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- PDB-3f56: The structure of a previously undetected carboxysome shell protei... -

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Basic information

Entry
Database: PDB / ID: 3f56
TitleThe structure of a previously undetected carboxysome shell protein: CsoS1D from Prochlorococcus marinus MED4
ComponentsCsoS1D
KeywordsSTRUCTURAL PROTEIN / Carboxysome / Hexamer
Function / homology
Function and homology information


structural constituent of carboxysome shell / carboxysome / carbon fixation / photosynthesis
Similarity search - Function
Bacterial microcompartment (BMC) circularly permuted domain / Bacterial microcompartment (BMC) circularly permuted domain profile. / BMC (bacterial microcompartment) domain / BMC domain / Bacterial microcompartment domain / CcmK-like superfamily / BMC / Alpha-Beta Plaits / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Carboxysome shell protein CsoS1D
Similarity search - Component
Biological speciesProchlorococcus marinus subsp. pastoris str. CCMP1986 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.303 Å
AuthorsKlein, M.G. / Zwart, P. / Kerfeld, C.A.
CitationJournal: J.Mol.Biol. / Year: 2009
Title: Identification and structural analysis of a novel carboxysome shell protein with implications for metabolite transport.
Authors: Klein, M.G. / Zwart, P. / Bagby, S.C. / Cai, F. / Chisholm, S.W. / Heinhorst, S. / Cannon, G.C. / Kerfeld, C.A.
History
DepositionNov 3, 2008Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 16, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Oct 25, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 1.3Dec 27, 2023Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_conn / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: CsoS1D
B: CsoS1D
C: CsoS1D
D: CsoS1D
E: CsoS1D
F: CsoS1D


Theoretical massNumber of molelcules
Total (without water)186,0096
Polymers186,0096
Non-polymers00
Water12,286682
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area19380 Å2
ΔGint-93 kcal/mol
Surface area38790 Å2
MethodPISA
Unit cell
Length a, b, c (Å)122.410, 131.286, 131.762
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein
CsoS1D / Carboxysome Shell Protein


Mass: 31001.518 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Prochlorococcus marinus subsp. pastoris str. CCMP1986 (bacteria)
Strain: MED4 / Gene: PMM0547 / Plasmid: pProEX_HTb / Production host: Escherichia coli (E. coli) / Strain (production host): B834 / References: UniProt: Q7V2D3
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 682 / 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: 2.85 Å3/Da / Density % sol: 56.78 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6.2
Details: 12% Tacsimate, pH 6.2, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.2.2 / Wavelength: 0.97680, 0.97960
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Apr 9, 2008
RadiationMonochromator: Double crystal, Si(111) / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.97681
20.97961
ReflectionResolution: 2.3→50 Å / Num. obs: 177663 / Redundancy: 4.4 % / Biso Wilson estimate: 29.15 Å2 / Rmerge(I) obs: 0.088 / Net I/σ(I): 16.7
Reflection shellResolution: 2.3→2.38 Å / Redundancy: 4.4 % / Rmerge(I) obs: 0.498 / Mean I/σ(I) obs: 2.9 / % possible all: 99.9

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Processing

Software
NameVersionClassification
BOSdata collection
PHENIXmodel building
SHARPphasing
PHENIX(phenix.refine)refinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing
RefinementMethod to determine structure: MAD / Resolution: 2.303→46.501 Å / Occupancy max: 1 / Occupancy min: 1 / SU ML: 0.3 / σ(F): 1.89 / Phase error: 21.66 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2167 8907 5.01 %
Rwork0.188 --
obs0.1895 93264 97.92 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 46.394 Å2 / ksol: 0.34 e/Å3
Displacement parametersBiso mean: 31.117 Å2
Baniso -1Baniso -2Baniso -3
1-8.196 Å2-0 Å2-0 Å2
2---4.402 Å20 Å2
3----3.794 Å2
Refine analyzeLuzzati sigma a obs: 0.29 Å
Refinement stepCycle: LAST / Resolution: 2.303→46.501 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9269 0 0 682 9951
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0099412
X-RAY DIFFRACTIONf_angle_d1.21712757
X-RAY DIFFRACTIONf_dihedral_angle_d16.7423402
X-RAY DIFFRACTIONf_chiral_restr0.0761510
X-RAY DIFFRACTIONf_plane_restr0.0051639
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.3032-2.32940.28422330.25194740X-RAY DIFFRACTION83
2.3294-2.35680.32472970.25325740X-RAY DIFFRACTION100
2.3568-2.38560.27553180.24285647X-RAY DIFFRACTION99
2.3856-2.41580.28382960.23675791X-RAY DIFFRACTION100
2.4158-2.44750.27183470.24225685X-RAY DIFFRACTION99
2.4475-2.48110.24382910.2265696X-RAY DIFFRACTION99
2.4811-2.51650.25922840.22125724X-RAY DIFFRACTION100
2.5165-2.55410.2752920.22645725X-RAY DIFFRACTION99
2.5541-2.5940.27862970.22995715X-RAY DIFFRACTION99
2.594-2.63650.27792500.22375703X-RAY DIFFRACTION99
2.6365-2.6820.24293040.21115752X-RAY DIFFRACTION99
2.682-2.73070.26382700.21875686X-RAY DIFFRACTION99
2.7307-2.78320.25543200.21145705X-RAY DIFFRACTION99
2.7832-2.840.26113170.20785611X-RAY DIFFRACTION99
2.84-2.90180.23492550.19425775X-RAY DIFFRACTION99
2.9018-2.96930.21273300.18815583X-RAY DIFFRACTION99
2.9693-3.04350.21373220.19565664X-RAY DIFFRACTION98
3.0435-3.12580.21883140.19545604X-RAY DIFFRACTION98
3.1258-3.21770.2343070.19765675X-RAY DIFFRACTION98
3.2177-3.32160.19912860.18365679X-RAY DIFFRACTION98
3.3216-3.44030.20023080.17375594X-RAY DIFFRACTION98
3.4403-3.57790.1983180.17015644X-RAY DIFFRACTION98
3.5779-3.74070.20242930.16485589X-RAY DIFFRACTION98
3.7407-3.93780.17622950.15775603X-RAY DIFFRACTION98
3.9378-4.18440.1792620.15395638X-RAY DIFFRACTION98
4.1844-4.50730.17332770.14825651X-RAY DIFFRACTION98
4.5073-4.96040.1583000.14025605X-RAY DIFFRACTION98
4.9604-5.67710.17563410.16215493X-RAY DIFFRACTION97
5.6771-7.14830.19742760.17575494X-RAY DIFFRACTION95
7.1483-46.510.1963070.1795545X-RAY DIFFRACTION97

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