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- PDB-4liw: CcmK1 Carboxysome Shell Protein from Synechocystis PCC6803, L11K ... -

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Basic information

Entry
Database: PDB / ID: 4liw
TitleCcmK1 Carboxysome Shell Protein from Synechocystis PCC6803, L11K Point Mutant
ComponentsCarbon dioxide-concentrating mechanism protein CcmK homolog 1
KeywordsTRANSPORT PROTEIN / bacterial microcompartment / carboxysome / BMC shell protein / twinning / translational NCS
Function / homology
Function and homology information


structural constituent of carboxysome shell / carboxysome / carbon fixation / photosynthesis
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 speciesSynechocystis sp. PCC 6803 substr. Kazusa (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.6 Å
AuthorsThompson, M.C. / Yeates, T.O.
CitationJournal: Acta Crystallogr.,Sect.D / Year: 2014
Title: A challenging interpretation of a hexagonally layered protein structure.
Authors: Thompson, M.C. / Yeates, T.O.
History
DepositionJul 3, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 8, 2014Provider: repository / Type: Initial release
Revision 1.1Feb 12, 2014Group: Database references
Revision 1.2Apr 4, 2018Group: Data collection / Source and taxonomy / Category: diffrn_source / entity_src_gen
Item: _diffrn_source.type / _entity_src_gen.pdbx_host_org_scientific_name / _entity_src_gen.pdbx_host_org_strain
Revision 1.3Sep 20, 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 CcmK homolog 1
B: Carbon dioxide-concentrating mechanism protein CcmK homolog 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,5773
Polymers21,4812
Non-polymers961
Water91951
1
A: Carbon dioxide-concentrating mechanism protein CcmK homolog 1
B: Carbon dioxide-concentrating mechanism protein CcmK homolog 1
hetero molecules

A: Carbon dioxide-concentrating mechanism protein CcmK homolog 1
B: Carbon dioxide-concentrating mechanism protein CcmK homolog 1
hetero molecules

A: Carbon dioxide-concentrating mechanism protein CcmK homolog 1
B: Carbon dioxide-concentrating mechanism protein CcmK homolog 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)64,7309
Polymers64,4426
Non-polymers2883
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_665-y+1,x-y+1,z1
crystal symmetry operation3_565-x+y,-x+1,z1
Buried area12070 Å2
ΔGint-109 kcal/mol
Surface area19960 Å2
MethodPISA
Unit cell
Length a, b, c (Å)70.020, 70.020, 56.250
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number173
Space group name H-MP63
DetailsTHE BIOLOGICAL UNIT IS A HEXAMER, WHICH CAN BE GENERATED BY APPLYING THE FOLLOWING SYMMETRY OPERATIONS TO THE TWO CHAINS (A AND B) IN THE ASYMMETRIC UNIT. CHAIN A: (X, Y, Z), (-X+Y, -X+1, Z), AND (-Y+1, X-Y+1, Z). CHAIN B: (X, Y, Z), (-Y-1, X-Y+1, Z), AND (-X+Y, -X+1, Z).

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Components

#1: Protein Carbon dioxide-concentrating mechanism protein CcmK homolog 1


Mass: 10740.304 Da / Num. of mol.: 2 / Mutation: L11K
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Synechocystis sp. PCC 6803 substr. Kazusa (bacteria)
Strain: PCC6803 / Gene: ccmK1, sll1029 / Plasmid: pET22b / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P72760
#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 51 / 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: 1.85 Å3/Da / Density % sol: 33.62 %
Crystal growTemperature: 298 K / pH: 9.5
Details: 0.1M N-cyclohexyl-2-aminoethanesulfonic acid, 1.26M ammonium sulfate, 0.15M sodium chloride, 0.01M guanidinium chloride, pH 9.5, vapor diffusion, hanging drop, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU FR-E+ SUPERBRIGHT / Wavelength: 1.5418
DetectorType: RIGAKU RAXIS HTC / Detector: IMAGE PLATE / Date: Nov 22, 2011
RadiationMonochromator: CONFOCAL MIRRORS VARIMAX HF / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
Reflection twinOperator: K,H,-L / Fraction: 0.6
ReflectionResolution: 1.6→41.24 Å / Num. obs: 20387 / % possible obs: 98 % / Observed criterion σ(I): -3 / Biso Wilson estimate: 25.05 Å2 / Rmerge(I) obs: 0.055 / Net I/σ(I): 34.07
Reflection shellResolution: 1.6→1.64 Å / Rmerge(I) obs: 0.244 / Mean I/σ(I) obs: 5.55 / % possible all: 84.6

