[English] 日本語
Yorodumi
- PDB-1ak9: SUBTILISIN MUTANT 8321 -

+
Open data


ID or keywords:

Loading...

no data

-
Basic information

Entry
Database: PDB / ID: 1ak9
TitleSUBTILISIN MUTANT 8321
ComponentsSUBTILISIN 8321
KeywordsSERINE PROTEASE / HYDROLASE / SPORULATION
Function / homologyPeptidase S8, subtilisin, Asp-active site / Peptidase S8/S53 domain superfamily / Serine proteases, subtilase family, serine active site. / Serine proteases, subtilase family, histidine active site. / Serine proteases, subtilase family, aspartic acid active site. / Peptidase inhibitor I9 / Subtilase family / Peptidase S8/S53 domain / Peptidase S8 propeptide/proteinase inhibitor I9 / Peptidase S8, subtilisin-related ...Peptidase S8, subtilisin, Asp-active site / Peptidase S8/S53 domain superfamily / Serine proteases, subtilase family, serine active site. / Serine proteases, subtilase family, histidine active site. / Serine proteases, subtilase family, aspartic acid active site. / Peptidase inhibitor I9 / Subtilase family / Peptidase S8/S53 domain / Peptidase S8 propeptide/proteinase inhibitor I9 / Peptidase S8, subtilisin-related / Peptidase S8, subtilisin, His-active site / Peptidase S8 propeptide/proteinase inhibitor I9 superfamily / Peptidase S8, subtilisin, Ser-active site / Subtilisin Carlsberg-like catalytic domain / subtilisin / sporulation resulting in formation of a cellular spore / fibrinolysis / proteolysis / serine-type endopeptidase activity / extracellular region / metal ion binding / Subtilisin BPN'
Function and homology information
Specimen sourceBacillus amyloliquefaciens (bacteria)
MethodX-RAY DIFFRACTION / DIFFERENCE MAP / 1.8 Å resolution
AuthorsWhitlow, M. / Howard, A.J. / Wood, J.F.
Citation
Journal: Biochemistry / Year: 1989
Title: Large increases in general stability for subtilisin BPN' through incremental changes in the free energy of unfolding.
Authors: Pantoliano, M.W. / Whitlow, M. / Wood, J.F. / Dodd, S.W. / Hardman, K.D. / Rollence, M.L. / Bryan, P.N.
#1: Journal: Biochemistry / Year: 1988
Title: The Engineering of Binding Affinity at Metal Ion Binding Sites for the Stabilization of Proteins: Subtilisin as a Test Case
Authors: Pantoliano, M.W. / Whitlow, M. / Wood, J.F. / Rollence, M.L. / Finzel, B.C. / Gilliland, G.L. / Poulos, T.L. / Bryan, P.N.
#2: Journal: Biochemistry / Year: 1987
Title: Protein Engineering of Subtilisin Bpn': Enhanced Stabilization Through the Introduction of Two Cysteines to Form a Disulfide Bond
Authors: Pantoliano, M.W. / Ladner, R.C. / Bryan, P.N. / Rollence, M.L. / Wood, J.F. / Poulos, T.L.
#3: Journal: Proteins / Year: 1986
Title: Proteases of Enhanced Stability: Characterization of a Thermostable Variant of Subtilisin
Authors: Bryan, P.N. / Rollence, M.L. / Pantoliano, M.W. / Wood, J. / Finzel, B.C. / Gilliland, G.L. / Howard, A.J. / Poulos, T.L.
#4: Journal: Biochem.Biophys.Res.Commun. / Year: 1971
Title: Atomic Coordinates for Subtilisin Bpn' (or Novo)
Authors: Alden, R.A. / Birktoft, J.J. / Kraut, J. / Robertus, J.D. / Wright, C.S.
Validation Report
SummaryFull reportAbout validation report
DateDeposition: May 30, 1997 / Release: Nov 12, 1997
RevisionDateData content typeGroupProviderType
1.0Nov 12, 1997Structure modelrepositoryInitial release
1.1Mar 3, 2008Structure modelVersion format compliance
1.2Jul 13, 2011Structure modelVersion format compliance

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: SUBTILISIN 8321
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,7636
Polyers27,5401
Non-polymers2235
Water3,567198
1


TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
γ
α
β
Length a, b, c (Å)41.640, 79.450, 37.260
Angle α, β, γ (deg.)90.00, 114.53, 90.00
Int Tables number4
Space group name H-MP 1 21 1

-
Components

#1: Protein/peptide SUBTILISIN 8321


Mass: 27539.617 Da / Num. of mol.: 1 / Mutation: T22C, M50F, S87C, G169A, Y217K, N218S / Source: (gene. exp.) Bacillus amyloliquefaciens (bacteria) / Genus: Bacillus / Plasmid name: PGX8321 / Genus (production host): Bacillus / Cellular location (production host): SECRETED / Production host: Bacillus subtilis (bacteria) / Strain (production host): GX8321 / References: UniProt: P00782, subtilisin
#2: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 2 / Formula: Ca / Calcium
#3: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Formula: Na / Sodium
#4: Chemical ChemComp-IPA / ISOPROPYL ALCOHOL / 2-PROPANOL


