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

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Basic information

Entry
Database: PDB / ID: 3fch
TitleThe structure of a previously undetected carboxysome shell protein: CsoS1D from Prochlorococcus marinus MED4
ComponentsCarboxysome shell protein CsoS1D
KeywordsSTRUCTURAL PROTEIN / carboxysome shell protein
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 / MOLECULAR REPLACEMENT / Resolution: 2.201 Å
AuthorsZwart, P.H. / Klein, M.G. / 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 21, 2008Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 16, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Dec 27, 2023Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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: Carboxysome shell protein CsoS1D
B: Carboxysome shell protein CsoS1D


Theoretical massNumber of molelcules
Total (without water)61,1592
Polymers61,1592
Non-polymers00
Water77543
1
A: Carboxysome shell protein CsoS1D

A: Carboxysome shell protein CsoS1D

A: Carboxysome shell protein CsoS1D

B: Carboxysome shell protein CsoS1D

B: Carboxysome shell protein CsoS1D

B: Carboxysome shell protein CsoS1D


Theoretical massNumber of molelcules
Total (without water)183,4776
Polymers183,4776
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 operation7_444x-2/3,y-1/3,z-1/31
crystal symmetry operation8_544-y+1/3,x-y-1/3,z-1/31
crystal symmetry operation9_554-x+y+1/3,-x+2/3,z-1/31
Buried area19390 Å2
ΔGint-88 kcal/mol
Surface area38790 Å2
MethodPISA
2
A: Carboxysome shell protein CsoS1D

B: Carboxysome shell protein CsoS1D


Theoretical massNumber of molelcules
Total (without water)61,1592
Polymers61,1592
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation8_544-y+1/3,x-y-1/3,z-1/31
Buried area1990 Å2
ΔGint-12 kcal/mol
Surface area17400 Å2
MethodPISA
3
A: Carboxysome shell protein CsoS1D

A: Carboxysome shell protein CsoS1D

A: Carboxysome shell protein CsoS1D


Theoretical massNumber of molelcules
Total (without water)91,7383
Polymers91,7383
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-y,x-y,z1
crystal symmetry operation3_555-x+y,-x,z1
Buried area6380 Å2
ΔGint-26 kcal/mol
Surface area23090 Å2
MethodPISA
4
B: Carboxysome shell protein CsoS1D

B: Carboxysome shell protein CsoS1D

B: Carboxysome shell protein CsoS1D


Theoretical massNumber of molelcules
Total (without water)91,7383
Polymers91,7383
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_655-y+1,x-y,z1
crystal symmetry operation3_665-x+y+1,-x+1,z1
Buried area5500 Å2
ΔGint-22 kcal/mol
Surface area23200 Å2
MethodPISA
Unit cell
Length a, b, c (Å)117.163, 117.163, 101.464
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number146
Space group name H-MH3

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Components

#1: Protein Carboxysome shell protein CsoS1D


Mass: 30579.467 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Prochlorococcus marinus subsp. pastoris str. CCMP1986 (bacteria)
Gene: PMM0547 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 / References: UniProt: Q7V2D3
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 43 / 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: 2.19 Å3/Da / Density % sol: 43.87 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 4.2
Details: 0.7M Ammonium Phosphate, 100mM CHES (pH 9.0), VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 200 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.2.2 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Apr 9, 2008
RadiationMonochromator: Double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
Reflection twinOperator: h,-h-k,-l / Fraction: 0.452
ReflectionResolution: 2.2→45.4 Å / Num. all: 25647 / Num. obs: 25647 / Observed criterion σ(F): 2 / Observed criterion σ(I): 2

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Processing

Software
NameVersionClassification
BOSdata collection
PHASERphasing
PHENIX(phenix.refine)refinement
DENZOdata reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.201→45.377 Å / σ(F): 0.13 / Stereochemistry target values: TWIN_LSQ_F
RfactorNum. reflection% reflection
Rfree0.259 1987 7.75 %
Rwork0.2039 --
all0.2082 25647 -
obs0.2082 25647 97.31 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 43.489 Å2 / ksol: 0.386 e/Å3
Refinement stepCycle: LAST / Resolution: 2.201→45.377 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6196 0 0 43 6239
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.2006-2.26010.36231330.32031647X-RAY DIFFRACTION98
2.2601-2.32660.35341390.29431718X-RAY DIFFRACTION98
2.3266-2.40170.30551560.28791767X-RAY DIFFRACTION98
2.4017-2.48750.34671530.27261822X-RAY DIFFRACTION98
2.4875-2.58710.32551480.24681808X-RAY DIFFRACTION98
2.5871-2.70480.30411500.26011838X-RAY DIFFRACTION98
2.7048-2.84740.26551500.23791865X-RAY DIFFRACTION98
2.8474-3.02580.27271550.23011884X-RAY DIFFRACTION98
3.0258-3.25930.2741550.2271835X-RAY DIFFRACTION98
3.2593-3.58720.26821480.20511878X-RAY DIFFRACTION98
3.5872-4.1060.23441550.17081886X-RAY DIFFRACTION98
4.106-5.17190.21981550.14441873X-RAY DIFFRACTION98
5.1719-45.38650.22321570.18361872X-RAY DIFFRACTION98
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
11.3472-1.35520.41021.0629-0.08980.5433-0.2141-0.2826-0.14380.13680.2010.1730.0120.01840.0030.1987-0.0185-0.01370.1742-0.02540.159115.044611.2955-44.0409
21.6203-0.2335-0.73020.56980.90132.48120.28690.29170.18180.02180.4803-0.1828-0.0775-0.1987-0.59690.1584-0.00720.06340.13920.05280.50718.49190.3652-45.7841
32.6531.31322.54814.8354-3.74343.48680.2939-0.1337-0.15321.4456-0.5205-0.5983-0.7685-0.2940.25410.5412-0.3028-0.19930.3760.11740.265128.47634.1984-38.069
40.4172-1.4978-0.06731.60830.88531.28810.12920.04320.1503-0.2644-0.1397-0.2218-0.0646-0.24250.01470.1306-0.02130.00650.15870.04890.205541.022525.4769-38.6979
51.0848-1.3377-1.6671-0.24741.44914.34331.0237-0.0180.92920.09780.489-0.2429-0.3479-0.6429-1.16760.12120.02680.18550.24360.11540.644748.86219.2446-39.1618
64.181-0.8626-1.37171.4703-0.94270.28490.431.11130.0816-0.15090.03720.0530.0341-0.3327-0.19620.3292-0.06020.03050.5232-0.06440.213640.000111.0063-45.2723
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain A and resid 50:217
2X-RAY DIFFRACTION2chain A and resid 218:236
3X-RAY DIFFRACTION3chain A and resid 237:254
4X-RAY DIFFRACTION4chain B and resid 54:220
5X-RAY DIFFRACTION5chain B and resid 221:235
6X-RAY DIFFRACTION6chain B and resid 236:256

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