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
XSCALEdata scaling
PHASER2.5.4phasing
PHENIXdev_1334refinement
PDB_EXTRACT3.11data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3DNC

3dnc


Resolution: 1.6→41.24 Å / Occupancy max: 1 / Occupancy min: 0.16 / σ(F): 1.37 / Phase error: 34.4 / Stereochemistry target values: TWIN_LSQ_F
Details: REFINEMENT WAS CARRIED OUT WITH HYDROGEN ATOMS IN THE RIDING POSITIONS FOR THE PURPOSES OF MAINTAINING GOOD GEOMETRY AND INCLUDING THEIR SCATTERING CONTRIBUTIONS IN CALCULATED STRUCTURE ...Details: REFINEMENT WAS CARRIED OUT WITH HYDROGEN ATOMS IN THE RIDING POSITIONS FOR THE PURPOSES OF MAINTAINING GOOD GEOMETRY AND INCLUDING THEIR SCATTERING CONTRIBUTIONS IN CALCULATED STRUCTURE FACTORS, BUT THEIR POSITIONS WERE NOT INDEPENDENTLY REFINED AGAINST THE X-RAY DATA. THESE H ATOMS WERE GENERATED USING PHENIX.REDUCE (WORD, J. M., ET AL. (1999). J. MOL. BIOL.) AND WERE REMOVED FROM THE MODEL PRIOR TO DEPOSITION.
RfactorNum. reflection% reflection
Rfree0.195 1034 5.07 %
Rwork0.18 --
obs0.192 20387 98 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 21.53 Å2
Refinement stepCycle: LAST / Resolution: 1.6→41.24 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1359 0 5 51 1415
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0121408
X-RAY DIFFRACTIONf_angle_d1.3151916
X-RAY DIFFRACTIONf_dihedral_angle_d16.749516
X-RAY DIFFRACTIONf_chiral_restr0.068235
X-RAY DIFFRACTIONf_plane_restr0.004247
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.6013-1.68570.28251340.28042493X-RAY DIFFRACTION85
1.6857-1.79130.28531490.282788X-RAY DIFFRACTION94
1.7913-1.92960.26051440.24972758X-RAY DIFFRACTION94
1.9296-2.12380.18161510.21282803X-RAY DIFFRACTION94
2.1238-2.43110.22341500.20112804X-RAY DIFFRACTION95
2.4311-3.06270.18981540.17772805X-RAY DIFFRACTION95
3.0627-41.25290.18011510.15052873X-RAY DIFFRACTION95
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)
12.6832-1.0445-0.46262.17350.23591.3208-0.06870.00870.05020.0934-0.03220.10050.0090.01430.08290.12330.0005-0.00410.11360.00330.0476-1.650960.05376.2345
20.37120.0298-0.0721.47290.79730.58170.0406-0.11170.08440.0488-0.15820.0811-0.0405-0.03010.09150.1137-0.02540.00160.12760.00970.10878.484462.9867.916
32.13160.73340.2380.9881-1.04541.71960.0153-0.44890.08610.2528-0.1435-0.0233-0.0368-0.0180.04790.12980.01170.030.1529-0.00730.18471.317559.046813.1891
41.7157-0.3169-0.31042.5399-0.25641.1079-0.06370.0248-0.03920.1052-0.1-0.05090.0946-0.07230.1960.0729-0.00580.00060.1256-0.0040.0871-0.483656.76868.0639
53.6991-1.722-2.13242.57161.05632.57270.0159-0.13760.3003-0.01290.11320.0651-0.34530.0227-0.09550.17280.0099-0.00440.127-0.01990.2191-0.492571.64636.5772
62.00482.892-2.62392.87831.41742.63020.15240.28290.3168-0.20160.00810.1634-0.32620.0232-0.01610.2281-0.00040.01010.13450.03130.10336.997465.1776-0.7478
72.53060.8475-0.89495.7469-0.28622.303-0.07970.02050.3445-0.1093-0.0918-0.1297-0.0562-0.03970.10380.16270.01730.01530.1770.03210.153312.336160.5357-2.7232
