,0921
Non-polymers961
Water5,386299
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)96.636, 96.636, 124.735
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number146
Space group name H-MH3
Components on special symmetry positions
IDModelComponents
11A-432-

HOH

21A-434-

HOH

31A-598-

HOH

Detailsbiological unit appears to be same as asymmetric unit.

-
Components

#1: Protein Chinitase A


Mass: 32092.445 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptomyces coelicolor (bacteria) / Gene: SCO5003, SCK15.05c / Plasmid: BC-pSGX4(BC) / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q9KY99, UniProt: Q9Z9M9*PLUS
#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 299 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 3.49 Å3/Da / Density % sol: 64.78 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 10.5
Details: 0.1 M CAPS pH 10.5, 2.0 M Ammonium sulfate, 0.2 M Lithium sulfate, Vapor diffusion, Sitting drop, temperature 298K, VAPOR DIFFUSION, SITTING DROP

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X29A / Wavelength: 0.979 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Jul 10, 2008
RadiationProtocol: SINGLE WAVELENGTH / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionRedundancy: 3.1 % / Av σ(I) over netI: 15.26 / Number: 435716 / Rmerge(I) obs: 0.054 / Χ2: 1.03 / D res high: 1.5 Å / D res low: 50 Å / Num. obs: 140060 / % possible obs: 99.8
Diffraction reflection shell
Highest resolution (Å)Lowest resolution (Å)% possible obs (%)IDRmerge(I) obsChi squaredRedundancy
3.235099.410.0331.0313.1
2.563.2310010.0521.0493.2
2.242.5610010.0570.993.2
2.042.2410010.0651.0133.2
1.892.0410010.081.0523.2
1.781.8910010.1070.9653.1
1.691.7810010.151.0563.1
1.621.6910010.2011.1063.1
1.551.6210010.2771.0623.1
1.51.5598.810.3891.022.9
ReflectionResolution: 1.5→50 Å / Num. all: 70137 / Num. obs: 70137 / % possible obs: 99.8 % / Redundancy: 6.2 % / Biso Wilson estimate: 16.5 Å2 / Rmerge(I) obs: 0.088 / Rsym value: 0.071 / Χ2: 1.034 / Net I/σ(I): 22.1
Reflection shellResolution: 1.5→1.55 Å / Redundancy: 5.8 % / Rmerge(I) obs: 0.454 / Mean I/σ(I) obs: 4.1 / Num. unique all: 13903 / Rsym value: 0.404 / Χ2: 1.02 / % possible all: 99.9

-
Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
REFMACrefinement
PDB_EXTRACT3.006data extraction
CBASSdata collection
HKL-2000data reduction
SHELXDphasing
SHELXEmodel building
CCP4phasing
RefinementResolution: 1.5→28.21 Å / Cor.coef. Fo:Fc: 0.971 / Cor.coef. Fo:Fc free: 0.967 / WRfactor Rfree: 0.186 / WRfactor Rwork: 0.172 / Occupancy max: 1 / Occupancy min: 0.3 / FOM work R set: 0.918 / SU B: 0.769 / SU ML: 0.03 / SU R Cruickshank DPI: 0.05 / SU Rfree: 0.05 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.05 / ESU R Free: 0.05 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.169 3535 5 %RANDOM
Rwork0.156 ---
obs0.157 70126 99.82 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso max: 47.55 Å2 / Biso mean: 16.785 Å2 / Biso min: 7.6 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refinement stepCycle: LAST / Resolution: 1.5→28.21 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2171 0 5 299 2475
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.0222224
X-RAY DIFFRACTIONr_angle_refined_deg1.4631.9443039
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.5625304
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.16225.29485
X-RAY DIFFRACTIONr_dihedral_angle_3_deg10.32715341
X-RAY DIFFRACTIONr_dihedral_angle_4_deg11.632156
X-RAY DIFFRACTIONr_chiral_restr0.1030.2351
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.021683
X-RAY DIFFRACTIONr_nbd_refined0.2080.21070
X-RAY DIFFRACTIONr_nbtor_refined0.3080.21582
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1180.2189
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2050.223
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1370.218
X-RAY DIFFRACTIONr_mcbond_it1.0321.51489
X-RAY DIFFRACTIONr_mcangle_it1.51522338
X-RAY DIFFRACTIONr_scbond_it2.3143841
X-RAY DIFFRACTIONr_scangle_it3.5374.5695
LS refinement shellResolution: 1.495→1.534 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.275 252 -
Rwork0.24 4829 -
all-5081 -
obs--97.92 %

+
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