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- PDB-3i71: Ethanolamine Utilization Microcompartment Shell Subunit, EutK C-t... -

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Basic information

Entry
Database: PDB / ID: 3i71
TitleEthanolamine Utilization Microcompartment Shell Subunit, EutK C-terminal domain
ComponentsEthanolamine utilization protein eutK
KeywordsUNKNOWN FUNCTION / helix-turn-helix
Function / homology
Function and homology information


ethanolamine degradation polyhedral organelle / ethanolamine catabolic process / response to X-ray / structural molecule activity
Similarity search - Function
EutK-Ctail domain / Ethanolamine utilization protein EutK C-terminus / EutK-Ctail domain profile. / 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 ...EutK-Ctail domain / Ethanolamine utilization protein EutK C-terminus / EutK-Ctail domain profile. / 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 / Winged helix-like DNA-binding domain superfamily/Winged helix DNA-binding domain / Arc Repressor Mutant, subunit A / Winged helix-like DNA-binding domain superfamily / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
CITRATE ANION / Bacterial microcompartment shell protein EutK
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SIRAS / 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 1.2Nov 1, 2017Group: Refinement description / Category: software
Revision 1.3Feb 21, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / 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 eutK
B: Ethanolamine utilization protein eutK
hetero molecules


Theoretical massNumber of molelcules
Total (without water)15,8804
Polymers15,5022
Non-polymers3782
Water1,00956
1
A: Ethanolamine utilization protein eutK
B: Ethanolamine utilization protein eutK
hetero molecules

A: Ethanolamine utilization protein eutK
B: Ethanolamine utilization protein eutK
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,7608
Polymers31,0034
Non-polymers7564
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation10_554-y,-x,-z-1/61
Buried area7850 Å2
ΔGint-41 kcal/mol
Surface area13180 Å2
MethodPISA
2


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2900 Å2
ΔGint-8 kcal/mol
Surface area7620 Å2
MethodPISA
3
A: Ethanolamine utilization protein eutK
hetero molecules


Theoretical massNumber of molelcules
Total (without water)8,1293
Polymers7,7511
Non-polymers3782
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
4
B: Ethanolamine utilization protein eutK

B: Ethanolamine utilization protein eutK


Theoretical massNumber of molelcules
Total (without water)15,5022
Polymers15,5022
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation10_554-y,-x,-z-1/61
Buried area1800 Å2
ΔGint-20 kcal/mol
Surface area9160 Å2
MethodPISA
Unit cell
Length a, b, c (Å)65.345, 65.345, 146.772
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number178
Space group name H-MP6122

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Components

#1: Protein Ethanolamine utilization protein eutK


Mass: 7750.819 Da / Num. of mol.: 2 / Fragment: residues 108-166
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Strain: K-12 / Gene: b2438, eutK, JW2431, yffI / Plasmid: pET22b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)Gold / References: UniProt: P76540
#2: Chemical ChemComp-FLC / CITRATE ANION


Mass: 189.100 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H5O7
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 56 / 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: 2.92 Å3/Da / Density % sol: 57.84 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 5.4
Details: 0.1M sodium citrate, 20.4% PEG4000, 16% isopropanol, pH 5.4, 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: 0.9717 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Jun 7, 2009
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9717 Å / Relative weight: 1
ReflectionRedundancy: 20.8 % / Av σ(I) over netI: 40.55 / Number: 308327 / Rmerge(I) obs: 0.09 / Χ2: 1.03 / D res high: 2.35 Å / D res low: 80 Å / Num. obs: 14853 / % possible obs: 99.9
Diffraction reflection shell
Highest resolution (Å)Lowest resolution (Å)% possible obs (%)IDRmerge(I) obsChi squaredRedundancy
5.068099.410.0481.01721.9
4.025.0610010.0591.02222.1
3.514.0210010.0680.97921.1
3.193.5110010.0871.04420.8
2.963.1910010.121.05920.6
2.792.9610010.1571.04720.4
2.652.7910010.2221.03320.3
2.532.6510010.3091.04720.2
2.432.5310010.371.04520.1
2.352.4310010.481.02720.1
ReflectionResolution: 2.1→90 Å / Num. obs: 11489 / % possible obs: 99.9 % / Redundancy: 19.7 % / Rmerge(I) obs: 0.07 / Χ2: 1.031 / Net I/σ(I): 13.4
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
2.1-2.1820.30.32611130.9991100
2.18-2.2620.40.27411161.041100
2.26-2.3720.40.20710991.0561100
2.37-2.4920.40.16611151.0651100
2.49-2.6520.30.13311231.0371100
2.65-2.8520.20.10611371.0441100
2.85-3.14200.0911490.9921100
3.14-3.5919.60.07911481.0781100
3.59-4.5218.90.05811891.0451100
4.52-9017.40.04513000.959199.3

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Phasing

PhasingMethod: SIRAS
Phasing MADD res high: 2.35 Å / D res low: 20 Å / FOM : 0.396 / FOM acentric: 0.376 / FOM centric: 0.455 / Reflection: 6979 / Reflection acentric: 5227 / Reflection centric: 1752
Phasing MAD setR cullis acentric: 0.88 / R cullis centric: 0.93 / Highest resolution: 2.35 Å / Lowest resolution: 20 Å / Loc acentric: 15 / Loc centric: 24.4 / Power acentric: 1.43 / Power centric: 1.17 / Reflection acentric: 5227 / Reflection centric: 1752
Phasing MAD set shell

