[English] 日本語
Yorodumi
- PDB-5wsl: Structural studies of keratinase from Meiothermus taiwanensis WR-220 -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 5wsl
TitleStructural studies of keratinase from Meiothermus taiwanensis WR-220
Componentskeratinase
KeywordsHYDROLASE / keratainase / protease
Function / homology
Function and homology information


serine-type endopeptidase activity / proteolysis / extracellular space / metal ion binding
Similarity search - Function
Proteinase K-like catalytic domain / Peptidase S8/S53 domain / Peptidase S8, subtilisin, His-active site / : / Serine proteases, subtilase family, histidine active site. / Serine proteases, subtilase family, aspartic acid active site. / Peptidase S8, subtilisin, Asp-active site / Serine proteases, subtilase family, serine active site. / Peptidase S8, subtilisin, Ser-active site / Peptidase S8, subtilisin-related ...Proteinase K-like catalytic domain / Peptidase S8/S53 domain / Peptidase S8, subtilisin, His-active site / : / Serine proteases, subtilase family, histidine active site. / Serine proteases, subtilase family, aspartic acid active site. / Peptidase S8, subtilisin, Asp-active site / Serine proteases, subtilase family, serine active site. / Peptidase S8, subtilisin, Ser-active site / Peptidase S8, subtilisin-related / Serine proteases, subtilase domain profile. / Peptidase S8/S53 domain superfamily / Subtilase family / Peptidase S8/S53 domain / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Biological speciesMeiothermus taiwanensis WR-220 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.5 Å
AuthorsHo, M.C. / Wu, S.H. / Chen, M.Y. / Tu, I.F.
CitationJournal: Sci Rep / Year: 2017
Title: The discovery of novel heat-stable keratinases from Meiothermus taiwanensis WR-220 and other extremophiles
Authors: Wu, W.L. / Chen, M.Y. / Tu, I.F. / Lin, Y.C. / EswarKumar, N. / Chen, M.Y. / Ho, M.C. / Wu, S.H.
History
DepositionDec 7, 2016Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Oct 18, 2017Provider: repository / Type: Initial release
Revision 1.1Nov 8, 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 / pdbx_struct_conn_angle / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.value / _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
Revision 1.2Oct 23, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: keratinase
B: keratinase
C: keratinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)93,50118
Polymers92,3963
Non-polymers1,10515
Water11,890660
1
A: keratinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,2637
Polymers30,7991
Non-polymers4646
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area10300 Å2
MethodPISA
2
B: keratinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,2637
Polymers30,7991
Non-polymers4646
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area170 Å2
ΔGint-13 kcal/mol
Surface area10280 Å2
MethodPISA
3
C: keratinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,9754
Polymers30,7991
Non-polymers1763
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area10290 Å2
MethodPISA
Unit cell
Length a, b, c (Å)59.210, 67.088, 92.857
Angle α, β, γ (deg.)90.000, 96.070, 90.000
Int Tables number4
Space group name H-MP1211

-
Components

#1: Protein keratinase


Mass: 30798.643 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Meiothermus taiwanensis WR-220 (bacteria)
Strain: WR-220 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A2H4A2Y5*PLUS
#2: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Ca
#3: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 660 / 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: 1.98 Å3/Da / Density % sol: 38.03 %
Crystal growTemperature: 292 K / Method: vapor diffusion, sitting drop / pH: 4.5
Details: 0.2M lithium sulfate, 0.1M sodium acetate, 50% PEG 400

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSRRC / Beamline: BL15A1 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Mar 29, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.5→30 Å / Num. obs: 115261 / % possible obs: 97.3 % / Redundancy: 3.9 % / Rsym value: 0.012 / Net I/σ(I): 10.5
Reflection shellResolution: 1.5→1.53 Å / Redundancy: 3.8 % / Mean I/σ(I) obs: 2.6 / % possible all: 95.6

-
Processing

Software
NameVersionClassification
HKL-2000data collection
REFMAC5.8.0155refinement
PDB_EXTRACT3.22data extraction
HKL-2000data reduction
HKL-2000data scaling
MOLREPphasing
HKLdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4DZT

4dzt


Resolution: 1.5→25.23 Å / Cor.coef. Fo:Fc: 0.97 / Cor.coef. Fo:Fc free: 0.96 / SU B: 1.336 / SU ML: 0.048 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.065 / ESU R Free: 0.068
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.1754 5617 5 %RANDOM
Rwork0.145 ---
obs0.1466 106459 97.16 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 75.08 Å2 / Biso mean: 12.966 Å2 / Biso min: 5.65 Å2
Baniso -1Baniso -2Baniso -3
1-0.03 Å20 Å2-0.06 Å2
2---0.01 Å20 Å2
3----0.01 Å2
Refinement stepCycle: final / Resolution: 1.5→25.23 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6021 0 51 660 6732
Biso mean--22.12 25.99 -
Num. residues----846
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0220.0196233
X-RAY DIFFRACTIONr_bond_other_d0.0030.025645
X-RAY DIFFRACTIONr_angle_refined_deg2.0441.9258531
X-RAY DIFFRACTIONr_angle_other_deg1.157312887
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.4685867
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.67623.457243
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.78915839
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.1931545
X-RAY DIFFRACTIONr_chiral_restr0.1370.21002
X-RAY DIFFRACTIONr_gen_planes_refined0.0120.027470
X-RAY DIFFRACTIONr_gen_planes_other0.0020.021503
LS refinement shellResolution: 1.502→1.541 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.202 398 -
Rwork0.198 7575 -
all-7973 -
obs--94.03 %

+
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