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- PDB-2a18: carboxysome shell protein ccmK4, crystal form 2 -

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Basic information

Entry
Database: PDB / ID: 2a18
Titlecarboxysome shell protein ccmK4, crystal form 2
ComponentsCarbon dioxide concentrating mechanism protein ccmK homolog 4
Keywordscarboxysome / cyclic hexamer / c6 point symmetry
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
AMMONIUM ION / Carboxysome shell protein CcmK4
Similarity search - Component
Biological speciesSynechocystis sp. (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.28 Å
AuthorsKerfeld, C.A. / Sawaya, M.R. / Tanaka, S. / Nguyen, C.V. / Phillips, M. / Beeby, M. / Yeates, T.O.
CitationJournal: Science / Year: 2005
Title: Protein structures forming the shell of primitive bacterial organelles
Authors: Kerfeld, C.A. / Sawaya, M.R. / Tanaka, S. / Nguyen, C.V. / Phillips, M. / Beeby, M. / Yeates, T.O.
History
DepositionJun 18, 2005Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 9, 2005Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Advisory / Derived calculations ...Advisory / Derived calculations / Source and taxonomy / Version format compliance
Revision 1.3Oct 11, 2017Group: Refinement description / Category: software
Revision 1.4Aug 23, 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_ncs_dom_lim / 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_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.end_auth_comp_id / _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: Carbon dioxide concentrating mechanism protein ccmK homolog 4
B: Carbon dioxide concentrating mechanism protein ccmK homolog 4
C: Carbon dioxide concentrating mechanism protein ccmK homolog 4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)40,4176
Polymers40,3633
Non-polymers543
Water1,44180
1
A: Carbon dioxide concentrating mechanism protein ccmK homolog 4
B: Carbon dioxide concentrating mechanism protein ccmK homolog 4
C: Carbon dioxide concentrating mechanism protein ccmK homolog 4
hetero molecules

A: Carbon dioxide concentrating mechanism protein ccmK homolog 4
B: Carbon dioxide concentrating mechanism protein ccmK homolog 4
C: Carbon dioxide concentrating mechanism protein ccmK homolog 4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)80,83412
Polymers80,7266
Non-polymers1086
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_655-x+1,-y,z1
Buried area13640 Å2
ΔGint-97 kcal/mol
Surface area23660 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)70.549, 125.040, 32.521
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Cell settingorthorhombic
Space group name H-MP21212
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
31C
12A
22B
32C
13A
23B
33C
14A
24B
34C
15A
25B
35C

NCS domain segments:

Component-ID: 1 / Refine code: 1

Dom-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11GLNGLNGLYGLYAA4 - 294 - 29
21GLNGLNGLYGLYBB4 - 294 - 29
31GLNGLNGLYGLYCC4 - 294 - 29
12ALAALAALAALAAA39 - 7239 - 72
22ALAALAALAALABB39 - 7239 - 72
32ALAALAALAALACC39 - 7239 - 72
13VALVALPROPROAA74 - 8174 - 81
23VALVALPROPROBB74 - 8174 - 81
33VALVALPROPROCC74 - 8174 - 81
14PROPROGLUGLUAA83 - 10783 - 107
24PROPROGLUGLUBB83 - 10783 - 107
34PROPROGLUGLUCC83 - 10783 - 107
15ILEILEILEILEAA31 - 3731 - 37
25ILEILEILEILEBB31 - 3731 - 37
35ILEILEILEILECC31 - 3731 - 37

NCS ensembles :
ID
1
2
3
4
5
DetailsThe biological assembly is generated by the two-fold axis: 1-x,-y,z

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Components

#1: Protein Carbon dioxide concentrating mechanism protein ccmK homolog 4 / ccmK4


Mass: 13454.331 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Synechocystis sp. (bacteria) / Strain: PCC 6803 / Gene: ccmK4 / Plasmid: pET22B / Production host: Escherichia coli (E. coli) / Strain (production host): BL21-Gold DE3 / References: UniProt: P73407
#2: Chemical ChemComp-NH4 / AMMONIUM ION


