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- PDB-3i6p: Ethanolamine Utilization Microcompartment Shell Subunit, EutM -

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Basic information

Entry
Database: PDB / ID: 3i6p
TitleEthanolamine Utilization Microcompartment Shell Subunit, EutM
ComponentsEthanolamine utilization protein eutM
KeywordsSTRUCTURAL PROTEIN
Function / homology
Function and homology information


ethanolamine degradation polyhedral organelle / ethanolamine catabolic process / protein hexamerization / structural molecule activity / identical protein binding
Similarity search - Function
BMC (bacterial microcompartment) domain / Bacterial microcompartments protein, conserved site / Bacterial microcompartment (BMC) domain signature. / CcmK/CsoS1, bacterial microcompartment domain / : / Bacterial microcompartment (BMC) domain profile. / BMC domain / Bacterial microcompartment domain / BMC / CcmK-like superfamily ...BMC (bacterial microcompartment) domain / Bacterial microcompartments protein, conserved site / Bacterial microcompartment (BMC) domain signature. / CcmK/CsoS1, bacterial microcompartment domain / : / Bacterial microcompartment (BMC) domain profile. / BMC domain / Bacterial microcompartment domain / BMC / CcmK-like superfamily / Alpha-Beta Plaits / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Bacterial microcompartment shell protein EutM
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.1 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 7, 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 2.0Nov 1, 2017Group: Advisory / Atomic model / Refinement description / Category: atom_site / pdbx_distant_solvent_atoms / software / Item: _atom_site.occupancy
Revision 2.1Sep 6, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ncs_dom_lim / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Ethanolamine utilization protein eutM
B: Ethanolamine utilization protein eutM
C: Ethanolamine utilization protein eutM
D: Ethanolamine utilization protein eutM
E: Ethanolamine utilization protein eutM
F: Ethanolamine utilization protein eutM
hetero molecules


Theoretical massNumber of molelcules
Total (without water)65,9809
Polymers65,6926
Non-polymers2883
Water3,063170
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area11080 Å2
ΔGint-83 kcal/mol
Surface area18850 Å2
MethodPISA
Unit cell
Length a, b, c (Å)99.480, 99.480, 113.870
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number94
Space group name H-MP42212
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21D
12B
22E
13C
23F

NCS domain segments:

Refine code: 3

Dom-IDComponent-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
111METMETLEULEUAA1 - 901 - 90
211METMETLEULEUDD1 - 901 - 90
112METMETALAALABB1 - 251 - 25
212METMETALAALAEE1 - 251 - 25
122LYSLYSALAALABB29 - 6229 - 62
222LYSLYSALAALAEE29 - 6229 - 62
132ILEILEILEILEBB66 - 7566 - 75
232ILEILEILEILEEE66 - 7566 - 75
142HISHISLEULEUBB79 - 9079 - 90
242HISHISLEULEUEE79 - 9079 - 90
113METMETALAALACC1 - 251 - 25
213METMETALAALAFF1 - 251 - 25
123LYSLYSALAALACC29 - 6229 - 62
223LYSLYSALAALAFF29 - 6229 - 62
133ILEILEILEILECC66 - 7566 - 75
233ILEILEILEILEFF66 - 7566 - 75
143HISHISLEULEUCC79 - 9079 - 90
243HISHISLEULEUFF79 - 9079 - 90

NCS ensembles :
ID
1
2
3

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Components

#1: Protein
Ethanolamine utilization protein eutM


Mass: 10948.691 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Strain: K-12 / Gene: b2457, cchA, eutM, JW2441, yffZ / Plasmid: pET22b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)Gold / References: UniProt: P0ABF4
#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 170 / 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: 2.14 Å3/Da / Density % sol: 42.64 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6
Details: 0.05M MES, 0.015M magnesium sulfate, 8% PEG 4000, 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: 0.97949 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Oct 7, 2008
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97949 Å / Relative weight: 1
ReflectionResolution: 2.1→90 Å / Num. obs: 34162 / % possible obs: 99.7 % / Redundancy: 7.6 % / Rmerge(I) obs: 0.097 / Χ2: 1.04 / Net I/σ(I): 11
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
2.1-2.187.60.49333620.9571100
2.18-2.267.60.47733581.3131100
2.26-2.377.70.33433671.122199.9
2.37-2.497.70.20433821.0231100
2.49-2.657.70.17133741.008199.9
2.65-2.857.70.13534011.015199.8
2.85-3.147.60.11534021.007199.9
3.14-3.597.60.09534291.004199.8
3.59-4.527.50.08734711.011199.5
4.52-907.10.06336160.945198.2

