[English] 日本語
Yorodumi
- PDB-3h8y: Crystal structure of carboxysome small shell protein CsoS1C from ... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 3h8y
TitleCrystal structure of carboxysome small shell protein CsoS1C from Halothiobacillus neapolitanus
ComponentsMajor carboxysome shell protein 1C
KeywordsSTRUCTURAL PROTEIN / bacterial microcompartment domain
Function / homology
Function and homology information


carboxysome / carbon fixation
Similarity search - Function
BMC (bacterial microcompartment) domain / Bacterial microcompartments protein, conserved site / Bacterial microcompartment (BMC) domain signature. / CcmK/CsoS1, bacterial microcompartment domain / : / Bacterial microcompartment (BMC) domain profile. / BMC domain / Bacterial microcompartment domain / BMC / CcmK-like superfamily ...BMC (bacterial microcompartment) domain / Bacterial microcompartments protein, conserved site / Bacterial microcompartment (BMC) domain signature. / CcmK/CsoS1, bacterial microcompartment domain / : / Bacterial microcompartment (BMC) domain profile. / BMC domain / Bacterial microcompartment domain / BMC / CcmK-like superfamily / Alpha-Beta Plaits / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Carboxysome shell protein CsoS1C
Similarity search - Component
Biological speciesHalothiobacillus neapolitanus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.51 Å
AuthorsTsai, Y. / Sawaya, M.R. / Yeates, T.O.
CitationJournal: Acta Crystallogr.,Sect.D / Year: 2009
Title: Analysis of lattice-translocation disorder in the layered hexagonal structure of carboxysome shell protein CsoS1C
Authors: Tsai, Y. / Sawaya, M.R. / Yeates, T.O.
History
DepositionApr 29, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 1, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 1, 2017Group: Refinement description / Category: software
Revision 1.3Sep 6, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Major carboxysome shell protein 1C


Theoretical massNumber of molelcules
Total (without water)9,9301
Polymers9,9301
Non-polymers00
Water43224
1
A: Major carboxysome shell protein 1C
x 6


Theoretical massNumber of molelcules
Total (without water)59,5836
Polymers59,5836
Non-polymers00
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-y,x-y,z1
crystal symmetry operation3_555-x+y,-x,z1
crystal symmetry operation4_555-x,-y,z1
crystal symmetry operation5_555y,-x+y,z1
crystal symmetry operation6_555x-y,x,z1
Buried area11990 Å2
ΔGint-95 kcal/mol
Surface area21390 Å2
MethodPISA
Unit cell
Length a, b, c (Å)66.675, 66.675, 63.007
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number168
Space group name H-MP6
Components on special symmetry positions
IDModelComponents
11A-122-

HOH

-
Components

#1: Protein Major carboxysome shell protein 1C


Mass: 9930.453 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Halothiobacillus neapolitanus (bacteria)
Gene: csoS1C / Plasmid: pPROEx-Htb / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)-RP / References: UniProt: P45688
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 24 / 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: 4.07 Å3/Da / Density % sol: 69.79 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: 0.1M Tris HCl pH 8.5, 0.15M Sodium Citrate, 25% PEG 400, 0.01M nickel (II) chloride, vapor diffusion, hanging drop, temperature 298K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 0.9792 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Feb 25, 2008
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 2.5→90 Å / Num. all: 5538 / Num. obs: 5538 / % possible obs: 100 % / Observed criterion σ(I): -3 / Redundancy: 8.3 % / Biso Wilson estimate: 37.6 Å2 / Rmerge(I) obs: 0.186 / Χ2: 1.272 / Net I/σ(I): 13.17
Reflection shellResolution: 2.5→2.69 Å / Redundancy: 8.4 % / Rmerge(I) obs: 0.359 / Mean I/σ(I) obs: 6.94 / Num. unique all: 1103 / Χ2: 1.18 / % possible all: 100

-
Phasing

PhasingMethod: molecular replacement
Phasing MRModel details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation2.21 Å57.76 Å
Translation2.21 Å57.76 Å

-
Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
PHASER1.3.2phasing
REFMACrefinement
PDB_EXTRACT3.005data extraction
ADSCQuantumdata collection
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 2G13

2g13


Resolution: 2.51→26.24 Å / Cor.coef. Fo:Fc: 0.909 / Cor.coef. Fo:Fc free: 0.833 / WRfactor Rfree: 0.322 / WRfactor Rwork: 0.274 / Occupancy max: 1 / Occupancy min: 0.17 / FOM work R set: 0.554 / SU B: 14.163 / SU ML: 0.342 / SU R Cruickshank DPI: 0.37 / SU Rfree: 0.301 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.37 / ESU R Free: 0.3 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.311 240 4.6 %RANDOM
Rwork0.255 ---
obs0.258 5271 95.16 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso max: 79.65 Å2 / Biso mean: 35.061 Å2 / Biso min: 2 Å2
Baniso -1Baniso -2Baniso -3
1--0.04 Å2-0.02 Å20 Å2
2---0.04 Å20 Å2
3---0.06 Å2
Refinement stepCycle: LAST / Resolution: 2.51→26.24 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms675 0 0 24 699
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0190.022681
X-RAY DIFFRACTIONr_bond_other_d0.0020.02443
X-RAY DIFFRACTIONr_angle_refined_deg1.9091.965924
X-RAY DIFFRACTIONr_angle_other_deg1.54331081
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.8594
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.12222.825
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.29715107
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.178157
X-RAY DIFFRACTIONr_chiral_restr0.1260.2114
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.02779
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02132
X-RAY DIFFRACTIONr_mcbond_it3.82465
X-RAY DIFFRACTIONr_mcbond_other0.7352198
X-RAY DIFFRACTIONr_mcangle_it5.4473737
X-RAY DIFFRACTIONr_scbond_it3.7462216
X-RAY DIFFRACTIONr_scangle_it5.6353187
LS refinement shellResolution: 2.509→2.574 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.608 15 -
Rwork0.292 366 -
all-381 -
obs--92.93 %

+
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