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- PDB-7d6c: Crystal structure of CcmM N-terminal domain in complex with CcmN -

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Basic information

Entry
Database: PDB / ID: 7d6c
TitleCrystal structure of CcmM N-terminal domain in complex with CcmN
Components
  • Carbon dioxide concentrating mechanism protein CcmM
  • Carboxysome assembly protein CcmN
KeywordsSTRUCTURAL PROTEIN / CO2-concentrating mechanism / carboxysome / scaffolding protein / complex
Function / homology
Function and homology information


structural constituent of carboxysome shell / carboxysome / carbon fixation / photosynthesis
Similarity search - Function
Carboxysome assembly protein CcmM / : / : / Ribulose bisphosphate carboxylase small subunit, domain / Ribulose bisphosphate carboxylase, small subunit superfamily / Ribulose bisphosphate carboxylase, small chain / Ribulose bisphosphate carboxylase, small chain / Trimeric LpxA-like superfamily
Similarity search - Domain/homology
Carboxysome assembly protein CcmN / Carboxysome assembly protein CcmM
Similarity search - Component
Biological speciesSynechococcus elongatus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.89 Å
AuthorsSun, H. / Cui, N. / Han, S.J. / Chen, Z.P. / Xia, L.Y. / Chen, Y. / Jiang, Y.L. / Zhou, C.Z.
Funding support China, 2items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)31630001 and 31621002 China
Chinese Academy of SciencesXDB37020301 and XDA24020302 China
CitationJournal: Protein Sci. / Year: 2021
Title: Complex structure reveals CcmM and CcmN form a heterotrimeric adaptor in beta-carboxysome.
Authors: Sun, H. / Cui, N. / Han, S.J. / Chen, Z.P. / Xia, L.Y. / Chen, Y. / Jiang, Y.L. / Zhou, C.Z.
History
DepositionSep 30, 2020Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Aug 4, 2021Provider: repository / Type: Initial release
Revision 1.1Nov 29, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
1: Carbon dioxide concentrating mechanism protein CcmM
2: Carbon dioxide concentrating mechanism protein CcmM
3: Carboxysome assembly protein CcmN
4: Carboxysome assembly protein CcmN
5: Carboxysome assembly protein CcmN
F: Carboxysome assembly protein CcmN


Theoretical massNumber of molelcules
Total (without water)94,8526
Polymers94,8526
Non-polymers00
Water1,18966
1
1: Carbon dioxide concentrating mechanism protein CcmM
4: Carboxysome assembly protein CcmN
F: Carboxysome assembly protein CcmN


Theoretical massNumber of molelcules
Total (without water)47,4263
Polymers47,4263
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4090 Å2
ΔGint-33 kcal/mol
Surface area15320 Å2
MethodPISA
2
2: Carbon dioxide concentrating mechanism protein CcmM
3: Carboxysome assembly protein CcmN
5: Carboxysome assembly protein CcmN


Theoretical massNumber of molelcules
Total (without water)47,4263
Polymers47,4263
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4060 Å2
ΔGint-33 kcal/mol
Surface area15720 Å2
MethodPISA
Unit cell
Length a, b, c (Å)84.180, 92.330, 125.380
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Space group name HallP2ac2ab
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x,y+1/2,-z+1/2
#4: -x+1/2,-y,z+1/2

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Components

#1: Protein Carbon dioxide concentrating mechanism protein CcmM


Mass: 23250.262 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Synechococcus elongatus (strain PCC 7942 / FACHB-805) (bacteria)
Gene: ccmM, Synpcc7942_1423 / Production host: Escherichia coli (E. coli) / References: UniProt: Q03513
#2: Protein
Carboxysome assembly protein CcmN / Carbon dioxide concentrating mechanism protein CcmN / ORF I


Mass: 12087.866 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Synechococcus elongatus (strain PCC 7942 / FACHB-805) (bacteria)
Gene: ccmN, Synpcc7942_1424 / Production host: Escherichia coli (E. coli) / References: UniProt: P46204
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 66 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsThe protein was expressed with sequence ...The protein was expressed with sequence MGSSHHHHHHMASMSDSEVNQEAKPEVKPEVKPETHINLKVSDGSSEIFFKIKKTTPLRRLMEAFAKRQGKEMDSLRFLYDGIRIQADQTPEDLDMEDNDIIEAHREQIGGIEENLYFQSNMHLPPLEPPISDRYFASGEVTIAADVVIAPGVLLIAEADSRIEIASGVCIGLGSVIHARGGAIIIQAGALLAAGVLIVGQSIVGRQACLGASTTLVNTSIEAGGVTAPGSLLSAETPPTTATVSSSEPAGRSPQSSAIAHPTKVYGKEQFLRMRQSMFPDR. However, N terminal SUMO-tag, the tag and the C terminal of the target protein were degraded during 4-month crystallization. FQSN were linker residues between the SUMO tag and the target protein.

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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: 2.57 Å3/Da / Density % sol: 52.11 %
Crystal growTemperature: 287.15 K / Method: vapor diffusion, sitting drop / Details: PEG 8000, N-(2-acetamido) iminodiacetic acid

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.97853 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Nov 10, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97853 Å / Relative weight: 1
ReflectionResolution: 2.89→44.16 Å / Num. obs: 22669 / % possible obs: 99.9 % / Redundancy: 6.6 % / Biso Wilson estimate: 63.28 Å2 / CC1/2: 0.998 / Net I/σ(I): 12
Reflection shellResolution: 2.89→3.06 Å / Num. unique obs: 3594 / CC1/2: 0.858

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Processing

Software
NameVersionClassification
PHENIX1.18.2_3874refinement
XDSdata reduction
SCALAdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3KWC

3kwc


Resolution: 2.89→44.16 Å / SU ML: 0.3787 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 30.6777
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.272 1104 4.89 %
Rwork0.2086 21477 -
obs0.2117 22581 99.79 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 63.57 Å2
Refinement stepCycle: LAST / Resolution: 2.89→44.16 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5630 0 0 66 5696
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01055714
X-RAY DIFFRACTIONf_angle_d1.23877788
X-RAY DIFFRACTIONf_chiral_restr0.0697949
X-RAY DIFFRACTIONf_plane_restr0.00741023
X-RAY DIFFRACTIONf_dihedral_angle_d25.6572836
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.89-3.020.33181470.28392628X-RAY DIFFRACTION99.64
3.02-3.180.32211360.25012631X-RAY DIFFRACTION99.82
3.18-3.370.30181300.23562666X-RAY DIFFRACTION99.86
3.37-3.630.3261190.2292667X-RAY DIFFRACTION99.89
3.63-40.2491210.20442691X-RAY DIFFRACTION99.96
4-4.580.23761520.17712663X-RAY DIFFRACTION99.89
4.58-5.770.23511530.1882696X-RAY DIFFRACTION99.79
5.77-44.160.2911460.20632835X-RAY DIFFRACTION99.47

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