81.7340.13910.30710.7325-0.62170.6587-0.04680.25060.1327-0.1485-0.020.1161-0.01880.06620.05140.11820.0018-0.0140.11350.0080.0615-3.542861.31421.8974
98.02573.6095-2.55557.5099-0.6160.9692-0.1386-0.338-0.19070.5026-0.128-0.051-0.21090.13570.1590.19610.11070.09160.0994-0.06330.2914-14.850366.304514.4491
103.3835-0.84550.67532.1144-0.05780.98-0.0116-0.3528-0.0576-0.0258-0.126-0.2109-0.0001-0.02440.19250.25140.00120.04560.23160.02090.0951-9.043558.091117.8335
111.93361.17580.73682.89391.25291.5163-0.0074-0.15180.35320.0495-0.0531-0.0570.03290.02170.00690.0948-0.0103-0.00160.1293-0.01410.116117.400754.44797.7962
121.44030.5379-0.02241.99780.34371.20740.0236-0.20060.0662-0.09850.0123-0.2120.04450.117-0.04670.09680.02680.01670.14150.01260.093420.427742.77835.982
134.6227-1.3833-2.32491.2648-0.25142.23140.0603-0.22340.31090.2363-0.0042-0.3595-0.14180.131-0.04170.10890.0099-0.03310.207-0.0730.165926.914651.386513.2618
142.01910.6087-0.00181.83420.18760.936-0.0294-0.26650.01150.0543-0.09130.0160.0638-0.03220.03040.0970.0089-0.00020.11480.00150.074112.368647.7878.9645
150.97870.1717-0.29983.19121.97531.5679-0.0273-0.10050.312-0.01080.0339-0.2383-0.08820.0715-0.03560.0132-0.00240.04080.1764-0.0010.446526.820957.63427.1057
162.8727-1.32671.95725.00652.36243.76070.07250.14090.2161-0.21850.0684-0.2744-0.18340.3099-0.05360.16650.00450.06190.23180.0090.13325.490547.2169-0.046
174.4725-1.0297-0.11214.50080.07233.613-0.07970.15910.0779-0.13120.0355-0.2854-0.15430.12880.03360.17510.00560.03420.1978-0.00730.079222.122840.2906-2.7527
182.17390.2870.21333.57610.94721.06780.040.11410.55830.00380.0106-0.2863-0.00480.201-0.12490.1096-0.00290.00620.05470.0120.181915.962459.82867.187
193.5347-1.7266-2.75260.86451.5573.9464-0.0546-0.25-0.30910.14960.0830.05310.3306-0.02090.02230.4290.02360.23190.234-0.0039-0.71899.719761.515418.4095
201.39720.26-1.08533.05030.24630.90820.0064-0.2077-0.10880.1890.0631-0.3260.08520.14160.01080.72840.30850.40860.1113-0.1686-0.064210.95555.780816.3933
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(chain A and resid 2:12)
2X-RAY DIFFRACTION2(chain A and resid 13:27)
3X-RAY DIFFRACTION3(chain A and resid 28:37)
4X-RAY DIFFRACTION4(chain A and resid 38:48)
5X-RAY DIFFRACTION5(chain A and resid 49:60)
6X-RAY DIFFRACTION6(chain A and resid 61:64)
7X-RAY DIFFRACTION7(chain A and resid 65:70)
8X-RAY DIFFRACTION8(chain A and resid 71:79)
9X-RAY DIFFRACTION9(chain A and resid 80:83)
10X-RAY DIFFRACTION10(chain A and resid 84:94)
11X-RAY DIFFRACTION11(chain B and resid 3:10)
12X-RAY DIFFRACTION12(chain B and resid 11:23)
13X-RAY DIFFRACTION13(chain B and resid 24:32)
14X-RAY DIFFRACTION14(chain B and resid 33:47)
15X-RAY DIFFRACTION15(chain B and resid 48:58)
16X-RAY DIFFRACTION16(chain B and resid 59:64)
17X-RAY DIFFRACTION17(chain B and resid 65:71)
18X-RAY DIFFRACTION18(chain B and resid 72:83)
19X-RAY DIFFRACTION19(chain B and resid 84:87)
20X-RAY DIFFRACTION20(chain B and resid 88:92)

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