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Basic information

Entry
Database: PDB / ID: 6xpi
TitleCutR flat hexamer, form 1
ComponentsEthanolamine utilization protein EutS
KeywordsSTRUCTURAL PROTEIN / microcompartment / MCP / shell protein / BMC
Function / homologyBacterial microcompartment shell protein EutS/PduU/CutR / bacterial microcompartment / BMC domain / Bacterial microcompartment domain / BMC / CcmK-like superfamily / Bacterial microcompartment shell protein CutR
Function and homology information
Biological speciesStreptococcus intermedius SK54 = ATCC 27335 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.6 Å
AuthorsOchoa, J.M. / Sawaya, M.R. / Nguyen, V.N. / Duilio, C. / Yeates, T.O.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID) United States
CitationJournal: Protein Sci. / Year: 2020
Title: Symmetry breaking and structural polymorphism in a bacterial microcompartment shell protein for choline utilization.
Authors: Ochoa, J.M. / Nguyen, V.N. / Nie, M. / Sawaya, M.R. / Bobik, T.A. / Yeates, T.O.
History
DepositionJul 8, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 22, 2020Provider: repository / Type: Initial release
Revision 1.1Sep 16, 2020Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.identifier_ORCID / _citation_author.name
Revision 1.2Nov 11, 2020Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title / _citation_author.identifier_ORCID
Revision 1.3Oct 18, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Ethanolamine utilization protein EutS
B: Ethanolamine utilization protein EutS
C: Ethanolamine utilization protein EutS
D: Ethanolamine utilization protein EutS
E: Ethanolamine utilization protein EutS
F: Ethanolamine utilization protein EutS


Theoretical massNumber of molelcules
Total (without water)79,4886
Polymers79,4886
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration, elutes at molecular weight consistent with other BMC hexamers
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area16760 Å2
ΔGint-89 kcal/mol
Surface area22460 Å2
MethodPISA
Unit cell
Length a, b, c (Å)135.360, 76.140, 67.810
Angle α, β, γ (deg.)90.000, 119.720, 90.000
Int Tables number5
Space group name H-MC121

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Components

#1: Protein
Ethanolamine utilization protein EutS


Mass: 13247.989 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptococcus intermedius SK54 = ATCC 27335 (bacteria)
Gene: HMPREF1654_00416 / Plasmid: pET-24a(+) / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0A0E2IV13

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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: 1.91 Å3/Da / Density % sol: 35.57 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 5.5 / Details: 2.0M ammonium sulfate, 0.1M BIS-Tris, pH 5.5

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 0.9717 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Dec 12, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9717 Å / Relative weight: 1
ReflectionResolution: 2.6→63.91 Å / Num. obs: 17277 / % possible obs: 92.8 % / Redundancy: 4.024 % / Biso Wilson estimate: 76.73 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.073 / Rrim(I) all: 0.084 / Χ2: 0.868 / Net I/σ(I): 10.31 / Num. measured all: 69528 / Scaling rejects: 13
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. possibleNum. unique obsCC1/2Rrim(I) all% possible all
2.6-2.674.1391.4391.045281134812760.7471.6594.7
2.67-2.744.1110.8751.525155132412540.9461.00594.7
2.74-2.824.1410.7571.735193131612540.9530.86795.3
2.82-2.914.0990.6662.034833125111790.930.76694.2
2.91-34.0740.5582.344697123611530.9530.64193.3
3-3.114.0380.3363.424381117810850.9880.38792.1
3.11-3.224.0390.2634.434193113110380.990.30391.8
3.22-3.363.9170.2115.15374510899560.990.24487.8
3.36-3.513.8690.1367.9336210588690.9940.15882.1
3.51-3.684.070.1049.84402910209900.9970.1297.1
3.68-3.884.0910.08312.6837849609250.9980.09696.4
3.88-4.114.0390.06814.8935309148740.9980.07895.6
4.11-4.393.950.05119.2531848458060.9990.0695.4
4.39-4.754.010.04124.5130728057660.9990.04895.2
4.75-5.23.8740.04523.127167547010.9980.05293
5.2-5.814.0050.04923.123396555840.9980.05689.2
5.81-6.713.7240.04323.7617805954780.9980.05180.3
6.71-8.223.8930.03132.3618615114780.9990.03693.5
8.22-11.633.9870.02438.1415353933850.9990.02898
11.63-63.913.7960.02333.7385823422610.02796.6

