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- PDB-4jw0: Structure of Gloeobacter violaceus CcmL -

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Basic information

Entry
Database: PDB / ID: 4jw0
TitleStructure of Gloeobacter violaceus CcmL
ComponentsCarbon dioxide concentrating mechanism protein
KeywordsSTRUCTURAL PROTEIN / OB fold
Function / homologyEutN/Ccml / Bacterial microcompartment vertex (BMV) domain profile. / Ethanolamine utilization protein EutN/carboxysome shell vertex protein CcmL / EutN/Ccml superfamily / Ethanolamine utilisation protein EutN/carboxysome / OB fold (Dihydrolipoamide Acetyltransferase, E2P) / Beta Barrel / Mainly Beta / Carboxysome vertex protein CcmL
Function and homology information
Biological speciesGloeobacter violaceus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.7 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_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_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

Downloads & links

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Assembly

Deposited unit
B: Carbon dioxide concentrating mechanism protein
A: 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)59,1686
Polymers59,0725
Non-polymers961
Water7,674426
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area12250 Å2
ΔGint-59 kcal/mol
Surface area18750 Å2
MethodPISA
Unit cell
Length a, b, c (Å)74.377, 81.619, 89.349
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein
Carbon dioxide concentrating mechanism protein


Mass: 11814.366 Da / Num. of mol.: 5
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Gloeobacter violaceus (bacteria) / Strain: PCC 7421 / Gene: ccmL, gll2094 / Production host: Escherichia coli (E. coli) / References: UniProt: Q7NIT8
#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.: 426 / 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: 2.3 Å3/Da / Density % sol: 46.42 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 5
Details: 0.2 M Lithium sulfate, 0.1 M Bis-Tris, 10% (w/v) PEG 3350, pH 5.0, VAPOR DIFFUSION, SITTING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.2 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Dec 16, 2012
RadiationMonochromator: Double-crystal, Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.7→38.3 Å / Num. obs: 58606 / % possible obs: 97.4 % / Observed criterion σ(I): -3
Reflection shellResolution: 1.7→1.8 Å / Redundancy: 3.6 % / Rmerge(I) obs: 0.01371 / Mean I/σ(I) obs: 0.9 / Num. unique all: 7115 / % possible all: 82.4

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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: 1.7→38.297 Å / SU ML: 0.21 / σ(F): 1.34 / Phase error: 19.04 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.1914 2000 3.44 %random
Rwork0.1614 ---
obs0.1624 58196 96.84 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.7→38.297 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3594 0 5 426 4025
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0053648
X-RAY DIFFRACTIONf_angle_d0.9444940
X-RAY DIFFRACTIONf_dihedral_angle_d13.911366
X-RAY DIFFRACTIONf_chiral_restr0.058574
X-RAY DIFFRACTIONf_plane_restr0.004646
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.7-1.74640.3511870.33942440X-RAY DIFFRACTION60
1.7464-1.79360.34341400.31213942X-RAY DIFFRACTION96
1.7936-1.84640.27711460.25324104X-RAY DIFFRACTION100
1.8464-1.9060.26491460.21054109X-RAY DIFFRACTION100
1.906-1.97410.24271460.19424086X-RAY DIFFRACTION100
1.9741-2.05310.19781460.17364086X-RAY DIFFRACTION100
2.0531-2.14660.20851460.16284121X-RAY DIFFRACTION100
2.1466-2.25970.20141470.15554134X-RAY DIFFRACTION100
2.2597-2.40130.1941460.14764122X-RAY DIFFRACTION100
2.4013-2.58670.21151480.15264133X-RAY DIFFRACTION100
2.5867-2.84690.17931470.15134142X-RAY DIFFRACTION100
2.8469-3.25860.17591490.1454182X-RAY DIFFRACTION100
3.2586-4.10480.14791500.13584208X-RAY DIFFRACTION100
4.1048-38.30680.16521560.15014387X-RAY DIFFRACTION100

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