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- PDB-4ht7: CO2 concentrating mechanism protein P, CcmP form 2 -

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Basic information

Entry
Database: PDB / ID: 4ht7
TitleCO2 concentrating mechanism protein P, CcmP form 2
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: 3.301 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
G: CO2 concentrating mechanism protein P
H: CO2 concentrating mechanism protein P
I: CO2 concentrating mechanism protein P
D: CO2 concentrating mechanism protein P
E: CO2 concentrating mechanism protein P
F: CO2 concentrating mechanism protein P
J: CO2 concentrating mechanism protein P
K: CO2 concentrating mechanism protein P
L: CO2 concentrating mechanism protein P


Theoretical massNumber of molelcules
Total (without water)298,15512
Polymers298,15512
Non-polymers00
Water34219
1
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
Water905
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area18900 Å2
ΔGint-50 kcal/mol
Surface area40440 Å2
MethodPISA
2
G: CO2 concentrating mechanism protein P
H: CO2 concentrating mechanism protein P
I: CO2 concentrating mechanism protein P
J: CO2 concentrating mechanism protein P
K: CO2 concentrating mechanism protein P
L: CO2 concentrating mechanism protein P


Theoretical massNumber of molelcules
Total (without water)149,0786
Polymers149,0786
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area18950 Å2
ΔGint-49 kcal/mol
Surface area40390 Å2
MethodPISA
Unit cell
Length a, b, c (Å)175.335, 176.204, 200.538
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-ID
11
21
31
41
51
61
12
22
32
42
52
62

NCS domain segments:
Dom-IDComponent-IDEns-IDSelection details
111chain 'A' and (resseq 17:219 )
211chain 'B' and (resseq 17:219 )
311chain 'C' and (resseq 17:219 )
411chain 'G' and (resseq 17:219 )
511chain 'H' and (resseq 17:219 )
611chain 'I' and (resseq 17:219 )
112chain 'D' and (resseq 17:219 )
212chain 'E' and (resseq 17:219 )
312chain 'F' and (resseq 17:219 )
412chain 'J' and (resseq 17:219 )
512chain 'K' and (resseq 17:219 )
612chain 'L' and (resseq 17:219 )

NCS ensembles :
ID
1
2

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Components

#1: Protein
CO2 concentrating mechanism protein P


Mass: 24846.258 Da / Num. of mol.: 12
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.: 19 / 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: 5.19 Å3/Da / Density % sol: 76.3 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 4.1
Details: 17% tacsimate, pH 4.1, 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: 0.9774 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Dec 2, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9774 Å / Relative weight: 1
ReflectionResolution: 3.3→39.412 Å / Num. obs: 92592 / % possible obs: 98.6 % / Rmerge(I) obs: 0.248 / Rsym value: 0.213 / Net I/σ(I): 9.71
Reflection shellResolution: 2.51→2.57 Å / Rmerge(I) obs: 0.806 / Mean I/σ(I) obs: 2.36 / Rsym value: 0.759 / % possible all: 96.3

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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: 3.301→39.412 Å / SU ML: 0.33 / σ(F): 0 / Phase error: 20.25 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2217 1900 2.18 %
Rwork0.1945 --
obs0.1951 87185 93.02 %
Solvent computationShrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 3.301→39.412 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms18636 0 0 19 18655
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00218864
X-RAY DIFFRACTIONf_angle_d0.54825500
X-RAY DIFFRACTIONf_dihedral_angle_d12.5967044
X-RAY DIFFRACTIONf_chiral_restr0.0362964
X-RAY DIFFRACTIONf_plane_restr0.0023348
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDTypeRms dev position (Å)
11A1553X-RAY DIFFRACTIONPOSITIONAL
12B1553X-RAY DIFFRACTIONPOSITIONAL0.006
13C1553X-RAY DIFFRACTIONPOSITIONAL0.007
14G1553X-RAY DIFFRACTIONPOSITIONAL0.005
15H1553X-RAY DIFFRACTIONPOSITIONAL0.005
16I1553X-RAY DIFFRACTIONPOSITIONAL0.007
21D1553X-RAY DIFFRACTIONPOSITIONAL
22E1553X-RAY DIFFRACTIONPOSITIONAL0.004
23F1553X-RAY DIFFRACTIONPOSITIONAL0.007
24J1553X-RAY DIFFRACTIONPOSITIONAL0.006
25K1553X-RAY DIFFRACTIONPOSITIONAL0.004
26L1553X-RAY DIFFRACTIONPOSITIONAL0.007
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.301-3.38360.35531230.28395318X-RAY DIFFRACTION82
3.3836-3.4750.27341220.26365670X-RAY DIFFRACTION87
3.475-3.57720.27791260.23215843X-RAY DIFFRACTION90
3.5772-3.69260.2431270.20995882X-RAY DIFFRACTION91
3.6926-3.82440.21641360.2045997X-RAY DIFFRACTION92
3.8244-3.97740.22681350.18636069X-RAY DIFFRACTION94
3.9774-4.15820.19621340.18176137X-RAY DIFFRACTION94
4.1582-4.37720.19611390.16086210X-RAY DIFFRACTION95
4.3772-4.6510.17781370.16066237X-RAY DIFFRACTION96
4.651-5.00950.1731450.15196336X-RAY DIFFRACTION97
5.0095-5.51240.2041440.18426290X-RAY DIFFRACTION96
5.5124-6.30730.24171400.21986278X-RAY DIFFRACTION95
6.3073-7.93580.25021430.20186406X-RAY DIFFRACTION96
7.9358-39.41490.20431490.18446612X-RAY DIFFRACTION96

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