[English] 日本語
Yorodumi
- PDB-2g0j: Crystal structure of SMU.848 from Streptococcus mutans -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 2g0j
TitleCrystal structure of SMU.848 from Streptococcus mutans
Componentshypothetical protein SMU.848
KeywordsUNKNOWN FUNCTION / 2-layer (alpha-beta)-sandwich
Function / homology
Function and homology information


cysteine-type peptidase activity / proteolysis / metal ion binding
Similarity search - Function
Cysteine protease Prp / Cysteine protease Prp / Cysteine protease Prp superfamily / Cysteine protease Prp / Alpha-Beta Plaits / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Ribosomal processing cysteine protease Prp
Similarity search - Component
Biological speciesStreptococcus mutans (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.8 Å
AuthorsHou, H.-F. / Gao, Z.-Q. / Li, L.-F. / Liang, Y.-H. / Su, X.-D. / Dong, Y.-H.
CitationJournal: To be Published
Title: Crystal structure of SMU.848 from Streptococcus mutans
Authors: Hou, H.-F. / Gao, Z.-Q. / Xu, J.-H. / Xu, R. / Li, L.-Q. / Li, L.-F. / Liang, Y.-H. / Su, X.-D. / Liu, P. / Xian, D.-C. / Dong, Y.-H.
History
DepositionFeb 13, 2006Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Aug 8, 2006Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 18, 2017Group: Refinement description / Category: software
Item: _software.classification / _software.contact_author ..._software.classification / _software.contact_author / _software.contact_author_email / _software.date / _software.language / _software.location / _software.name / _software.type / _software.version
Revision 2.0Mar 13, 2024Group: Atomic model / Data collection / Database references
Category: atom_site / chem_comp_atom ...atom_site / chem_comp_atom / chem_comp_bond / database_2 / struct_ref_seq_dif
Item: _atom_site.occupancy / _database_2.pdbx_DOI ..._atom_site.occupancy / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: hypothetical protein SMU.848
B: hypothetical protein SMU.848
C: hypothetical protein SMU.848
D: hypothetical protein SMU.848


Theoretical massNumber of molelcules
Total (without water)62,8314
Polymers62,8314
Non-polymers00
Water1,33374
1
A: hypothetical protein SMU.848
B: hypothetical protein SMU.848


Theoretical massNumber of molelcules
Total (without water)31,4162
Polymers31,4162
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1810 Å2
ΔGint-19 kcal/mol
Surface area10690 Å2
MethodPISA
2
C: hypothetical protein SMU.848
D: hypothetical protein SMU.848


Theoretical massNumber of molelcules
Total (without water)31,4162
Polymers31,4162
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1930 Å2
ΔGint-21 kcal/mol
Surface area11010 Å2
MethodPISA
3
A: hypothetical protein SMU.848
B: hypothetical protein SMU.848

A: hypothetical protein SMU.848
B: hypothetical protein SMU.848

C: hypothetical protein SMU.848
D: hypothetical protein SMU.848

C: hypothetical protein SMU.848
D: hypothetical protein SMU.848


Theoretical massNumber of molelcules
Total (without water)125,6638
Polymers125,6638
Non-polymers00
Water1448
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation5_554x-y,-y,-z-1/31
crystal symmetry operation3_454-x+y-1,-x,z-1/31
crystal symmetry operation4_455y-1,x,-z1
Buried area12170 Å2
ΔGint-111 kcal/mol
Surface area38710 Å2
MethodPISA
Unit cell
Length a, b, c (Å)78.160, 78.160, 130.157
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number152
Space group name H-MP3121

-
Components

#1: Protein
hypothetical protein SMU.848


Mass: 15707.851 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptococcus mutans (bacteria) / Plasmid: Pet28(a) / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q8DUQ5
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 74 / 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: 1.83 Å3/Da / Density % sol: 32.65 %
Crystal growTemperature: 289 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 0.1M HEPES-NaOH, PH 7.5, 28% PEG 400, 0.2M CaCl2, VAPOR DIFFUSION, HANGING DROP, temperature 289K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: BSRF / Beamline: 3W1A / Wavelength: 1 Å
DetectorType: MARRESEARCH / Detector: CCD / Date: Feb 20, 2005
RadiationMonochromator: Si(111) double-crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionRedundancy: 6 % / Av σ(I) over netI: 7 / Number: 71233 / Rmerge(I) obs: 0.11 / Χ2: 1.06 / D res high: 2.8 Å / D res low: 50 Å / Num. obs: 11810 / % possible obs: 99.7
Diffraction reflection shell

ID: 1

Highest resolution (Å)Lowest resolution (Å)Num. obs% possible obs (%)Rmerge(I) obsChi squaredRedundancy
6.0350127298.70.0440.9325.6
4.796.03121099.80.0631.1136.1
4.184.79119699.70.0591.1036.1
3.84.18118199.80.0881.0776
3.533.8116099.80.1181.1156.1
3.323.53117399.80.1541.0936.1
3.153.32116599.90.2361.0696.1
3.023.15114899.90.3381.0846.2
2.93.02115699.90.4631.0286.2
2.82.9114999.70.5991.0016
ReflectionResolution: 2.8→50 Å / Num. all: 11846 / Num. obs: 11810 / % possible obs: 99.7 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Redundancy: 6 % / Rmerge(I) obs: 0.11 / Χ2: 1.062 / Net I/σ(I): 7
Reflection shellResolution: 2.8→2.9 Å / % possible obs: 99.7 % / Redundancy: 6 % / Rmerge(I) obs: 0.599 / Num. unique obs: 1149 / Χ2: 1.001 / % possible all: 99.7

-
Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
CNSrefinement
PDB_EXTRACT1.701data extraction
MAR345data collection
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.8→50 Å / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.259 1160 9.8 %RANDOM
Rwork0.226 ---
all0.264 11229 --
obs0.24 11196 94.8 %-
Solvent computationBsol: 41.63 Å2
Displacement parametersBiso mean: 38.197 Å2
Baniso -1Baniso -2Baniso -3
1--8.102 Å2-10.422 Å20 Å2
2---8.102 Å20 Å2
3---16.203 Å2
Refinement stepCycle: LAST / Resolution: 2.8→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3466 0 0 74 3540
Xplor file
Refine-IDSerial noParam file
X-RAY DIFFRACTION1protein_rep.param
X-RAY DIFFRACTION2water_rep.param

+
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