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- PDB-3i96: Ethanolamine Utilization Microcompartment Shell Subunit, EutS -

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Basic information

Entry
Database: PDB / ID: 3i96
TitleEthanolamine Utilization Microcompartment Shell Subunit, EutS
ComponentsEthanolamine utilization protein eutS
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
Bacterial microcompartment shell protein EutS/PduU/CutR / 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 EutS
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.65 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 10, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 12, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Refinement description / Version format compliance
Revision 1.2Nov 1, 2017Group: Refinement description / Category: software
Revision 1.3Sep 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_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_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 eutS
B: Ethanolamine utilization protein eutS
C: Ethanolamine utilization protein eutS
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,27414
Polymers38,1983
Non-polymers1,07611
Water4,918273
1
A: Ethanolamine utilization protein eutS
B: Ethanolamine utilization protein eutS
C: Ethanolamine utilization protein eutS
hetero molecules

A: Ethanolamine utilization protein eutS
B: Ethanolamine utilization protein eutS
C: Ethanolamine utilization protein eutS
hetero molecules


Theoretical massNumber of molelcules
Total (without water)78,54728
Polymers76,3966
Non-polymers2,15122
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation6_555-x,-x+y,-z+1/31
Buried area16370 Å2
ΔGint-107 kcal/mol
Surface area24590 Å2
MethodPISA
2


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5180 Å2
ΔGint-38 kcal/mol
Surface area15300 Å2
MethodPISA
Unit cell
Length a, b, c (Å)60.455, 60.455, 191.458
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number152
Space group name H-MP3121

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Components

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Protein , 1 types, 3 molecules ABC

#1: Protein Ethanolamine utilization protein eutS


Mass: 12732.680 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Strain: K-12 / Gene: b2462, eutS, JW2446, ypfE / Plasmid: pET22b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)Gold / References: UniProt: P63746

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Non-polymers , 5 types, 284 molecules

#2: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#3: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C3H8O3
#4: Chemical ChemComp-NHE / 2-[N-CYCLOHEXYLAMINO]ETHANE SULFONIC ACID / N-CYCLOHEXYLTAURINE / CHES


Mass: 207.290 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H17NO3S / Comment: pH buffer*YM
#5: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 273 / 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: 2.64 Å3/Da / Density % sol: 53.48 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 9.5
Details: 0.1M CHES, 1.22M ammonium sulfate, 0.15M sodium chloride, pH 9.5, 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: 0.97919 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Nov 26, 2008
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97919 Å / Relative weight: 1
ReflectionResolution: 1.65→55 Å / Num. obs: 49926 / % possible obs: 99.9 % / Redundancy: 13.1 % / Rmerge(I) obs: 0.067 / Χ2: 1.262 / Net I/σ(I): 14.1
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
1.65-1.7113.30.53148981.011100
1.71-1.7813.30.3949511.0581100
1.78-1.8613.30.25348951.0891100
1.86-1.9613.30.16749181.251100
1.96-2.0813.30.12149681.3731100
2.08-2.2413.30.09549541.5191100
2.24-2.4613.20.08249501.6121100
2.46-2.8213.20.08450271.6181100
2.82-3.5512.90.06451041.2121100
3.55-5512.30.04552610.864198.7

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Phasing

PhasingMethod: molecular replacement
Phasing MRModel details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation2.5 Å63.8 Å
Translation2.5 Å63.8 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: 3CGI

3cgi


Resolution: 1.65→40.49 Å / Cor.coef. Fo:Fc: 0.969 / Cor.coef. Fo:Fc free: 0.959 / WRfactor Rfree: 0.184 / WRfactor Rwork: 0.163 / Occupancy max: 1 / Occupancy min: 0.38 / FOM work R set: 0.902 / SU B: 2.823 / SU ML: 0.045 / SU R Cruickshank DPI: 0.076 / SU Rfree: 0.076 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.077 / ESU R Free: 0.076 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS; U VALUES: RESIDUAL ONLY
RfactorNum. reflection% reflectionSelection details
Rfree0.185 2546 5.1 %RANDOM
Rwork0.162 ---
obs0.163 49844 99.85 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso max: 79.61 Å2 / Biso mean: 18.956 Å2 / Biso min: 2 Å2
Baniso -1Baniso -2Baniso -3
1-0.9 Å20.45 Å20 Å2
2--0.9 Å20 Å2
3----1.35 Å2
Refinement stepCycle: LAST / Resolution: 1.65→40.49 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2410 0 67 273 2750
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0222619
X-RAY DIFFRACTIONr_bond_other_d0.0010.021756
X-RAY DIFFRACTIONr_angle_refined_deg1.4012.0073557
X-RAY DIFFRACTIONr_angle_other_deg0.85234361
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.0285363
X-RAY DIFFRACTIONr_dihedral_angle_2_deg30.72624.65988
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.915454
X-RAY DIFFRACTIONr_dihedral_angle_4_deg9.847159
X-RAY DIFFRACTIONr_chiral_restr0.0820.2426
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0212874
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02479
X-RAY DIFFRACTIONr_mcbond_it1.88321674
X-RAY DIFFRACTIONr_mcbond_other0.5542702
X-RAY DIFFRACTIONr_mcangle_it3.07632693
X-RAY DIFFRACTIONr_scbond_it2.9982945
X-RAY DIFFRACTIONr_scangle_it4.7473845
LS refinement shellResolution: 1.65→1.693 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.266 183 -
Rwork0.204 3444 -
all-3627 -
obs--99.94 %
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)
10.8564-0.22460.79850.4464-0.21341.8644-0.00730.09880.0149-0.07260.048-0.02490.00090.2979-0.04070.0731-0.0432-0.00380.0794-0.00230.0459-3.601919.18512.4617
20.60460.0350.48010.8335-0.46652.2363-0.0778-0.02890.0764-0.0160.0469-0.0021-0.22140.18520.03090.0338-0.0326-0.00530.0591-0.01490.03631.957325.124331.3848
31.34660.39840.8190.26610.48291.35120.02970.0061-0.1046-0.03350.0529-0.05910.11320.0679-0.08260.1105-0.0412-0.02570.03020.00440.0688-18.03284.688411.3403
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A6 - 114
2X-RAY DIFFRACTION2B2 - 111
3X-RAY DIFFRACTION3C5 - 113

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