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- PDB-3sss: CcmK1 with residues 103-113 deleted -

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Basic information

Entry
Database: PDB / ID: 3sss
TitleCcmK1 with residues 103-113 deleted
ComponentsCarbon dioxide concentrating mechanism protein
KeywordsSTRUCTURAL PROTEIN / Bacterial Microcompartment Fold / Shell forming / structural / pore forming
Function / homology
Function and homology information


structural constituent of carboxysome shell / carboxysome / carbon fixation / photosynthesis / identical protein binding
Similarity search - Function
Carboxysome shell protein CcmK / 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 ...Carboxysome shell protein CcmK / 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 CcmK1
Similarity search - Component
Biological speciesThermosynechococcus elongatus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.05 Å
AuthorsKimber, M.S. / Samborska, B.
CitationJournal: Structure / Year: 2012
Title: A CcmK2 double layer is the dominant architectural feature of the beta-carboxysomal shell facet
Authors: Samborska, B. / Kimber, M.S.
History
DepositionJul 8, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 11, 2012Provider: repository / Type: Initial release
Revision 1.1Nov 8, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 1.2Sep 13, 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

Downloads & links

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Assembly

Deposited unit
A: Carbon dioxide concentrating mechanism protein
B: Carbon dioxide concentrating mechanism protein
C: Carbon dioxide concentrating mechanism protein
D: Carbon dioxide concentrating mechanism protein
E: Carbon dioxide concentrating mechanism protein
F: Carbon dioxide concentrating mechanism protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)72,0587
Polymers72,0226
Non-polymers351
Water3,837213
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area13500 Å2
ΔGint-109 kcal/mol
Surface area23250 Å2
MethodPISA
Unit cell
Length a, b, c (Å)78.400, 78.600, 110.800
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
Carbon dioxide concentrating mechanism protein


Mass: 12003.721 Da / Num. of mol.: 6 / Fragment: unp residues 1-102
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermosynechococcus elongatus (bacteria)
Strain: BP-1 / Gene: ccmK1, tll0946 / Plasmid: pET-28a / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta / References: UniProt: Q8DKB3
#2: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 213 / 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: 2.37 Å3/Da / Density % sol: 48.1 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 5.5
Details: 25% PEG 3350, 0.2 M (NH4)2SO4,0.1M bis-Tris , pH 5.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: CLSI / Beamline: 08ID-1 / Wavelength: 0.97949 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Mar 1, 2011
Details: DCM with cryo-cooled 1st crystal sagittally bent 2nd crystal followed by vertically focusing mirror
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97949 Å / Relative weight: 1
ReflectionResolution: 2.05→50 Å / Num. all: 43990 / Num. obs: 43990 / % possible obs: 98.2 % / Observed criterion σ(F): -3 / Observed criterion σ(I): -3 / Redundancy: 7.7 % / Biso Wilson estimate: 30.99 Å2 / Rsym value: 0.087 / Net I/σ(I): 14.9
Reflection shellResolution: 2.05→2.1 Å / Mean I/σ(I) obs: 3.1 / Rsym value: 0.664 / % possible all: 83.6

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Processing

Software
NameVersionClassification
MxDCdata collection
PHASERphasing
PHENIX(phenix.refine: 1.6.4_486)refinement
XDSdata reduction
XSCALEdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: pdb entry 3SSQ

3ssq


Resolution: 2.05→45.282 Å / SU ML: 0.23 / σ(F): 2.01 / Phase error: 19.94 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2111 2149 5 %random
Rwork0.1629 ---
obs0.1653 42961 98.39 %-
all-42961 --
Solvent computationShrinkage radii: 0.89 Å / VDW probe radii: 1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 40.568 Å2 / ksol: 0.4 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-2.858 Å20 Å2-0 Å2
2--0.7015 Å20 Å2
3----3.5595 Å2
Refinement stepCycle: LAST / Resolution: 2.05→45.282 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4710 0 1 213 4924
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0194793
X-RAY DIFFRACTIONf_angle_d1.7856509
X-RAY DIFFRACTIONf_dihedral_angle_d16.0441745
X-RAY DIFFRACTIONf_chiral_restr0.11787
X-RAY DIFFRACTIONf_plane_restr0.008844
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.05-2.12330.24721870.19333541X-RAY DIFFRACTION86
2.1233-2.20830.23962130.18464054X-RAY DIFFRACTION99
2.2083-2.30880.26012170.184114X-RAY DIFFRACTION100
2.3088-2.43050.24442130.184059X-RAY DIFFRACTION100
2.4305-2.58280.24462160.17534099X-RAY DIFFRACTION100
2.5828-2.78220.22752160.17114105X-RAY DIFFRACTION100
2.7822-3.06210.21522170.18514121X-RAY DIFFRACTION100
3.0621-3.5050.2332190.17914154X-RAY DIFFRACTION100
3.505-4.41540.19582210.14084203X-RAY DIFFRACTION100
4.4154-45.29340.16882300.1444362X-RAY DIFFRACTION100
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)
10.87870.215-0.09350.7552-0.18422.6185-0.09980.0032-0.0943-0.1686-0.01060.1290.2275-0.3701-0.00010.2138-0.0712-0.03880.2866-0.03250.285-24.7876-35.065914.3147
21.41051.2313-0.95131.9736-0.57440.8131-0.18360.38880.1792-0.30.27940.2199-0.0739-0.1828-00.2321-0.0154-0.07740.30140.03210.2053-15.5711-19.28340.941
30.45280.4560.48210.89131.12831.73640.0581-0.0008-0.01-0.14180.01180.0318-0.1999-0.20780.00010.23250.04820.00440.23390.04250.226-5.7499-1.22619.486
40.83840.0881-0.59461.0791-0.69611.6160.0351-0.01520.12320.1112-0.04350.0209-0.1512-0.13610.00010.23970.0157-0.00650.1811-0.00670.2363-4.51511.830231.4777
50.73420.14440.39121.1524-0.6481.1871-0.0246-0.14480.01810.29830.09190.1565-0.1359-0.1570.00010.28430.05180.080.2477-0.00830.2346-13.8999-13.177745.722
60.47080.37880.991.22810.94412.49780.0626-0.08320.01860.0862-0.0640.23360.2151-0.4271-0.00010.2068-0.04660.0460.29720.02060.2808-23.4427-31.88536.7977
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A'
2X-RAY DIFFRACTION2chain 'B'
3X-RAY DIFFRACTION3chain 'C'
4X-RAY DIFFRACTION4chain 'D'
5X-RAY DIFFRACTION5chain 'E'
6X-RAY DIFFRACTION6chain 'F'

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