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Phasing

PhasingMethod: molecular replacement
Phasing MRModel details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation5 Å74.92 Å
Translation5 Å74.92 Å

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
PHASER1.3.2phasing
REFMACrefinement
PDB_EXTRACT3.005data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3BN4

3bn4


Resolution: 2.1→74.95 Å / Cor.coef. Fo:Fc: 0.962 / Cor.coef. Fo:Fc free: 0.948 / WRfactor Rfree: 0.28 / WRfactor Rwork: 0.228 / Occupancy max: 1 / FOM work R set: 0.694 / SU B: 14.342 / SU ML: 0.179 / SU R Cruickshank DPI: 0.246 / SU Rfree: 0.205 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.246 / ESU R Free: 0.204 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.258 1639 5.1 %RANDOM
Rwork0.214 ---
obs0.216 32287 94.69 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso max: 101.61 Å2 / Biso mean: 38.661 Å2 / Biso min: 19.19 Å2
Baniso -1Baniso -2Baniso -3
1-0.28 Å20 Å20 Å2
2--0.28 Å20 Å2
3----0.55 Å2
Refinement stepCycle: LAST / Resolution: 2.1→74.95 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3822 0 15 170 4007
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0223921
X-RAY DIFFRACTIONr_bond_other_d0.0020.022619
X-RAY DIFFRACTIONr_angle_refined_deg1.3461.9925300
X-RAY DIFFRACTIONr_angle_other_deg0.91436450
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.9015551
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.4723.171123
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.26815693
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.4611533
X-RAY DIFFRACTIONr_chiral_restr0.0650.2652
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.024382
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02708
X-RAY DIFFRACTIONr_mcbond_it2.14922673
X-RAY DIFFRACTIONr_mcbond_other0.42321131
X-RAY DIFFRACTIONr_mcangle_it3.3934236
X-RAY DIFFRACTIONr_scbond_it2.62421248
X-RAY DIFFRACTIONr_scangle_it4.17431055
Refine LS restraints NCS

Dom-ID: 1 / Refine-ID: X-RAY DIFFRACTION

Ens-IDAuth asym-IDNumberTypeRms dev position (Å)Weight position
1A525TIGHT POSITIONAL0.020.05
1A543LOOSE POSITIONAL0.025
1A525TIGHT THERMAL0.140.5
1A543LOOSE THERMAL0.1110
2B469TIGHT POSITIONAL0.030.05
2B440LOOSE POSITIONAL0.035
2B469TIGHT THERMAL0.170.5
2B440LOOSE THERMAL0.1310
3C471TIGHT POSITIONAL0.020.05
3C448LOOSE POSITIONAL0.035
3C471TIGHT THERMAL0.140.5
3C448LOOSE THERMAL0.1310
LS refinement shellResolution: 2.1→2.153 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.357 40 -
Rwork0.293 919 -
all-959 -
obs--38.86 %
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)
11.0585-0.77820.18180.956-0.13552.0473-0.014-0.1042-0.1387-0.1165-0.0420.13380.0457-0.12590.056-0.13520.0452-0.0071-0.13010.0007-0.050716.1702-33.656126.9152
21.7409-1.5570.40651.5515-0.40290.79940.0856-0.0398-0.2185-0.158-0.04220.19650.0449-0.0388-0.0434-0.1254-0.005-0.0101-0.1207-0.0005-0.019415.9359-33.914726.937
31.5156-1.184-0.43141.1440.49851.39940.0953-0.1314-0.1361-0.09970.09260.1140.09850.053-0.1878-0.08720.006-0.0174-0.13860.0271-0.044315.8363-33.958826.9631
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 90
2X-RAY DIFFRACTION1D1 - 90
3X-RAY DIFFRACTION2B1 - 90
4X-RAY DIFFRACTION2E1 - 90
5X-RAY DIFFRACTION3C1 - 90
6X-RAY DIFFRACTION3F1 - 90

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