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- PDB-4jvz: Structure of Thermosynechococcus elongatus CcmL -

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Basic information

Entry
Database: PDB / ID: 4jvz
TitleStructure of Thermosynechococcus elongatus CcmL
ComponentsCarbon dioxide concentrating mechanism protein
KeywordsSTRUCTURAL PROTEIN / OB Fold
Function / homology
Function and homology information


structural constituent of carboxysome shell / carboxysome / carbon fixation / photosynthesis
Similarity search - Function
Carboxysome shell vertex protein CcmL / EutN/Ccml / Ethanolamine utilization protein EutN/carboxysome shell vertex protein CcmL / EutN/Ccml superfamily / Ethanolamine utilisation protein EutN/carboxysome / Bacterial microcompartment vertex (BMV) domain profile. / OB fold (Dihydrolipoamide Acetyltransferase, E2P) / Beta Barrel / Mainly Beta
Similarity search - Domain/homology
Carboxysome shell vertex protein CcmL
Similarity search - Component
Biological speciesThermosynechococcus elongatus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.01 Å
AuthorsSutter, M. / Kerfeld, C.A.
CitationJournal: Photosynth.Res. / Year: 2013
Title: Two new high-resolution crystal structures of carboxysome pentamer proteins reveal high structural conservation of CcmL orthologs among distantly related cyanobacterial species.
Authors: Sutter, M. / Wilson, S.C. / Deutsch, S. / Kerfeld, C.A.
History
DepositionMar 26, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 4, 2013Provider: repository / Type: Initial release
Revision 1.1Nov 27, 2013Group: Database references
Revision 1.2Feb 28, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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
B: Carbon dioxide concentrating mechanism protein
C: Carbon dioxide concentrating mechanism protein
D: Carbon dioxide concentrating mechanism protein
E: Carbon dioxide concentrating mechanism protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)54,3526
Polymers54,2565
Non-polymers961
Water8,071448
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area11860 Å2
ΔGint-43 kcal/mol
Surface area18910 Å2
MethodPISA
Unit cell
Length a, b, c (Å)72.445, 72.445, 197.449
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212

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Components

#1: Protein
Carbon dioxide concentrating mechanism protein


Mass: 10851.188 Da / Num. of mol.: 5
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermosynechococcus elongatus (bacteria)
Strain: BP-1 / Gene: ccmL / Production host: Escherichia coli (E. coli) / References: UniProt: Q8DKB4
#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.: 448 / 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: 2.39 Å3/Da / Density % sol: 48.48 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 6.4
Details: 0.1 M MES, 1.4 M MgSO4, pH 6.4, VAPOR DIFFUSION, SITTING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.1 / Wavelength: 0.977408 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Mar 4, 2013
RadiationMonochromator: Single crystal, cylindrically bent, Si(220) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.977408 Å / Relative weight: 1
ReflectionResolution: 2.01→39.49 Å / Num. obs: 35901 / % possible obs: 99.2 % / Observed criterion σ(I): -3 / Redundancy: 28.3 % / Rmerge(I) obs: 0.22
Reflection shellResolution: 2.01→2.12 Å / Redundancy: 28.5 % / Rmerge(I) obs: 0.0144 / Mean I/σ(I) obs: 3.1 / Num. unique all: 5124 / % possible all: 99.5

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Processing

Software
NameVersionClassification
ADSCQuantumdata collection
AutoSolphasing
PHENIX(phenix.refine: 1.8.1_1168)refinement
XDSdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.01→36.222 Å / SU ML: 0.27 / σ(F): 1.33 / Phase error: 28.51 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2957 1992 5.9 %random
Rwork0.2464 ---
obs0.2493 33784 93.56 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.01→36.222 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3588 0 5 448 4041
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0043640
X-RAY DIFFRACTIONf_angle_d0.8394945
X-RAY DIFFRACTIONf_dihedral_angle_d13.2221297
X-RAY DIFFRACTIONf_chiral_restr0.051598
X-RAY DIFFRACTIONf_plane_restr0.003627
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.01-2.05760.37561460.31352329X-RAY DIFFRACTION99
2.0576-2.11330.29071480.28272355X-RAY DIFFRACTION100
2.1133-2.17540.3771490.28732389X-RAY DIFFRACTION100
2.1754-2.24560.4648900.45671433X-RAY DIFFRACTION60
2.2456-2.32590.5929930.4511488X-RAY DIFFRACTION62
2.3259-2.4190.34331510.26772402X-RAY DIFFRACTION100
2.419-2.52910.31581490.2562380X-RAY DIFFRACTION100
2.5291-2.66240.30131500.24312412X-RAY DIFFRACTION100
2.6624-2.82910.25811510.22212398X-RAY DIFFRACTION100
2.8291-3.04740.25881530.22232440X-RAY DIFFRACTION100
3.0474-3.35390.27051520.20892424X-RAY DIFFRACTION100
3.3539-3.83880.3111530.22712438X-RAY DIFFRACTION99
3.8388-4.83460.18211400.17412247X-RAY DIFFRACTION90
4.8346-36.22840.26261670.23092657X-RAY DIFFRACTION100

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