[English] 日本語
Yorodumi
- PDB-7ltd: X-ray radiation damage series on Proteinase K at 100K, crystal st... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 7ltd
TitleX-ray radiation damage series on Proteinase K at 100K, crystal structure, dataset 1
ComponentsProteinase K
KeywordsHYDROLASE / radiation damage / conformational heterogeneity / protease
Function / homology
Function and homology information


peptidase K / serine-type endopeptidase activity / proteolysis / extracellular space / metal ion binding
Similarity search - Function
Proteinase K-like catalytic domain / Peptidase S8 propeptide/proteinase inhibitor I9 / Peptidase inhibitor I9 / : / Peptidase S8 propeptide/proteinase inhibitor I9 superfamily / 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. ...Proteinase K-like catalytic domain / Peptidase S8 propeptide/proteinase inhibitor I9 / Peptidase inhibitor I9 / : / Peptidase S8 propeptide/proteinase inhibitor I9 superfamily / 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 / Peptidase S8/S53 domain / Subtilase family
Similarity search - Domain/homology
NITRATE ION / Proteinase K
Similarity search - Component
Biological speciesParengyodontium album (fungus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 0.9 Å
AuthorsYabukarski, F. / Doukov, T. / Herschlag, D.
Funding support United States, 1items
OrganizationGrant numberCountry
National Science Foundation (NSF, United States)MCB-1714723 United States
CitationJournal: Acta Crystallogr D Struct Biol / Year: 2022
Title: Evaluating the impact of X-ray damage on conformational heterogeneity in room-temperature (277 K) and cryo-cooled protein crystals.
Authors: Yabukarski, F. / Doukov, T. / Mokhtari, D.A. / Du, S. / Herschlag, D.
History
DepositionFeb 19, 2021Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 17, 2022Provider: repository / Type: Initial release
Revision 1.1Oct 18, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Proteinase K
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,3097
Polymers28,9591
Non-polymers3506
Water8,305461
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)67.721, 67.721, 101.423
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number96
Space group name H-MP43212
Space group name HallP4nw2abw
Symmetry operation#1: x,y,z
#2: -y+1/2,x+1/2,z+3/4
#3: y+1/2,-x+1/2,z+1/4
#4: x+1/2,-y+1/2,-z+1/4
#5: -x+1/2,y+1/2,-z+3/4
#6: -x,-y,z+1/2
#7: y,x,-z
#8: -y,-x,-z+1/2

-
Components

#1: Protein Proteinase K / Endopeptidase K / Tritirachium alkaline proteinase


Mass: 28958.791 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Parengyodontium album (fungus) / References: UniProt: P06873, peptidase K
#2: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca
#3: Chemical
ChemComp-NO3 / NITRATE ION


Mass: 62.005 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: NO3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 461 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN
Sequence detailsthe residue at position 207 was modeled as aspartate instead of serine because the electron density ...the residue at position 207 was modeled as aspartate instead of serine because the electron density unambiguously indicates an aspartate at this position. This is consistent with other high-resolution crystal structures with aspartate at this position

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.01 Å3/Da / Density % sol: 38.74 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: Proteinase K was dissolved in 10 mM Calcium Chloride, 50 mM Tris pH 7.5 at a final concentration of 30 mg/ml. 1-2 microliters of this protein solution was mixed with an equivalent volume of ...Details: Proteinase K was dissolved in 10 mM Calcium Chloride, 50 mM Tris pH 7.5 at a final concentration of 30 mg/ml. 1-2 microliters of this protein solution was mixed with an equivalent volume of precipitant solution (0.5 M Sodium Nitrate).

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL9-2 / Wavelength: 0.88557 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Dec 4, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.88557 Å / Relative weight: 1
ReflectionResolution: 0.9→34.82 Å / Num. obs: 173186 / % possible obs: 99.6 % / Redundancy: 6.9 % / Biso Wilson estimate: 5.85 Å2 / Rmerge(I) obs: 0.076 / Rpim(I) all: 0.029 / Net I/σ(I): 10.3
Reflection shellResolution: 0.9→0.92 Å / Redundancy: 2.2 % / Rmerge(I) obs: 0.716 / Mean I/σ(I) obs: 1 / Num. unique obs: 7909 / Rpim(I) all: 0.519 / % possible all: 93

-
Processing

Software
NameVersionClassification
PHENIX1.18.2_3874refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 7LN7

7ln7


Resolution: 0.9→33.86 Å / SU ML: 0.0917 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 17.3753
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.172 8457 4.89 %
Rwork0.1574 164573 -
obs0.1582 173030 99.56 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 9.99 Å2
Refinement stepCycle: LAST / Resolution: 0.9→33.86 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2032 0 21 461 2514
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00542586
X-RAY DIFFRACTIONf_angle_d0.89933558
X-RAY DIFFRACTIONf_chiral_restr0.0744379
X-RAY DIFFRACTIONf_plane_restr0.0059498
X-RAY DIFFRACTIONf_dihedral_angle_d12.9486939
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
0.9-0.910.3242740.33574854X-RAY DIFFRACTION89.53
0.91-0.920.33562460.29645361X-RAY DIFFRACTION98.01
0.92-0.930.27452860.26615381X-RAY DIFFRACTION99.7
0.93-0.940.26762990.24815445X-RAY DIFFRACTION99.93
0.94-0.960.25342760.24245458X-RAY DIFFRACTION99.97
0.96-0.970.24632890.23365452X-RAY DIFFRACTION99.98
0.97-0.980.2432720.23065475X-RAY DIFFRACTION99.91
0.98-10.24872750.21755430X-RAY DIFFRACTION99.93
1-1.010.22842820.21515444X-RAY DIFFRACTION100
1.01-1.030.25062810.21155474X-RAY DIFFRACTION99.98
1.03-1.050.22172710.20675449X-RAY DIFFRACTION99.97
1.05-1.070.20662870.1965458X-RAY DIFFRACTION100
1.07-1.090.20042980.19225458X-RAY DIFFRACTION99.93
1.09-1.110.19472930.18025466X-RAY DIFFRACTION100
1.11-1.130.19562920.17395447X-RAY DIFFRACTION100
1.13-1.160.1743030.16755448X-RAY DIFFRACTION100
1.16-1.190.17962790.16585497X-RAY DIFFRACTION100
1.19-1.220.16252830.15795482X-RAY DIFFRACTION99.98
1.22-1.260.18272800.15845513X-RAY DIFFRACTION100
1.26-1.30.15572590.15245513X-RAY DIFFRACTION100
1.3-1.340.16663130.15085463X-RAY DIFFRACTION100
1.34-1.40.17592630.15355534X-RAY DIFFRACTION100
1.4-1.460.17062600.14635537X-RAY DIFFRACTION99.97
1.46-1.540.15422790.13525564X-RAY DIFFRACTION100
1.54-1.640.15822830.13615525X-RAY DIFFRACTION100
1.64-1.760.152380.13985620X-RAY DIFFRACTION100
1.76-1.940.16043050.13845593X-RAY DIFFRACTION100
1.94-2.220.14483100.13065585X-RAY DIFFRACTION100
2.22-2.80.13882910.12795674X-RAY DIFFRACTION99.98
2.8-33.860.14032900.13295973X-RAY DIFFRACTION99.98

+
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