Mass: 18.038 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: H4N
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 80 / 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: 2.2 Å3/Da / Density % sol: 43.6 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 4.6
Details: 0.1M sodium citrate, pH 4.6, 30% PEG 4000, 0.2M ammonium acetate, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.2.1 / Wavelength: 0.95373 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Jun 11, 2005
RadiationMonochromator: Double Crystal Si 111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.95373 Å / Relative weight: 1
ReflectionResolution: 2.28→90 Å / Num. all: 13846 / Num. obs: 13846 / % possible obs: 99.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 13.6 % / Biso Wilson estimate: 42.5 Å2 / Rsym value: 0.113 / Net I/σ(I): 23.2
Reflection shellResolution: 2.28→2.36 Å / Redundancy: 13.9 % / Mean I/σ(I) obs: 8.7 / Num. unique all: 1346 / Rsym value: 0.373 / % possible all: 100

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Processing

Software
NameVersionClassification
Blu-Icesoftwaredata collection
SCALEPACKdata scaling
PHASERphasing
REFMAC5.2refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2A10

2a10


Resolution: 2.28→62.5 Å / Cor.coef. Fo:Fc: 0.942 / Cor.coef. Fo:Fc free: 0.936 / SU B: 13.331 / SU ML: 0.163 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.395 / ESU R Free: 0.222 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.22236 686 5 %RANDOM
Rwork0.20262 ---
all0.20364 13071 --
obs0.20364 13071 99.81 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 35.61 Å2
Baniso -1Baniso -2Baniso -3
1--1.78 Å20 Å20 Å2
2--1.3 Å20 Å2
3---0.48 Å2
Refinement stepCycle: LAST / Resolution: 2.28→62.5 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2325 0 3 80 2408
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0222367
X-RAY DIFFRACTIONr_angle_refined_deg1.0061.9583222
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.2925309
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.43723.43896
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.37415375
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.7791521
X-RAY DIFFRACTIONr_chiral_restr0.0640.2381
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.021797
X-RAY DIFFRACTIONr_nbd_refined0.190.21109
X-RAY DIFFRACTIONr_nbtor_refined0.2910.21689
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1030.2132
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1580.269
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.120.28
X-RAY DIFFRACTIONr_mcbond_it0.6351.51597
X-RAY DIFFRACTIONr_mcangle_it1.12922505
X-RAY DIFFRACTIONr_scbond_it1.1613858
X-RAY DIFFRACTIONr_scangle_it2.0194.5717
Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION

Ens-IDDom-IDAuth asym-IDNumberTypeRms dev position (Å)Weight position
11A172tight positional0.010.05
12B172tight positional0.020.05
13C172tight positional0.010.05
21A244tight positional0.010.05
22B244tight positional0.010.05
23C244tight positional0.010.05
31A67tight positional0.010.05
32B67tight positional0.010.05
33C67tight positional0.010.05
41A198tight positional0.010.05
42B198tight positional0.010.05
43C198tight positional0.010.05
51A54tight positional0.010.05
52B54tight positional0.010.05
53C54tight positional0.010.05
11A172tight thermal0.030.5
12B172tight thermal0.030.5
13C172tight thermal0.030.5
21A244tight thermal0.030.5
22B244tight thermal0.030.5
23C244tight thermal0.030.5
31A67tight thermal0.020.5
32B67tight thermal0.020.5
33C67tight thermal0.020.5
41A198tight thermal0.020.5
42B198tight thermal0.020.5
43C198tight thermal0.020.5
51A54tight thermal0.030.5
52B54tight thermal0.030.5
53C54tight thermal0.030.5
LS refinement shellResolution: 2.28→2.339 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.265 57 -
Rwork0.234 935 -
obs--100 %
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)
12.93371.4596-0.75922.85-0.98921.82710.0031-0.06240.09590.1783-0.0980.025-0.2089-0.07710.0949-0.08260.0401-0.0268-0.0507-0.0778-0.086916.484812.538615.5039
21.9296-1.39080.44114.067-0.7962.2511-0.0972-0.09-0.06380.1536-0.06730.14360.1044-0.2310.1644-0.1024-0.07260.0523-0.017-0.0837-0.060314.9823-9.983115.5258
34.3042-0.4545-0.97521.8517-0.03291.7798-0.0186-0.17830.13930.0892-0.089-0.065-0.16830.11240.1075-0.0091-0.0373-0.091-0.0944-0.0152-0.075836.765522.471715.54
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA4 - 1074 - 107
2X-RAY DIFFRACTION2BB4 - 1074 - 107
3X-RAY DIFFRACTION3CC4 - 1074 - 107

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