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- PDB-2g13: CsoS1A with sulfate ion -

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Basic information

Entry
Database: PDB / ID: 2g13
TitleCsoS1A with sulfate ion
ComponentsMajor carboxysome shell protein 1A
KeywordsCARBOXYSOME / bacterial microcompartment domain
Function / homology
Function and homology information


structural constituent of carboxysome shell / 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
Major carboxysome shell protein CsoS1A
Similarity search - Component
Biological speciesHalothiobacillus neapolitanus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 1.61 Å
AuthorsTsai, Y. / Sawaya, M.R. / Cannon, G.C. / Williams, E.B. / Kerfeld, C.A. / Yeates, T.O.
CitationJournal: Plos Biol. / Year: 2007
Title: Structural Analysis of CsoS1A and the Protein Shell of the Halothiobacillus neapolitanus Carboxysome.
Authors: Tsai, Y. / Sawaya, M.R. / Cannon, G.C. / Cai, F. / Williams, E.B. / Heinhorst, S. / Kerfeld, C.A. / Yeates, T.O.
History
DepositionFeb 13, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 27, 2007Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Advisory / Derived calculations / 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 1.4Aug 30, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Major carboxysome shell protein 1A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)10,2624
Polymers9,9731
Non-polymers2883
Water50428
1
A: Major carboxysome shell protein 1A
hetero molecules
x 6


Theoretical massNumber of molelcules
Total (without water)61,57024
Polymers59,8416
Non-polymers1,72918
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 area14110 Å2
ΔGint-287 kcal/mol
Surface area20850 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)66.196, 66.196, 27.421
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number168
Space group name H-MP6
Components on special symmetry positions
IDModelComponents
11A-4770-

SO4

21A-4770-

SO4

31A-4771-

SO4

41A-4771-

SO4

51A-4772-

SO4

61A-4780-

HOH

71A-4798-

HOH

DetailsThe biological assembly is a hexamer generated from the monomer in the asymmetric unit by the operations: -Y,X-Y,Z; Y-X,-X,Z;-X,-Y,Z;Y,Y-X,Z;X-Y,X,Z.

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Components

#1: Protein Major carboxysome shell protein 1A


Mass: 9973.478 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Halothiobacillus neapolitanus (bacteria)
Gene: csoS1A / Plasmid: pProEx / Production host: Escherichia coli (E. coli) / Strain (production host): DH5alpha / References: UniProt: P45689
#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 28 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

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

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Sample preparation

CrystalDensity Matthews: 1.73 Å3/Da / Density % sol: 29.24 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 9.5
Details: The reservoir contained 30% PEG 400, 0.1M 2(cyclohexylamino)ethanosulfonic acid. The crystal was then move to a reservoir containing 30% PEG 400, 0.1M 2(cyclohexylamino)ethanosulfonic acid, ...Details: The reservoir contained 30% PEG 400, 0.1M 2(cyclohexylamino)ethanosulfonic acid. The crystal was then move to a reservoir containing 30% PEG 400, 0.1M 2(cyclohexylamino)ethanosulfonic acid, and 0.2M Na2SO4., pH 9.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.2.2 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Dec 7, 2005
RadiationMonochromator: Double crystal, Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.6→90 Å / Num. all: 9134 / Num. obs: 9134 / % possible obs: 99.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 14.4 % / Biso Wilson estimate: 27.7 Å2 / Rmerge(I) obs: 0.104 / Χ2: 1.188 / Net I/σ(I): 12.7
Reflection shellResolution: 1.6→1.66 Å / % possible obs: 98.5 % / Redundancy: 12.1 % / Rmerge(I) obs: 0.388 / Num. unique all: 891 / Num. unique obs: 891 / Χ2: 1.014 / % possible all: 98.5

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
REFMACrefinement
PDB_EXTRACT1.701data extraction
BOSdata collection
RefinementMethod to determine structure: FOURIER SYNTHESIS
Starting model: 2EWH

2ewh


Resolution: 1.61→57.35 Å / Cor.coef. Fo:Fc: 0.954 / Cor.coef. Fo:Fc free: 0.953 / SU B: 9.023 / SU ML: 0.128 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.127 / ESU R Free: 0.123 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.26 432 4.8 %RANDOM
Rwork0.218 ---
all0.22 9066 --
obs0.22 9066 99.03 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 15.949 Å2
Baniso -1Baniso -2Baniso -3
1--2.89 Å2-1.45 Å20 Å2
2---2.89 Å20 Å2
3---4.34 Å2
Refinement stepCycle: LAST / Resolution: 1.61→57.35 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms675 0 15 28 718
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.022699
X-RAY DIFFRACTIONr_angle_refined_deg1.6131.98952
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.665596
X-RAY DIFFRACTIONr_dihedral_angle_2_deg27.35323.07726
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.47215108
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.182157
X-RAY DIFFRACTIONr_chiral_restr0.1060.2115
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.02514
X-RAY DIFFRACTIONr_nbd_refined0.2110.2300
X-RAY DIFFRACTIONr_nbtor_refined0.2960.2472
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.0950.234
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2050.261
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1560.211
X-RAY DIFFRACTIONr_mcbond_it2.5552480
X-RAY DIFFRACTIONr_mcangle_it3.4713743
X-RAY DIFFRACTIONr_scbond_it2.8142236
X-RAY DIFFRACTIONr_scangle_it4.4483208
LS refinement shellResolution: 1.607→1.649 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.416 26 -
Rwork0.348 619 -
obs-645 97.29 %
Refinement TLS params.Method: refined / Origin x: 19.5263 Å / Origin y: 8.7852 Å / Origin z: -11.6912 Å
111213212223313233
T-0.0052 Å20.0022 Å2-0.005 Å2--0.0026 Å20.025 Å2---0.0929 Å2
L3.4456 °20.6769 °20.0211 °2-3.2528 °20.5279 °2--0.2854 °2
S0.0043 Å °-0.0593 Å °-0.0004 Å °0.033 Å °0.0253 Å °-0.1236 Å °0.0145 Å °-0.0172 Å °-0.0296 Å °
Refinement TLS groupSelection: ALL

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