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- PDB-5suh: The structure of double ringed trimeric shell protein MSM0271 fro... -

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Basic information

Entry
Database: PDB / ID: 5suh
TitleThe structure of double ringed trimeric shell protein MSM0271 from the RMM microcompartment
ComponentsMSM0271 protein
KeywordsSTRUCTURAL PROTEIN / Bacterial microcompartment / shell / BMC-FP
Function / homologyBacterial microcompartment (BMC) circularly permuted domain / Bacterial microcompartment (BMC) circularly permuted domain profile. / BMC (bacterial microcompartment) domain / bacterial microcompartment / CcmK-like superfamily / Alpha-Beta Plaits / 2-Layer Sandwich / Alpha Beta / BMC circularly permuted domain-containing protein
Function and homology information
Biological speciesMycobacterium smegmatis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.7 Å
AuthorsMallette, E. / Kimber, M.S.
CitationJournal: J. Biol. Chem. / Year: 2017
Title: A Complete Structural Inventory of the Mycobacterial Microcompartment Shell Proteins Constrains Models of Global Architecture and Transport.
Authors: Mallette, E. / Kimber, M.S.
History
DepositionAug 3, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 14, 2016Provider: repository / Type: Initial release
Revision 1.1Feb 1, 2017Group: Database references
Revision 1.2Feb 8, 2017Group: Database references
Revision 1.3Mar 6, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
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: MSM0271 protein
B: MSM0271 protein
C: MSM0271 protein


Theoretical massNumber of molelcules
Total (without water)78,0593
Polymers78,0593
Non-polymers00
Water46826
1
A: MSM0271 protein
B: MSM0271 protein
C: MSM0271 protein

A: MSM0271 protein
B: MSM0271 protein
C: MSM0271 protein


Theoretical massNumber of molelcules
Total (without water)156,1176
Polymers156,1176
Non-polymers00
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_555y,x,-z1
Buried area19080 Å2
ΔGint-65 kcal/mol
Surface area40670 Å2
MethodPISA
Unit cell
Length a, b, c (Å)139.890, 139.890, 150.120
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number182
Space group name H-MP6322

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Components

#1: Protein MSM0271 protein


Mass: 26019.549 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium smegmatis (strain ATCC 700084 / mc(2)155) (bacteria)
Strain: ATCC 700084 / mc(2)155 / Gene: MSMEG_0271, MSMEI_0264 / Plasmid: pET28a / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: A0QP48
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 26 / 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: 2.72 Å3/Da / Density % sol: 54.71 % / Description: hexagonal prisms
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: 10 mg/mL protein, 0.8 M Na/K tartrate, 0.1 M Tris, 0.5% (w/v) PEG 2000MME

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: CLSI / Beamline: 08ID-1 / Wavelength: 0.97949 Å
DetectorType: RAYONIX MX-300 / Detector: CCD / Date: Jul 10, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97949 Å / Relative weight: 1
ReflectionResolution: 2.7→47.2 Å / Num. obs: 24387 / % possible obs: 99.9 % / Redundancy: 9.6 % / Biso Wilson estimate: 69.4 Å2 / CC1/2: 0.997 / Rsym value: 0.133 / Net I/σ(I): 19.2
Reflection shellResolution: 2.7→2.77 Å / Redundancy: 11.1 % / Mean I/σ(I) obs: 2.1 / CC1/2: 0.752 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: MSM0275

Resolution: 2.7→47.139 Å / SU ML: 0.37 / Cross valid method: THROUGHOUT / σ(F): 1.37 / Phase error: 22.9
RfactorNum. reflection% reflection
Rfree0.2243 1219 5 %
Rwork0.1729 --
obs0.1755 24385 99.93 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.7→47.139 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4685 0 0 26 4711
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.014756
X-RAY DIFFRACTIONf_angle_d1.2786471
X-RAY DIFFRACTIONf_dihedral_angle_d14.9951753
X-RAY DIFFRACTIONf_chiral_restr0.055770
X-RAY DIFFRACTIONf_plane_restr0.007854
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.7-2.80810.33851330.24922514X-RAY DIFFRACTION100
2.8081-2.93590.29941320.23572516X-RAY DIFFRACTION100
2.9359-3.09070.30011320.21352514X-RAY DIFFRACTION100
3.0907-3.28430.23341340.20872536X-RAY DIFFRACTION100
3.2843-3.53780.27531340.19062553X-RAY DIFFRACTION100
3.5378-3.89360.24441350.17032557X-RAY DIFFRACTION100
3.8936-4.45670.23031360.15092589X-RAY DIFFRACTION100
4.4567-5.61350.15891380.13742614X-RAY DIFFRACTION100
5.6135-47.1460.20611450.17322773X-RAY DIFFRACTION99
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)
12.2121-0.60411.07571.5195-0.58610.78060.13020.13510.1617-0.2634-0.1707-0.0615-0.0085-0.1130.0440.48870.10470.05080.5287-0.01730.386-26.2158-62.2425-13.0682
21.58910.03180.15521.8892-0.29740.9488-0.03170.10220.64170.15490.0505-0.1341-0.27440.2031-0.03560.502-0.00750.02510.5950.02810.74770.6622-43.8532-4.5234
32.05460.12280.72751.6511-0.04630.67030.1550.50950.84-0.1773-0.155-0.2136-0.30370.08520.03510.7790.05880.1390.71010.21360.7688-24.2874-29.8807-22.2467
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A'
2X-RAY DIFFRACTION2chain 'B'
3X-RAY DIFFRACTION3chain 'C'

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