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- PDB-6xpl: CutR Screw, form 2 with 33.8 angstrom pitch -

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Basic information

Entry
Database: PDB / ID: 6xpl
TitleCutR Screw, form 2 with 33.8 angstrom pitch
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: 3.3 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 1.3Jun 30, 2021Group: Data collection / Category: pdbx_reflns_twin
Item: _pdbx_reflns_twin.crystal_id / _pdbx_reflns_twin.diffrn_id
Revision 1.4Oct 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

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Assembly

Deposited unit
A: Ethanolamine utilization protein EutS


Theoretical massNumber of molelcules
Total (without water)13,2801
Polymers13,2801
Non-polymers00
Water00
1
A: Ethanolamine utilization protein EutS

A: Ethanolamine utilization protein EutS

A: Ethanolamine utilization protein EutS

A: Ethanolamine utilization protein EutS

A: Ethanolamine utilization protein EutS

A: Ethanolamine utilization protein EutS


Theoretical massNumber of molelcules
Total (without water)79,6806
Polymers79,6806
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-y,x-y,z+1/31
crystal symmetry operation3_555-x+y,-x,z+2/31
crystal symmetry operation4_555-x,-y,z+1/21
crystal symmetry operation5_555y,-x+y,z+5/61
crystal symmetry operation6_555x-y,x,z+1/61
Unit cell
Length a, b, c (Å)64.910, 64.910, 33.780
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number169
Space group name H-MP61

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Components

#1: Protein Ethanolamine utilization protein EutS


Mass: 13280.055 Da / Num. of mol.: 1
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: 1.55 Å3/Da / Density % sol: 20.49 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop
Details: 0.2M potassium sodium tartrate tetrahydrate, 0.1M Bis-Tris propane, 8.52% w/v PEG 3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-E / Wavelength: 0.97918 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Dec 6, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97918 Å / Relative weight: 1
Reflection twin
TypeCrystal-IDIDOperatorDomain-IDFraction
pseudo-merohedral11H, K, L10.7363
pseudo-merohedral11-K, -H, -L20.2637
ReflectionResolution: 3.3→56.214 Å / Num. obs: 1286 / % possible obs: 99.3 % / Redundancy: 4.579 % / Biso Wilson estimate: 81.695 Å2 / CC1/2: 0.992 / Rmerge(I) obs: 0.236 / Rrim(I) all: 0.268 / Χ2: 0.755 / Net I/σ(I): 4.63
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique obsCC1/2Rrim(I) all% possible all
3.3-3.54.5431.3370.982080.5111.5199.5
3.5-3.764.2290.9311.52050.4641.06799
3.76-3.975.0850.6362.231180.8750.709100
3.97-4.214.8780.5052.621230.880.565100
4.21-4.864.7650.3254.672210.9240.365100
4.86-5.954.7860.3024.731820.9530.34100
5.95-8.44.2070.168.151450.9790.18498.6
8.4-56.2144.0710.04721.23840.9960.05495.5

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Phasing

PhasingMethod: molecular replacement
Phasing MRModel details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation3.7 Å56.21 Å
Translation3.7 Å56.21 Å

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Processing

Software
NameVersionClassificationNB
XDSdata reduction
XSCALEdata scaling
PHASER2.8.3phasing
REFMAC5.8.0258refinement
PDB_EXTRACT3.25data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6XPK

6xpk


Resolution: 3.3→56.214 Å / Cor.coef. Fo:Fc: 0.923 / Cor.coef. Fo:Fc free: 0.918 / SU B: 30.858 / SU ML: 0.464 / Cross valid method: FREE R-VALUE / ESU R Free: 0.151
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.2654 151 11.797 %
Rwork0.2193 1129 -
all0.225 --
obs-1280 99.533 %
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT
Displacement parametersBiso mean: 123.909 Å2
Baniso -1Baniso -2Baniso -3
1--50.17 Å2-0 Å2-0 Å2
2---50.17 Å2-0 Å2
3---100.34 Å2
Refinement stepCycle: LAST / Resolution: 3.3→56.214 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms720 0 0 0 720
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0050.013731
X-RAY DIFFRACTIONr_bond_other_d0.0010.017686
X-RAY DIFFRACTIONr_ext_dist_refined_d0.0110.012762
X-RAY DIFFRACTIONr_angle_refined_deg1.3061.623997
X-RAY DIFFRACTIONr_angle_other_deg1.0691.5651589
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.26597
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.0125.35728
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.0315114
X-RAY DIFFRACTIONr_dihedral_angle_4_deg9.338151
X-RAY DIFFRACTIONr_chiral_restr0.0370.2109
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.02827
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02136
X-RAY DIFFRACTIONr_nbd_refined0.1530.2123
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1590.2622
X-RAY DIFFRACTIONr_nbtor_refined0.1440.2351
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0740.2354
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.0770.211
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.1970.27
X-RAY DIFFRACTIONr_nbd_other0.1850.241
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.2170.22
X-RAY DIFFRACTIONr_mcbond_it19.98212.853391
X-RAY DIFFRACTIONr_mcbond_other19.95512.851390
X-RAY DIFFRACTIONr_mcangle_it28.38619.01487
X-RAY DIFFRACTIONr_mcangle_other28.37719.009488
X-RAY DIFFRACTIONr_scbond_it19.9914.232340
X-RAY DIFFRACTIONr_scbond_other20.00614.234339
X-RAY DIFFRACTIONr_scangle_it29.57720.748510
X-RAY DIFFRACTIONr_scangle_other29.55920.739510
X-RAY DIFFRACTIONr_lrange_it39.99313.8332833
X-RAY DIFFRACTIONr_lrange_other40.001313.8232829
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.3-3.3860.296130.33479X-RAY DIFFRACTION96.8421
3.386-3.4780.27570.33991X-RAY DIFFRACTION100
3.478-3.5790.335100.25966X-RAY DIFFRACTION97.4359
3.579-3.6880.34890.29979X-RAY DIFFRACTION100
3.688-3.8090.214160.25167X-RAY DIFFRACTION100
3.809-3.9420.271100.21764X-RAY DIFFRACTION100
3.942-4.090.21450.25484X-RAY DIFFRACTION100
4.09-4.2560.45880.25363X-RAY DIFFRACTION100
4.256-4.4440.207120.17558X-RAY DIFFRACTION100
4.444-4.6590.16950.16667X-RAY DIFFRACTION100
4.659-4.910.15570.14160X-RAY DIFFRACTION100
4.91-5.2050.31160.15456X-RAY DIFFRACTION100
5.205-5.5610.5780.24150X-RAY DIFFRACTION100
5.561-6.0010.38970.20549X-RAY DIFFRACTION100
6.001-6.5670.39760.25147X-RAY DIFFRACTION100
6.567-7.3290.23650.19542X-RAY DIFFRACTION97.9167
7.329-8.4390.3560.13834X-RAY DIFFRACTION100
8.439-10.2780.10750.12332X-RAY DIFFRACTION100
10.278-14.2990.15340.17124X-RAY DIFFRACTION100
14.299-56.2140.47620.42517X-RAY DIFFRACTION100

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