ID: 1

Resolution (Å)R cullis acentricR cullis centricLoc acentricLoc centricPower acentricPower centricReflection acentricReflection centric
10.32-201.091.4749.864.31.981.424193
6.95-10.321.361.1537.848.32.191.47142123
5.24-6.951.130.9428.434.92.171.64298170
4.21-5.240.84120.828.61.971.2510223
3.51-4.210.760.6917.722.41.451.1793274
3.02-3.510.80.7914.317.81.150.791131316
2.64-3.020.860.8210.112.70.890.661510381
2.35-2.640.920.9810.90.690.46802172
Phasing MAD set site
IDAtom type symbolB isoFract xFract yFract zOccupancy
1I-68.080.3610.7750.0360.243
2I-66.9470.3040.9260.0480.244
3I-73.0040.5781.0190.0690.213
4I-66.670.3230.9790.0060.24
5I-76.130.3691.1720.0930.201
6I-77.2210.1930.7790.0840.203
7I-79.3550.2430.6850.0370.193
8I-77.7710.4520.8480.1620.195
9I-250.5450.3950.50
10I-91.7490.590.8920.3720.149
11I-79.410.40.5050.1180.196
Phasing MAD shell
Resolution (Å)FOM FOM acentricFOM centricReflectionReflection acentricReflection centric
10.32-200.4250.4980.3941344193
6.95-10.320.5180.5790.449265142123
5.24-6.950.5430.5420.545468298170
4.21-5.240.5350.5540.492733510223
3.51-4.210.4970.4730.5641067793274
3.02-3.510.4030.3890.45414471131316
2.64-3.020.3110.2910.38918911510381
2.35-2.640.2280.2070.324974802172
Phasing dmMethod: Solvent flattening and Histogram matching / Reflection: 6959
Phasing dm shell
Resolution (Å)Delta phi finalFOM Reflection
6.28-10056.10.783505
4.92-6.2849.20.886506
4.28-4.9251.40.914501
3.86-4.2843.40.926509
3.57-3.8650.60.907501
3.35-3.57540.912501
3.17-3.3550.10.79512
3.03-3.1758.70.825505
2.91-3.0351.80.847502
2.81-2.9167.30.816503
2.71-2.8167.10.793502
2.63-2.7167.50.776511
2.35-2.6367.70.697901

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
MLPHAREphasing
DM6.1phasing
REFMACrefinement
PDB_EXTRACT3.005data extraction
ADSCQuantumdata collection
RefinementMethod to determine structure: SIRAS / Resolution: 2.1→44.81 Å / Cor.coef. Fo:Fc: 0.944 / Cor.coef. Fo:Fc free: 0.933 / WRfactor Rfree: 0.241 / WRfactor Rwork: 0.221 / Occupancy max: 1 / Occupancy min: 0.5 / FOM work R set: 0.848 / SU B: 7.588 / SU ML: 0.094 / SU R Cruickshank DPI: 0.164 / SU Rfree: 0.147 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.164 / ESU R Free: 0.146 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS; U VALUES: RESIDUAL ONLY
RfactorNum. reflection% reflectionSelection details
Rfree0.23 546 4.8 %RANDOM
Rwork0.206 ---
obs0.207 11420 99.76 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso max: 95.21 Å2 / Biso mean: 38.226 Å2 / Biso min: 15.01 Å2
Baniso -1Baniso -2Baniso -3
1-1.01 Å20.51 Å20 Å2
2--1.01 Å20 Å2
3----1.52 Å2
Refinement stepCycle: LAST / Resolution: 2.1→44.81 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms886 0 26 56 968
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.021924
X-RAY DIFFRACTIONr_bond_other_d0.0010.02658
X-RAY DIFFRACTIONr_angle_refined_deg1.4352.0031243
X-RAY DIFFRACTIONr_angle_other_deg0.81831582
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.5675112
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.28821.28239
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.65315162
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.4561512
X-RAY DIFFRACTIONr_chiral_restr0.0840.2136
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.021016
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02198
X-RAY DIFFRACTIONr_mcbond_it2.1381.5568
X-RAY DIFFRACTIONr_mcbond_other0.6581.5234
X-RAY DIFFRACTIONr_mcangle_it3.9062897
X-RAY DIFFRACTIONr_scbond_it5.3213356
X-RAY DIFFRACTIONr_scangle_it8.8344.5346
LS refinement shellResolution: 2.1→2.157 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.252 41 -
Rwork0.2 768 -
all-809 -
obs--99.14 %
Refinement TLS params.Method: refined / Origin x: 27.578 Å / Origin y: -11.1134 Å / Origin z: 6.1857 Å
111213212223313233
T0.0708 Å20.0398 Å20.0065 Å2-0.0399 Å20.0168 Å2--0.03 Å2
L0.6397 °2-0.0076 °20.3893 °2-1.3146 °2-0.3057 °2--1.8672 °2
S-0.0907 Å °-0.0321 Å °-0.0668 Å °0.1518 Å °0.1845 Å °0.0274 Å °-0.0372 Å °-0.1044 Å °-0.0938 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A109 - 165
2X-RAY DIFFRACTION1B108 - 165

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