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- PDB-3i82: Ethanolamine Utilization Microcompartment Shell Subunit, EutL Clo... -

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Basic information

Entry
Database: PDB / ID: 3i82
TitleEthanolamine Utilization Microcompartment Shell Subunit, EutL Closed Form
ComponentsEthanolamine utilization protein eutL
KeywordsSTRUCTURAL PROTEIN
Function / homology
Function and homology information


ethanolamine degradation polyhedral organelle / ethanolamine catabolic process / structural molecule activity / zinc ion binding / identical protein binding
Similarity search - Function
Bacterial microcompartment shell protein EutL / Bacterial microcompartment shell protein, EutL/PduB type / Bacterial microcompartment (BMC) circularly permuted domain / Bacterial microcompartment (BMC) circularly permuted domain profile. / BMC (bacterial microcompartment) domain / BMC domain / Bacterial microcompartment domain / CcmK-like superfamily / BMC / Alpha-Beta Plaits ...Bacterial microcompartment shell protein EutL / Bacterial microcompartment shell protein, EutL/PduB type / Bacterial microcompartment (BMC) circularly permuted domain / Bacterial microcompartment (BMC) circularly permuted domain profile. / BMC (bacterial microcompartment) domain / BMC domain / Bacterial microcompartment domain / CcmK-like superfamily / BMC / Alpha-Beta Plaits / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Bacterial microcompartment shell protein EutL
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.31 Å
AuthorsTanaka, S. / Sawaya, M.R. / Yeates, T.O.
CitationJournal: Science / Year: 2010
Title: Structure and Mechanisms of a Protein-Based Organelle in Escherichia coli.
Authors: Tanaka, S. / Sawaya, M.R. / Yeates, T.O.
History
DepositionJul 9, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 12, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2Nov 1, 2017Group: Refinement description / Category: software
Revision 1.3Sep 6, 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 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Ethanolamine utilization protein eutL


Theoretical massNumber of molelcules
Total (without water)23,8761
Polymers23,8761
Non-polymers00
Water79344
1
A: Ethanolamine utilization protein eutL

A: Ethanolamine utilization protein eutL

A: Ethanolamine utilization protein eutL


Theoretical massNumber of molelcules
Total (without water)71,6283
Polymers71,6283
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_565-y,x-y+1,z1
crystal symmetry operation3_455-x+y-1,-x,z1
Buried area8380 Å2
ΔGint-59 kcal/mol
Surface area22870 Å2
MethodPISA
Unit cell
Length a, b, c (Å)67.260, 67.260, 79.800
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number150
Space group name H-MP321

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Components

#1: Protein Ethanolamine utilization protein eutL


Mass: 23875.928 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Strain: K-12 / Gene: b2439, eutL, JW2432, yffJ / Plasmid: pET22b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)Gold / References: UniProt: P76541
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 44 / 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: 2.18 Å3/Da / Density % sol: 43.64 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6
Details: 0.1M sodium/potassium phosphate, 2.5M sodium chloride, pH 6.0, 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: 0.97942 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Oct 21, 2008
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97942 Å / Relative weight: 1
ReflectionResolution: 2.3→90 Å / Num. obs: 9144 / % possible obs: 94.7 % / Redundancy: 9.5 % / Rmerge(I) obs: 0.167 / Net I/σ(I): 5.8
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsDiffraction-ID% possible all
2.3-2.389.50.576197.1
2.38-2.489.40.489196.5
2.48-2.599.50.423196.6
2.59-2.739.50.327196.2
2.73-2.99.50.25195.8
2.9-3.129.60.196195
3.12-3.449.50.148194.7
3.44-3.939.40.108194.1
3.93-4.959.20.075192.3
4.95-909.50.066189.6

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Phasing

PhasingMethod: molecular replacement
Phasing MRModel details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation4 Å58.25 Å
Translation4 Å58.25 Å

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
PHASER1.3.2phasing
REFMACrefinement
PDB_EXTRACT3.005data extraction
ADSCQuantumdata collection
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3I87

3i87


Resolution: 2.31→79.81 Å / Cor.coef. Fo:Fc: 0.905 / Cor.coef. Fo:Fc free: 0.867 / Occupancy max: 1 / Occupancy min: 0 / SU B: 15.743 / SU ML: 0.173 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.859 / ESU R Free: 0.297 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.24378 356 4.8 %RANDOM
Rwork0.20597 ---
obs0.20782 7091 77.52 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 10.967 Å2
Baniso -1Baniso -2Baniso -3
1-0.96 Å20.48 Å20 Å2
2--0.96 Å20 Å2
3----1.44 Å2
Refinement stepCycle: LAST / Resolution: 2.31→79.81 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1576 0 0 44 1620
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0221610
X-RAY DIFFRACTIONr_bond_other_d0.0020.021025
X-RAY DIFFRACTIONr_angle_refined_deg1.2751.9692205
X-RAY DIFFRACTIONr_angle_other_deg2.26732519
X-RAY DIFFRACTIONr_dihedral_angle_1_deg2.6525215
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.02724.42661
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.20215230
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.694158
X-RAY DIFFRACTIONr_chiral_restr0.0840.2261
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0211836
X-RAY DIFFRACTIONr_gen_planes_other0.0030.02303
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.96521081
X-RAY DIFFRACTIONr_mcbond_other0.1062433
X-RAY DIFFRACTIONr_mcangle_it1.59331728
X-RAY DIFFRACTIONr_scbond_it1.0982529
X-RAY DIFFRACTIONr_scangle_it1.7173477
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.306→2.366 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.329 10 -
Rwork0.223 148 -
obs--22.54 %
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)
10.84540.1282-0.152.28540.48470.4859-0.0191-0.0116-0.01140.05660.01480.02140.0557-0.050.00430.0139-0.0007-0.01380.02140.0170.1021-14.280912.605418.0941
21.2427-0.5939-0.20891.8962-0.28230.83240.0630.02980.1019-0.107-0.0404-0.0119-0.0298-0.0157-0.02260.0133-0.0018-0.01160.01530.00090.1092-16.973433.651817.3081
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A2 - 115
2X-RAY DIFFRACTION2A116 - 217

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