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Phasing

PhasingMethod: molecular replacement
Phasing MRModel details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation2.3 Å63.91 Å
Translation2.3 Å63.91 Å

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Processing

Software
NameVersionClassificationNB
XDSdata reduction
XSCALEdata scaling
PHASER2.8.3phasing
BUSTER2.10.3 (20-MAY-2020)refinement
PDB_EXTRACT3.25data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6XPK

6xpk


Resolution: 2.6→63.91 Å / Cor.coef. Fo:Fc: 0.911 / Cor.coef. Fo:Fc free: 0.898 / Cross valid method: FREE R-VALUE / σ(F): 0 / SU Rfree Blow DPI: 0.325
RfactorNum. reflection% reflectionSelection details
Rfree0.2417 1728 10 %RANDOM
Rwork0.2007 ---
obs0.2049 17276 93.2 %-
Displacement parametersBiso max: 157.87 Å2 / Biso mean: 105.52 Å2 / Biso min: 77.32 Å2
Baniso -1Baniso -2Baniso -3
1-17.1003 Å20 Å2-10.5739 Å2
2---56.7905 Å20 Å2
3---39.6901 Å2
Refine analyzeLuzzati coordinate error obs: 0.83 Å
Refinement stepCycle: final / Resolution: 2.6→63.91 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4808 0 0 0 4808
Num. residues----649
Refine LS restraints
Refine-IDTypeNumberRestraint functionWeightDev ideal
X-RAY DIFFRACTIONt_dihedral_angle_d1623SINUSOIDAL2
X-RAY DIFFRACTIONt_trig_c_planes
X-RAY DIFFRACTIONt_gen_planes841HARMONIC5
X-RAY DIFFRACTIONt_it4880HARMONIC10
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_chiral_improper_torsion722SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact4105SEMIHARMONIC4
X-RAY DIFFRACTIONt_bond_d4880HARMONIC20.008
X-RAY DIFFRACTIONt_angle_deg6653HARMONIC21.06
X-RAY DIFFRACTIONt_omega_torsion3
X-RAY DIFFRACTIONt_other_torsion19.79
LS refinement shellResolution: 2.6→2.62 Å / Rfactor Rfree error: 0 / Total num. of bins used: 51
RfactorNum. reflection% reflection
Rfree0.492 35 10.12 %
Rwork0.2863 311 -
all0.3065 346 -
obs--93.77 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
13.705-1.0626-1.67341.02390.66754.9719-0.024-0.03710.0214-0.2512-0.0193-0.04890.0531-0.78450.0433-0.1297-0.07870.05430.07260.0201-0.1333-2.22530.390636.8009
24.1018-1.5566-0.46450.6359-0.80263.6915-0.10140.53350.1230.0992-0.0037-0.22450.275-0.67670.105-0.1343-0.06180.01210.1118-0.1016-0.13550.6991.059716.5233
33.0374-1.2766-0.4010.7161-1.45034.5707-0.13140.68840.00620.2393-0.1509-0.10750.04270.11590.2824-0.0852-0.03690.03170.1066-0.072-0.105719.6371-0.0429.005
44.5151.0085-2.61930.7379-1.07836.7768-0.1894-0.0594-0.12550.1063-0.00240.05940.07071.21460.1917-0.21470.08820.00390.223-0.0172-0.208735.5454-2.042321.5821
54.44781.303-0.30580.73440.23052.7572-0.3886-0.66970.0346-0.0210.11370.21460.21820.87110.2749-0.16960.19210.02350.3520.1262-0.296432.4049-3.232241.5216
64.03660.5406-1.328600.98844.6584-0.1591-0.7944-0.0131-0.1954-0.07060.13360.12930.41980.2297-0.07370.07580.06020.06940.0881-0.148713.7326-1.836949.5326
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1{ A|* }A9 - 116
2X-RAY DIFFRACTION2{ B|* }B9 - 116
3X-RAY DIFFRACTION3{ C|* }C9 - 116
4X-RAY DIFFRACTION4{ D|* }D9 - 116
5X-RAY DIFFRACTION5{ E|* }E8 - 116
6X-RAY DIFFRACTION6{ F|* }F9 - 116

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