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- PDB-4ht5: CO2 concentrating mechanism protein P, CcmP form 1 -

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Basic information

Entry
Database: PDB / ID: 4ht5
TitleCO2 concentrating mechanism protein P, CcmP form 1
ComponentsCO2 concentrating mechanism protein P
KeywordsPROTEIN BINDING / BMC / carboxysome
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 / Bacterial microcompartment domain / BMC / CcmK-like superfamily / Alpha-Beta Plaits / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Carboxysome shell protein CcmP / Uncharacterized protein
Similarity search - Component
Biological speciesSynechococcus elongatus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.51 Å
AuthorsCai, F. / Sutter, M. / Kerfeld, C.A.
CitationJournal: J.Biol.Chem. / Year: 2013
Title: The structure of CcmP, a tandem bacterial microcompartment domain protein from the beta-carboxysome, forms a subcompartment within a microcompartment.
Authors: Cai, F. / Sutter, M. / Cameron, J.C. / Stanley, D.N. / Kinney, J.N. / Kerfeld, C.A.
History
DepositionOct 31, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 17, 2013Provider: repository / Type: Initial release
Revision 1.1Sep 4, 2013Group: Database references
Revision 1.2Jan 24, 2018Group: Structure summary / Category: audit_author / Item: _audit_author.name
Revision 1.3Feb 28, 2024Group: 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: CO2 concentrating mechanism protein P
B: CO2 concentrating mechanism protein P
C: CO2 concentrating mechanism protein P
D: CO2 concentrating mechanism protein P
E: CO2 concentrating mechanism protein P
F: CO2 concentrating mechanism protein P


Theoretical massNumber of molelcules
Total (without water)149,0786
Polymers149,0786
Non-polymers00
Water7,260403
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area18700 Å2
ΔGint-51 kcal/mol
Surface area39800 Å2
MethodPISA
Unit cell
Length a, b, c (Å)119.350, 137.355, 152.688
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212
Components on special symmetry positions
IDModelComponents
11A-375-

HOH

21D-359-

HOH

31F-311-

HOH

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Components

#1: Protein
CO2 concentrating mechanism protein P


Mass: 24846.258 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Synechococcus elongatus (bacteria) / Strain: ATCC 27144 / PCC 6301 / SAUG 1402/1 / Gene: syc1000_c / Plasmid: pCOLADuet-1 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q5N3D0, UniProt: Q31QW7*PLUS
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 403 / 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: 4.2 Å3/Da / Density % sol: 70.7 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 4.6
Details: 100 mM sodium acetate, 1.2 M sodium formate, and 20% PEG 400 , pH 4.6, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.1 / Wavelength: 0.9765 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Feb 5, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9765 Å / Relative weight: 1
ReflectionResolution: 2.51→97.864 Å / Num. obs: 86082 / % possible obs: 97.3 % / Redundancy: 6.3 % / Rmerge(I) obs: 0.256 / Rsym value: 0.23
Reflection shellResolution: 2.51→2.57 Å / Redundancy: 5.2 % / Rmerge(I) obs: 1.122 / Mean I/σ(I) obs: 1.411 / % possible all: 86.9

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Processing

Software
NameVersionClassification
PHENIXautoMRmodel building
PHENIX(phenix.refine: 1.8.1_1168)refinement
XDSdata reduction
SCALAdata scaling
PHENIXautoMRphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.51→39.265 Å / SU ML: 0.41 / σ(F): 0.96 / Phase error: 31.93 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2908 1273 1.5 %
Rwork0.2567 --
obs0.2572 86082 96.35 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.2 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.51→39.265 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9328 0 0 403 9731
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0059443
X-RAY DIFFRACTIONf_angle_d0.83312765
X-RAY DIFFRACTIONf_dihedral_angle_d14.1973525
X-RAY DIFFRACTIONf_chiral_restr0.0541483
X-RAY DIFFRACTIONf_plane_restr0.0031676
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.51-2.56120.42351370.3248644X-RAY DIFFRACTION90
2.5612-2.61690.28221340.29728682X-RAY DIFFRACTION91
2.6169-2.67780.31781350.28028880X-RAY DIFFRACTION92
2.6778-2.74470.36421360.29818883X-RAY DIFFRACTION93
2.7447-2.81890.28221310.29379032X-RAY DIFFRACTION94
2.8189-2.90180.35871410.28159104X-RAY DIFFRACTION95
2.9018-2.99550.34321350.27899253X-RAY DIFFRACTION96
2.9955-3.10250.29841420.2839201X-RAY DIFFRACTION96
3.1025-3.22670.32131470.27619392X-RAY DIFFRACTION97
3.2267-3.37340.35741440.25719380X-RAY DIFFRACTION98
3.3734-3.55120.29271410.25059449X-RAY DIFFRACTION98
3.5512-3.77350.24121440.23579497X-RAY DIFFRACTION99
3.7735-4.06460.23741400.22989514X-RAY DIFFRACTION99
4.0646-4.47310.2561490.23519614X-RAY DIFFRACTION100
4.4731-5.11920.24091460.22359584X-RAY DIFFRACTION100
5.1192-6.4450.31421460.25259605X-RAY DIFFRACTION100
6.445-39.270.25871520.24759584X-RAY DIFFRACTION100

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