[English] 日本語
Yorodumi
- PDB-3bpp: 1510-N membrane protease K138A mutant specific for a stomatin hom... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 3bpp
Title1510-N membrane protease K138A mutant specific for a stomatin homolog from Pyrococcus horikoshii
Components1510-N membrane protease
KeywordsHYDROLASE / membrane protease / specific for a stomatin homolog / archaea / Pyrococcus / thermostable / catalytic dyad
Function / homology
Function and homology information


Hydrolases; Acting on peptide bonds (peptidases); Serine endopeptidases / serine-type peptidase activity / proteolysis / membrane
Similarity search - Function
Archaeal protein PH0471, N-terminal / : / : / NfeD integral membrane domain / NfeD1b, N-terminal domain / NfeD-like, C-terminal domain / : / NfeD-like C-terminal, partner-binding domain / 2-enoyl-CoA Hydratase; Chain A, domain 1 / 2-enoyl-CoA Hydratase; Chain A, domain 1 ...Archaeal protein PH0471, N-terminal / : / : / NfeD integral membrane domain / NfeD1b, N-terminal domain / NfeD-like, C-terminal domain / : / NfeD-like C-terminal, partner-binding domain / 2-enoyl-CoA Hydratase; Chain A, domain 1 / 2-enoyl-CoA Hydratase; Chain A, domain 1 / ClpP/crotonase-like domain superfamily / Nucleic acid-binding, OB-fold / Alpha-Beta Complex / Alpha Beta
Similarity search - Domain/homology
Membrane-bound protease PH1510
Similarity search - Component
Biological speciesPyrococcus horikoshii (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
AuthorsYokoyama, H. / Hamamatsu, S. / Fujii, S. / Matsui, I.
Citation
Journal: J.SYNCHROTRON RADIAT. / Year: 2008
Title: Novel dimer structure of a membrane-bound protease with a catalytic Ser-Lys dyad and its linkage to stomatin
Authors: Yokoyama, H. / Hamamatsu, S. / Fujii, S. / Matsui, I.
#1: Journal: J.Mol.Biol. / Year: 2006
Title: Molecular structure of a novel membrane protease specific for a stomatin homolog from the hyperthermophilic archaeon Pyrococcus horikoshii
Authors: Yokoyama, H. / Matsui, E. / Akiba, T. / Harata, K. / Matsui, I.
History
DepositionDec 19, 2007Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Apr 29, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 10, 2021Group: Database references / Category: database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details
Revision 1.3Nov 1, 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: 1510-N membrane protease


Theoretical massNumber of molelcules
Total (without water)25,3681
Polymers25,3681
Non-polymers00
Water1,13563
1
A: 1510-N membrane protease

A: 1510-N membrane protease


Theoretical massNumber of molelcules
Total (without water)50,7362
Polymers50,7362
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation16_555-y+1/2,-x+1/2,-z+1/21
2
A: 1510-N membrane protease

A: 1510-N membrane protease


Theoretical massNumber of molelcules
Total (without water)50,7362
Polymers50,7362
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_555y,x,-z1
3


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)106.261, 106.261, 128.994
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number97
Space group name H-MI422

-
Components

#1: Protein 1510-N membrane protease / 441aa long hypothetical nfeD protein


Mass: 25368.025 Da / Num. of mol.: 1 / Fragment: Residues 16-236 / Mutation: K138A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pyrococcus horikoshii (archaea) / Gene: PH1510 / Plasmid: pET21b / Production host: Escherichia coli (E. coli) / References: UniProt: O59179
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 63 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 3.59 Å3/Da / Density % sol: 65.72 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 4.5
Details: 18% PEG4000, 0.1M magnesium chloride, 0.1M sodium acetate, pH 4.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-6A / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Mar 17, 2006 / Details: mirror
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.3→20 Å / Num. obs: 16792 / % possible obs: 99 % / Redundancy: 14.1 % / Biso Wilson estimate: 45.7 Å2 / Rmerge(I) obs: 0.049 / Net I/σ(I): 71.8
Reflection shellResolution: 2.3→2.38 Å / Rmerge(I) obs: 0.33 / Mean I/σ(I) obs: 11.9 / % possible all: 100

-
Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
HKL-2000data collection
HKL-2000data reduction
HKL-2000data scaling
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2DEO

2deo


Resolution: 2.3→19.51 Å / Cor.coef. Fo:Fc: 0.933 / Cor.coef. Fo:Fc free: 0.882 / SU B: 8.011 / SU ML: 0.194 / Cross valid method: THROUGHOUT / ESU R: 0.259 / ESU R Free: 0.25 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.30976 1694 10.1 %RANDOM
Rwork0.23669 ---
obs0.24374 15063 99.78 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 47.985 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.36 Å0.34 Å
Luzzati d res low-5 Å
Luzzati sigma a0.33 Å0.34 Å
Refinement stepCycle: LAST / Resolution: 2.3→19.51 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1663 0 0 63 1726
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.0221693
X-RAY DIFFRACTIONr_angle_refined_deg1.5071.9742301
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.7365215
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.64524.70668
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.60915290
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.271158
X-RAY DIFFRACTIONr_chiral_restr0.090.2270
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.021257
X-RAY DIFFRACTIONr_nbd_refined0.2210.2774
X-RAY DIFFRACTIONr_nbtor_refined0.3130.21162
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1880.299
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1890.221
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.060.23
X-RAY DIFFRACTIONr_mcbond_it6.59621114
X-RAY DIFFRACTIONr_mcangle_it8.56231747
X-RAY DIFFRACTIONr_scbond_it6.4962669
X-RAY DIFFRACTIONr_scangle_it8.2023554
LS refinement shellResolution: 2.297→2.356 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.46 139 -
Rwork0.321 1070 -
obs--99.92 %

+
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