[English] 日本語
Yorodumi
- PDB-1snp: PROTEIN STABILITY IN STAPHYLOCOCCAL NUCLEASE -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1snp
TitlePROTEIN STABILITY IN STAPHYLOCOCCAL NUCLEASE
ComponentsSTAPHYLOCOCCAL NUCLEASE
KeywordsHYDROLASE / NUCLEASE / ENDONUCLEASE / CALCIUM
Function / homology
Function and homology information


micrococcal nuclease / : / nucleic acid binding / extracellular region / metal ion binding / membrane
Similarity search - Function
OB fold (Dihydrolipoamide Acetyltransferase, E2P) - #90 / Thermonuclease family signature 1. / Thermonuclease active site / Thermonuclease family signature 2. / Staphylococcal nuclease (SNase-like), OB-fold / Staphylococcal nuclease homologue / Thermonuclease domain profile. / Staphylococcal nuclease homologues / SNase-like, OB-fold superfamily / OB fold (Dihydrolipoamide Acetyltransferase, E2P) ...OB fold (Dihydrolipoamide Acetyltransferase, E2P) - #90 / Thermonuclease family signature 1. / Thermonuclease active site / Thermonuclease family signature 2. / Staphylococcal nuclease (SNase-like), OB-fold / Staphylococcal nuclease homologue / Thermonuclease domain profile. / Staphylococcal nuclease homologues / SNase-like, OB-fold superfamily / OB fold (Dihydrolipoamide Acetyltransferase, E2P) / Beta Barrel / Mainly Beta
Similarity search - Domain/homology
Biological speciesStaphylococcus aureus (bacteria)
MethodX-RAY DIFFRACTION / Resolution: 1.95 Å
AuthorsTruckses, D.M. / Somoza, J.R. / Markley, J.L.
Citation
Journal: Protein Sci. / Year: 1996
Title: Coupling between trans/cis proline isomerization and protein stability in staphylococcal nuclease.
Authors: Truckses, D.M. / Somoza, J.R. / Prehoda, K.E. / Miller, S.C. / Markley, J.L.
#1: Journal: Biochemistry / Year: 1994
Title: Engineering Alternative Beta-Turn Types in Staphylococcal Nuclease
Authors: Hynes, T.R. / Hodel, A. / Fox, R.O.
#2: Journal: Proteins / Year: 1991
Title: The Crystal Structure of Staphylococcal Nuclease Refined at 1.7 A Resolution
Authors: Hynes, T.R. / Fox, R.O.
#3: Journal: Biochemistry / Year: 1990
Title: Coupling between Local Structure and Global Stability of a Protein: Mutants of Staphylococcal Nuclease
Authors: Alexandrescu, A.T. / Hinck, A.P. / Markley, J.L.
History
DepositionJul 6, 1996Processing site: BNL
Revision 1.0Feb 12, 1997Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Nov 3, 2021Group: Database references / Other
Category: database_2 / pdbx_database_status / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.process_site / _struct_ref_seq_dif.details
Revision 1.4Feb 14, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: STAPHYLOCOCCAL NUCLEASE


Theoretical massNumber of molelcules
Total (without water)16,7781
Polymers16,7781
Non-polymers00
Water57632
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)49.010, 49.010, 63.660
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number76
Space group name H-MP41

-
Components

#1: Protein STAPHYLOCOCCAL NUCLEASE / MICROCOCCAL NUCLEASE


Mass: 16778.277 Da / Num. of mol.: 1 / Mutation: P117G
Source method: isolated from a genetically manipulated source
Details: THIS STAPH NUCLEASE IS FROM THE V8 STRAIN, THEREFORE RESIDUE 124 IS LEU, NOT HIS AS IN THE FOGGI STRAIN
Source: (gene. exp.) Staphylococcus aureus (bacteria) / Strain: V8 / Description: PET SYSTEM / Gene: NUC / Plasmid: PET3A / Gene (production host): NUC / Production host: Escherichia coli (E. coli) / Strain (production host): PET / References: UniProt: P00644, micrococcal nuclease
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 32 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION

-
Sample preparation

CrystalDensity Matthews: 2.28 Å3/Da / Density % sol: 46 %
Crystal growpH: 8.15
Details: 10.5 MM POTASSIUM PHOSPHATE, 20% - 30% 2-METHYL-2,4-PENTANEDIOL, pH 8.15
Crystal grow
*PLUS
Temperature: 4 ℃ / Method: vapor diffusion
Details: Loll, P.J., (1989) Proteins: Struct.,Funct., Genet., 5, 183.
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
120 mg/mlprotein1drop
210.5 mMpotassium phosphate1drop
317 %(w/w)MPD1drop
410 mM1dropCaCl2
520 mMpotassium citrate1drop
610.5 mMpotassium phosphate1reservoir
720-30 %(w/w)MPD1reservoir

-
Data collection

DiffractionMean temperature: 277 K
Diffraction sourceWavelength: 1.5418
DetectorType: RIGAKU / Detector: IMAGE PLATE / Date: Feb 1, 1993
RadiationMonochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionNum. obs: 11126 / % possible obs: 98.9 % / Observed criterion σ(I): 0 / Rmerge(I) obs: 0.062
Reflection
*PLUS
Highest resolution: 1.95 Å / Lowest resolution: 9999 Å / Num. measured all: 36225 / Rmerge(I) obs: 0.062
Reflection shell
*PLUS
Highest resolution: 1.95 Å / Lowest resolution: 2 Å / % possible obs: 97.1 %

-
Processing

Software
NameClassification
X-PLORmodel building
X-PLORrefinement
R-AXISdata reduction
X-PLORphasing
RefinementResolution: 1.95→6 Å / σ(F): 2
RfactorNum. reflection
Rfree0.255 -
Rwork0.184 -
obs0.184 11126
Displacement parametersBiso mean: 34.6 Å2
Refinement stepCycle: LAST / Resolution: 1.95→6 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1039 0 0 32 1071
Software
*PLUS
Name: X-PLOR / Classification: refinement
Refinement
*PLUS
Num. reflection all: 11126 / Num. reflection obs: 10171
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.01
X-RAY DIFFRACTIONx_angle_deg1.632
X-RAY DIFFRACTIONx_dihedral_angle_deg22.73
X-RAY DIFFRACTIONx_improper_angle_deg1.218
LS refinement shell
*PLUS
Highest resolution: 1.95 Å / Lowest resolution: 2 Å

+
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