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- PDB-5l39: The structure of the fused permuted hexameric shell protein MSM02... -

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Basic information

Entry
Database: PDB / ID: 5l39
TitleThe structure of the fused permuted hexameric shell protein MSM0275 from the RMM microcompartment
ComponentsRMM microcompartment shell protein MSM0275
KeywordsSTRUCTURAL PROTEIN / bacterial microcompartment / fused permuted hexameric shell protein
Function / homology
Function and homology information


bacterial microcompartment
Similarity search - Function
Bacterial microcompartment (BMC) circularly permuted domain / Bacterial microcompartment (BMC) circularly permuted domain profile. / BMC (bacterial microcompartment) domain / BMC domain / Bacterial microcompartment domain / BMC / CcmK-like superfamily / Alpha-Beta Plaits / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Bacterial microcompartments protein family protein
Similarity search - Component
Biological speciesMycobacterium smegmatis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 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 1.3Oct 4, 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: RMM microcompartment shell protein MSM0275
B: RMM microcompartment shell protein MSM0275
C: RMM microcompartment shell protein MSM0275
D: RMM microcompartment shell protein MSM0275
E: RMM microcompartment shell protein MSM0275
F: RMM microcompartment shell protein MSM0275
hetero molecules


Theoretical massNumber of molelcules
Total (without water)138,3798
Polymers138,3086
Non-polymers712
Water6,377354
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area17110 Å2
ΔGint-75 kcal/mol
Surface area40510 Å2
MethodPISA
Unit cell
Length a, b, c (Å)132.140, 143.480, 116.990
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221

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Components

#1: Protein
RMM microcompartment shell protein MSM0275 / Microcompartments protein


Mass: 23051.328 Da / Num. of mol.: 6
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_0275, MSMEI_0268 / Plasmid: pET28a / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 / References: UniProt: A0QP52
#2: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 354 / 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 Å3/Da / Density % sol: 38.64 % / Description: needles
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 5.6 / Details: 20 mg/mL protein, 0.5 M Na citrate, 20% PEG3350

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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: Mar 16, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97949 Å / Relative weight: 1
ReflectionResolution: 2.1→48.6 Å / Num. obs: 64985 / % possible obs: 100 % / Redundancy: 7.5 % / Biso Wilson estimate: 36.7 Å2 / CC1/2: 0.997 / Rsym value: 0.109 / Net I/σ(I): 11.96
Reflection shellResolution: 2.1→2.15 Å / Redundancy: 7.5 % / Rmerge(I) obs: 0.897 / Mean I/σ(I) obs: 2.4 / CC1/2: 0.834 / % 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: 4HT5

4ht5


Resolution: 2.1→48.6 Å / SU ML: 0.23 / Cross valid method: THROUGHOUT / σ(F): 1.36 / Phase error: 23.32
RfactorNum. reflection% reflection
Rfree0.2239 3247 5 %
Rwork0.1817 --
obs0.1838 64967 99.96 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.1→48.6 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9031 0 2 354 9387
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0059172
X-RAY DIFFRACTIONf_angle_d0.87212442
X-RAY DIFFRACTIONf_dihedral_angle_d13.9943296
X-RAY DIFFRACTIONf_chiral_restr0.0311460
X-RAY DIFFRACTIONf_plane_restr0.0031627
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.1-2.13130.27661470.2412673X-RAY DIFFRACTION100
2.1313-2.16460.33241250.2372686X-RAY DIFFRACTION100
2.1646-2.20010.27691380.22272601X-RAY DIFFRACTION100
2.2001-2.23810.29051510.22452666X-RAY DIFFRACTION100
2.2381-2.27880.261400.21862661X-RAY DIFFRACTION100
2.2788-2.32260.30621360.2222680X-RAY DIFFRACTION100
2.3226-2.370.2791460.2152647X-RAY DIFFRACTION100
2.37-2.42150.24541320.20492666X-RAY DIFFRACTION100
2.4215-2.47790.25481390.19932634X-RAY DIFFRACTION100
2.4779-2.53980.25471550.2012682X-RAY DIFFRACTION100
2.5398-2.60850.28671290.20552649X-RAY DIFFRACTION100
2.6085-2.68530.24621430.20142663X-RAY DIFFRACTION100
2.6853-2.77190.26111380.20282695X-RAY DIFFRACTION100
2.7719-2.8710.24391410.20032689X-RAY DIFFRACTION100
2.871-2.98590.22281400.20042672X-RAY DIFFRACTION100
2.9859-3.12180.23961430.19922670X-RAY DIFFRACTION100
3.1218-3.28630.23531360.19132677X-RAY DIFFRACTION100
3.2863-3.49220.23811470.18572700X-RAY DIFFRACTION100
3.4922-3.76170.21671400.1612695X-RAY DIFFRACTION100
3.7617-4.14010.19311400.15032699X-RAY DIFFRACTION100
4.1401-4.73870.17161430.14432726X-RAY DIFFRACTION100
4.7387-5.96860.19651460.15882744X-RAY DIFFRACTION100
5.9686-48.61260.17441520.16752845X-RAY DIFFRACTION100
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)
10.91870.00870.02183.73660.92241.66680.04520.2267-0.0224-0.4963-0.04580.085-0.152-0.02530.01770.27340.0374-0.00030.26840.00990.150448.290966.144413.2907
20.935-0.88110.09972.8272-0.951.6111-0.0697-0.1595-0.01360.25550.0854-0.0424-0.08220.0076-0.00960.2039-0.0383-0.00990.2118-0.00280.140448.799563.212947.1635
31.352-0.5561-0.14031.3824-0.43082.30850.12440.1151-0.456-0.2662-0.05370.22670.5840.0478-0.06360.37770.0214-0.10660.2042-0.04890.359848.027435.61127.5894
42.1766-0.2741-0.13842.1146-1.33391.81730.23170.4601-0.6831-0.5429-0.02510.24790.5075-0.1226-0.20470.45120.0388-0.21010.4194-0.15620.562719.012346.943111.9095
52.0617-0.12570.78951.6004-0.50464.18920.0354-0.0410.18040.0263-0.01850.1869-0.3747-0.2225-0.04190.21120.03530.0110.19740.01150.261818.856673.83931.0914
61.9757-0.31020.10391.95790.58232.04090.0585-0.4328-0.79470.19020.01510.41680.3915-0.2058-0.06260.3629-0.1269-0.06440.40760.23850.63418.11242.795444.6751
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A'
2X-RAY DIFFRACTION2chain 'B'
3X-RAY DIFFRACTION3chain 'C'
4X-RAY DIFFRACTION4chain 'D'
5X-RAY DIFFRACTION5chain 'E'
6X-RAY DIFFRACTION6chain 'F'

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