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- PDB-4i7a: GrpN pentameric microcompartment shell protein from Rhodospirillu... -

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Basic information

Entry
Database: PDB / ID: 4i7a
TitleGrpN pentameric microcompartment shell protein from Rhodospirillum rubrum
ComponentsEthanolamine utilization protein EutN/carboxysome structural protein Ccml
KeywordsSTRUCTURAL PROTEIN / microcompartments / ccmL / eutN / glycyl radical propanediol microcompartment
Function / homologyEutN/Ccml / OB fold (Dihydrolipoamide Acetyltransferase, E2P) / Beta Barrel / Mainly Beta / :
Function and homology information
Biological speciesRhodospirillum rubrum (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 3.2 Å
AuthorsWheatley, N.M. / Gidaniyan, S.D. / Cascio, D. / Yeates, T.O.
CitationJournal: Protein Sci. / Year: 2013
Title: Bacterial microcompartment shells of diverse functional types possess pentameric vertex proteins.
Authors: Wheatley, N.M. / Gidaniyan, S.D. / Liu, Y. / Cascio, D. / Yeates, T.O.
History
DepositionNov 30, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 1, 2013Provider: repository / Type: Initial release
Revision 1.1May 8, 2013Group: Database references
Revision 1.2Sep 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / 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
A: Ethanolamine utilization protein EutN/carboxysome structural protein Ccml
B: Ethanolamine utilization protein EutN/carboxysome structural protein Ccml
C: Ethanolamine utilization protein EutN/carboxysome structural protein Ccml
D: Ethanolamine utilization protein EutN/carboxysome structural protein Ccml
E: Ethanolamine utilization protein EutN/carboxysome structural protein Ccml
hetero molecules


Theoretical massNumber of molelcules
Total (without water)49,5078
Polymers49,4015
Non-polymers1063
Water181
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area10100 Å2
ΔGint-67 kcal/mol
Surface area16970 Å2
MethodPISA
Unit cell
Length a, b, c (Å)150.710, 150.710, 150.710
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number197
Space group name H-MI23

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Components

#1: Protein
Ethanolamine utilization protein EutN/carboxysome structural protein Ccml / GrpN


Mass: 9880.153 Da / Num. of mol.: 5
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rhodospirillum rubrum (bacteria) / Strain: F11 / Gene: F11_04705, grpN / Plasmid: pET22b(+) / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: G2TCY2
#2: Chemical ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Cl
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 1 / 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: 2.89 Å3/Da / Density % sol: 57.4 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.2
Details: 0.1 M sodium chloride, 0.1 M HEPES, pH 7.2, 1.5 M ammonium sulfate, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 0.9791 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Oct 27, 2012
RadiationMonochromator: double crystal Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9791 Å / Relative weight: 1
ReflectionResolution: 3.2→106.57 Å / Num. obs: 9248 / % possible obs: 96.6 % / Observed criterion σ(I): -3 / Redundancy: 5.4 % / Biso Wilson estimate: 73.556 Å2 / Rmerge(I) obs: 0.066 / Net I/σ(I): 21.02
Reflection shell
Resolution (Å)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. unique obsDiffraction-ID% possible all
3.2-3.280.562.993856700199.6
3.28-3.370.4623.723646669197.8
3.37-3.470.3454.993495664198.5
3.47-3.580.2736.13066599195.8
3.58-3.70.2297.432711581191.9
3.7-3.820.1799.763259579196.8
3.82-3.970.14111.653378590197.5
3.97-4.130.08718.63043530198.5
4.13-4.310.07819.393124548198.4
4.31-4.530.05427.222779498198.2
4.53-4.770.04531.832609476197.7
4.77-5.060.04433.382441472198.7
5.06-5.410.04630.521896410194.3
5.41-5.840.04331.272213411197.9
5.84-6.40.04331.842119369198.9
6.4-7.160.03339.11961345196.9
7.16-8.260.02352.61650289194.4
8.26-10.120.01765.741324256195.9
10.12-14.310.01667.831003187192.1
14.31-106.570.01476.4341375158.1

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Phasing

PhasingMethod: molecular replacement
Phasing MRModel details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation3.2 Å19.79 Å
Translation3.2 Å19.79 Å

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Processing

Software
NameVersionClassificationNB
XSCALEdata scaling
PHASER2.3.0phasing
PHENIX1.8.1_1168refinement
PDB_EXTRACT3.11data extraction
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2QW7

2qw7


Resolution: 3.2→19.789 Å / Occupancy max: 1 / Occupancy min: 1 / FOM work R set: 0.7272 / SU ML: 0.39 / Cross valid method: THROUGHOUT / σ(F): 1.99 / Phase error: 33 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2885 461 4.99 %RANDOM
Rwork0.2671 ---
obs0.2682 9242 97.03 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 160.25 Å2 / Biso mean: 87.6177 Å2 / Biso min: 51.97 Å2
Refinement stepCycle: LAST / Resolution: 3.2→19.789 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2926 0 3 1 2930
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0042928
X-RAY DIFFRACTIONf_angle_d0.6933979
X-RAY DIFFRACTIONf_chiral_restr0.037551
X-RAY DIFFRACTIONf_plane_restr0.001493
X-RAY DIFFRACTIONf_dihedral_angle_d11.7391007
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 3

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
3.2-3.66060.37551510.33042889304097
3.6606-4.60240.26951540.2712926308098
4.6024-19.78960.27331560.24332966312297
Refinement TLS params.Method: refined / Origin x: 47.2819 Å / Origin y: 29.815 Å / Origin z: 0.0653 Å
111213212223313233
T0.5117 Å2-0.0846 Å20.0262 Å2-0.506 Å2-0.025 Å2--0.5633 Å2
L1.6619 °2-1.1662 °2-0.0022 °2-2.7206 °2-0.2138 °2--2.4408 °2
S-0.0012 Å °-0.0573 Å °0.1111 Å °0.0108 Å °0.0506 Å °-0.1443 Å °-0.0148 Å °-0.0713 Å °-0.0576 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1allA1 - 88
2X-RAY DIFFRACTION1allB1 - 201
3X-RAY DIFFRACTION1allC1 - 101
4X-RAY DIFFRACTION1allD1 - 101
5X-RAY DIFFRACTION1allE1 - 91

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