[English] 日本語
Yorodumi
- PDB-3u2g: Crystal structure of the C-terminal DUF1608 domain of the Methano... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 3u2g
TitleCrystal structure of the C-terminal DUF1608 domain of the Methanosarcina acetivorans S-layer (MA0829) protein
ComponentsS-layer protein MA0829
KeywordsSTRUCTURAL PROTEIN / DUF1608 domain / cell envelop / surface layer / S-layer / UNKNOWN FUNCTION
Function / homology
Function and homology information


S-layer / cell wall organization / extracellular region / identical protein binding / plasma membrane
Similarity search - Function
Immunoglobulin-like - #4190 / DU1608 C-terminal domain / S-layer family duplication domain / S-layer protein / PGF-CTERM archaeal protein-sorting signal / PGF-CTERM motif / Tick-borne Encephalitis virus Glycoprotein; domain 1 / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
CITRIC ACID / AMMONIUM ION / Major S-layer protein
Similarity search - Component
Biological speciesMethanosarcina acetivorans (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.3 Å
AuthorsChan, S. / Phan, T. / Ahn, C.J. / Shin, A. / Rohlin, L. / Gunsalus, R.P. / Arbing, M.A.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2012
Title: Structure of the surface layer of the methanogenic archaean Methanosarcina acetivorans.
Authors: Arbing, M.A. / Chan, S. / Shin, A. / Phan, T. / Ahn, C.J. / Rohlin, L. / Gunsalus, R.P.
History
DepositionOct 3, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 4, 2012Provider: repository / Type: Initial release
Revision 1.1Aug 8, 2012Group: Database references

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: S-layer protein MA0829
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,7845
Polymers32,3901
Non-polymers3944
Water3,027168
1
A: S-layer protein MA0829
hetero molecules

A: S-layer protein MA0829
hetero molecules


Theoretical massNumber of molelcules
Total (without water)65,56910
Polymers64,7802
Non-polymers7898
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_665-x+1,-y+1,z1
Buried area3200 Å2
ΔGint-5 kcal/mol
Surface area24540 Å2
MethodPISA
Unit cell
Length a, b, c (Å)120.995, 120.995, 88.978
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number177
Space group name H-MP622
Detailsthe full-length natural protein consists of a tandem repeats of two DUF1608 domains of highly similar sequences

-
Components

#1: Protein S-layer protein MA0829 /


Mass: 32389.953 Da / Num. of mol.: 1 / Fragment: C-terminal DUF1608 domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Methanosarcina acetivorans (archaea) / Strain: C2A / Gene: MA0829, MA_0829 / Plasmid: pET22b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 Rosetta (DE3) / References: UniProt: Q8TSG7
#2: Chemical ChemComp-CIT / CITRIC ACID / Citric acid


Mass: 192.124 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H8O7
#3: Chemical ChemComp-NH4 / AMMONIUM ION / Ammonium


Mass: 18.038 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: H4N
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 168 / 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: 2.9 Å3/Da / Density % sol: 57.62 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.4
Details: 0.4 M ammonium citrate, 20% PEG3350, pH 7.4, VAPOR DIFFUSION, HANGING DROP, temperature 293K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 0.979028 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Feb 20, 2010
RadiationMonochromator: Si(111) double crystal monochromator (Kohzu HLD8-24 Monochromator)
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979028 Å / Relative weight: 1
ReflectionResolution: 2.3→90 Å / Num. obs: 17588 / % possible obs: 99.9 % / Redundancy: 10.4 % / Rsym value: 0.092 / Net I/σ(I): 21.1
Reflection shellResolution: 2.3→2.38 Å / Redundancy: 10.7 % / Mean I/σ(I) obs: 6.2 / Num. unique all: 1715 / Rsym value: 0.494 / % possible all: 100

-
Processing

Software
NameVersionClassificationNB
REFMAC5.5.0109refinement
PDB_EXTRACT3.1data extraction
ADSCQuantumdata collection
DENZOdata reduction
SCALEPACKdata scaling
SHELXphasing
RefinementMethod to determine structure: SAD / Resolution: 2.3→90 Å / Cor.coef. Fo:Fc: 0.944 / Cor.coef. Fo:Fc free: 0.924 / Occupancy max: 1 / Occupancy min: 0.5 / SU B: 10.602 / SU ML: 0.118 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.195 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : RESIDUAL ONLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2208 921 5.2 %RANDOM
Rwork0.178 ---
obs0.1802 17584 99.8 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso max: 69.78 Å2 / Biso mean: 27.182 Å2 / Biso min: 8.81 Å2
Baniso -1Baniso -2Baniso -3
1--1.18 Å2-0.59 Å20 Å2
2---1.18 Å20 Å2
3---1.78 Å2
Refinement stepCycle: LAST / Resolution: 2.3→90 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2162 0 26 168 2356
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0222236
X-RAY DIFFRACTIONr_bond_other_d0.0010.021398
X-RAY DIFFRACTIONr_angle_refined_deg1.2541.9553046
X-RAY DIFFRACTIONr_angle_other_deg0.77133432
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.6335275
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.43426.557122
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.65615349
X-RAY DIFFRACTIONr_dihedral_angle_4_deg10.904154
X-RAY DIFFRACTIONr_chiral_restr0.0770.2333
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.022558
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02433
X-RAY DIFFRACTIONr_mcbond_it0.6351.51358
X-RAY DIFFRACTIONr_mcbond_other0.1061.5562
X-RAY DIFFRACTIONr_mcangle_it1.28722198
X-RAY DIFFRACTIONr_scbond_it2.2643878
X-RAY DIFFRACTIONr_scangle_it3.3994.5847
LS refinement shellResolution: 2.3→2.36 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.269 78 -
Rwork0.204 1169 -
all-1247 -
obs--98.97 %
Refinement TLS params.Method: refined / Origin x: 12.7909 Å / Origin y: 45.2377 Å / Origin z: 19.8265 Å
111213212223313233
T0.0304 Å20.0254 Å2-0.0135 Å2-0.0244 Å2-0.0051 Å2--0.0541 Å2
L0.3346 °20.5451 °2-0.1844 °2-1.3346 °2-0.6096 °2--0.3984 °2
S-0.0065 Å °-0.0282 Å °-0.0122 Å °0.0607 Å °0.0271 Å °-0.0631 Å °-0.0195 Å °-0.0231 Å °-0.0205 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