Mass: 60.095 Da / Num. of mol.: 2 / Formula: C3H8O / Isopropyl alcohol
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 198 / Formula: H2O / Water

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.03 / Density percent sol: 39.56 %
Crystal growMethod: vapor diffusion / pH: 9
Details: CRYSTAL WERE GROWN BY VAPOR DIFFUSION OF 10 MG/ML PROTEIN IN 50 MM GLYCINE PH 9.0 (1 MM EDTA, 25 MM CACL2 OF 50 MM KCL) AGAINST 2-PROPANOL OR ACETONE., vapor diffusion
Crystal grow
*PLUS
Method: vapor diffusion, hanging drop
Details: Bryan, P.N., (1986) Proteins: Struct.,Funct., Genet., 1, 326.
components of the solutions
*PLUS
Conc: 55 % / Common name: acetone

-
Data collection

DiffractionMean temperature: 290 kelvins
SourceSource: ROTATING ANODE / Type: ELLIOTT GX-21 / Wavelength: 1.5418
DetectorType: SIEMENS / Details: HUBER MONOCHROMATOR / Detector: AREA DETECTOR / Collection date: Apr 22, 1987
RadiationMonochromatic or laue m l: M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionD resolution high: 1.75 Å / D resolution low: 1 Å / Number obs: 17227 / Observed criterion sigma I: 2 / Rsym value: 0.0548 / NetI over sigmaI: 16.9 / Redundancy: 2.7 % / Percent possible obs: 78.6
Reflection shellHighest resolution: 1.75 Å / Lowest resolution: 1.86 Å / MeanI over sigI obs: 1.4 / Rsym value: 0.3234 / Percent possible all: 55.9

-
Processing

Software
NameClassification
XENGENdata collection
XENGENdata reduction
PROLSQ/PROFFTmodel building
PROFFTrefinement
PROLSQrefinement
XENGENdata scaling
RefineMethod to determine structure: DIFFERENCE MAP / Sigma F: 2
Least-squares processR factor R work: 0.148 / Highest resolution: 1.8 Å / Lowest resolution: 1 Å / Number reflection all: 31520 / Number reflection obs: 14232
Refine hist #LASTHighest resolution: 1.8 Å / Lowest resolution: 1 Å
Number of atoms included #LASTProtein: 1950 / Nucleic acid: 0 / Ligand: 11 / Solvent: 198 / Total: 2159
Refine LS restraints
Refine IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONp_bond_d0.0200.030
X-RAY DIFFRACTIONp_angle_d0.0300.040
X-RAY DIFFRACTIONp_angle_deg
X-RAY DIFFRACTIONp_planar_d0.0400.050
X-RAY DIFFRACTIONp_hb_or_metal_coord
X-RAY DIFFRACTIONp_mcbond_it0.6151.00
X-RAY DIFFRACTIONp_mcangle_it1.0092.00
X-RAY DIFFRACTIONp_scbond_it1.7572.00
X-RAY DIFFRACTIONp_scangle_it2.5514.00
X-RAY DIFFRACTIONp_plane_restr0.0200.030
X-RAY DIFFRACTIONp_chiral_restr0.2030.300
X-RAY DIFFRACTIONp_singtor_nbd0.1620.200
X-RAY DIFFRACTIONp_multtor_nbd0.1340.200
X-RAY DIFFRACTIONp_xhyhbond_nbd0.200
X-RAY DIFFRACTIONp_xyhbond_nbd0.1450.200
X-RAY DIFFRACTIONp_planar_tor3.57.5
X-RAY DIFFRACTIONp_staggered_tor12.410.0
X-RAY DIFFRACTIONp_orthonormal_tor
X-RAY DIFFRACTIONp_transverse_tor29.410.0
X-RAY DIFFRACTIONp_special_tor0.6
Software
*PLUS
Name: PROFFT / Classification: refinement
Least-squares process
*PLUS
R factor obs: 0.148

+
About Yorodumi

-
News

-
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. (see PDBe EMDB page)
  • 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 at PDBe / 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. See below links for details.
  • 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

+
Jun 16, 2017. Omokage search with filter

Omokage search with filter

  • Result of Omokage search can be filtered by keywords and the database types

Related info.: Omokage search

+
Sep 15, 2016. EM Navigator & Yorodumi renewed

EM Navigator & Yorodumi renewed

  • New versions of EM Navigator and Yorodumi started

Related info.: Changes in new EM Navigator and Yorodumi

+
Aug 31, 2016. New EM Navigator & Yorodumi

New EM Navigator & Yorodumi

  • In 15th Sep 2016, the development versions of EM Navigator and Yorodumi will replace the official versions.
  • Current version will continue as 'legacy version' for some time.

Related info.: Changes in new EM Navigator and Yorodumi / EM Navigator / Yorodumi

Read more

-
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.

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