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- PDB-3i87: Ethanolamine Utilization Microcompartment Shell Subunit, EutL Ope... -

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Basic information

Entry
Database: PDB / ID: 3i87
TitleEthanolamine Utilization Microcompartment Shell Subunit, EutL Open 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 / SAD / Resolution: 2.3 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 1.3Feb 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 eutL
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,9112
Polymers23,8761
Non-polymers351
Water91951
1
A: Ethanolamine utilization protein eutL
hetero molecules

A: Ethanolamine utilization protein eutL
hetero molecules

A: Ethanolamine utilization protein eutL
hetero molecules


Theoretical massNumber of molelcules
Total (without water)71,7346
Polymers71,6283
Non-polymers1063
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 area6400 Å2
ΔGint-40 kcal/mol
Surface area24820 Å2
MethodPISA
Unit cell
Length a, b, c (Å)67.799, 67.799, 80.520
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number150
Space group name H-MP321
Components on special symmetry positions
IDModelComponents
11A-261-

HOH

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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: Chemical ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 51 / 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: 2.24 Å3/Da / Density % sol: 45.03 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6
Details: 0.1M sodium/potassium phosphate, 2.2M 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: 0.9792 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Mar 29, 2009
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionRedundancy: 6.3 % / Av σ(I) over netI: 14.11 / Number: 88176 / Rmerge(I) obs: 0.119 / Χ2: 1.07 / D res high: 2.5 Å / D res low: 90 Å / Num. obs: 14100 / % possible obs: 100
Diffraction reflection shell
Highest resolution (Å)Lowest resolution (Å)% possible obs (%)IDRmerge(I) obsChi squaredRedundancy
5.399099.610.0641.0546.4
4.275.3910010.0611.0586.1
3.734.2710010.0810.9736.2
3.393.7310010.1131.1096.3
3.153.3910010.1461.1146.2
2.963.1510010.191.0576.3
2.822.9610010.2481.0716.3
2.692.8210010.3261.0926.3
2.592.6910010.3941.0676.3
2.52.5910010.4711.0736.2
ReflectionResolution: 2.3→90 Å / Num. obs: 8975 / % possible obs: 90.9 % / Redundancy: 6 % / Rmerge(I) obs: 0.131 / Χ2: 1.06 / Net I/σ(I): 7.5
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
2.3-2.385.90.4939121.217193.6
2.38-2.4860.3988901.101193.2
2.48-2.596.10.3519031.058192.5
2.59-2.7360.2489071.025192.8
2.73-2.960.1898951.099192.1
2.9-3.126.10.148820.966191.3
3.12-3.446.10.1048931.059190.8
3.44-3.936.10.098911.034190.2
3.93-4.956.10.0768951.063188.4
4.95-9060.0489070.982184.7

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Phasing

PhasingMethod: SAD
Phasing MADD res high: 2.5 Å / D res low: 19.97 Å / FOM : 0.259 / FOM acentric: 0.266 / FOM centric: 0.22 / Reflection: 7608 / Reflection acentric: 6455 / Reflection centric: 1153
Phasing MAD set

Highest resolution: 2.5 Å / Lowest resolution: 19.97 Å

IDR cullis acentricR cullis centricLoc acentricLoc centricPower acentricPower centricReflection acentricReflection centric
11.921000064551153
20.970.9313.119.10.470.3563321144
Phasing MAD set shell
IDResolution (Å)R cullis acentricR cullis centricLoc acentricLoc centricPower acentricPower centricReflection acentricReflection centric
110.66-19.971.33100005549
17.27-10.661.3210.100016072
15.52-7.272.2410.100032499
14.45-5.521.3610000529132
13.72-4.451.3110000808160
13.2-3.721.78100001127188
12.81-3.22.88100001518212
12.5-2.817.01100001934241
210.66-19.970.950.8216.322.50.970.865549
27.27-10.660.930.851522.50.990.6916072
25.52-7.270.850.8313.317.70.980.6732499
24.45-5.520.930.8914.319.30.730.45528132
23.72-4.450.970.9616.422.10.510.29807160
23.2-3.720.970.9713.920.60.440.241124188
22.81-3.20.980.9812.218.60.370.21508211
22.5-2.810.990.9911.414.80.270.181826233
Phasing MAD set site
IDAtom type symbolB isoFract xFract yFract zOccupancy
1Hg43.6280.5960.1510.290
2Hg45.0580.5950.1510.290.107
Phasing MAD shell
Resolution (Å)FOM FOM acentricFOM centricReflectionReflection acentricReflection centric
10.66-19.970.5780.6220.5281045549
7.27-10.660.5350.5820.43223216072
5.52-7.270.5540.5930.42642332499
4.45-5.520.4520.4860.318661529132
3.72-4.450.3360.3630.2968808160
3.2-3.720.2660.280.18613151127188
2.81-3.20.1890.1970.13217301518212
2.5-2.810.1140.1190.07521751934241
Phasing dmMethod: Solvent flattening and Histogram matching / Reflection: 7608
Phasing dm shell
Resolution (Å)Delta phi finalFOM Reflection
6.37-10056.40.738503
5.01-6.3756.70.786502
4.35-5.0153.20.777506
3.95-4.3560.40.711504
3.66-3.9561.20.689501
3.43-3.6673.40.501520
3.25-3.4375.40.522511
3.11-3.2571.10.471504
2.98-3.1177.30.545508
2.88-2.9877.70.46506
2.78-2.8880.60.539503
2.7-2.7878.40.38506
2.63-2.780.20.447502
2.57-2.6383.10.373504
2.5-2.5779.80.393528

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
MLPHAREphasing
DM6phasing
REFMACrefinement
PDB_EXTRACT3.005data extraction
ADSCQuantumdata collection
RefinementMethod to determine structure: SAD / Resolution: 2.3→80.58 Å / Cor.coef. Fo:Fc: 0.942 / Cor.coef. Fo:Fc free: 0.9 / WRfactor Rfree: 0.231 / WRfactor Rwork: 0.183 / Occupancy max: 1 / Occupancy min: 0.4 / FOM work R set: 0.843 / SU B: 14.222 / SU ML: 0.156 / SU R Cruickshank DPI: 0.382 / SU Rfree: 0.243 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.382 / ESU R Free: 0.243 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS; U VALUES: RESIDUAL ONLY
RfactorNum. reflection% reflectionSelection details
Rfree0.234 435 4.9 %RANDOM
Rwork0.188 ---
obs0.19 8966 90.68 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso max: 56.14 Å2 / Biso mean: 20.198 Å2 / Biso min: 2 Å2
Baniso -1Baniso -2Baniso -3
1--1.98 Å2-0.99 Å20 Å2
2---1.98 Å20 Å2
3---2.97 Å2
Refinement stepCycle: LAST / Resolution: 2.3→80.58 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1517 0 1 51 1569
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0060.0221555
X-RAY DIFFRACTIONr_bond_other_d0.0010.02992
X-RAY DIFFRACTIONr_angle_refined_deg0.8731.9672128
X-RAY DIFFRACTIONr_angle_other_deg0.78632440
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.9645208
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.10724.57659
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.95215224
X-RAY DIFFRACTIONr_dihedral_angle_4_deg23.653158
X-RAY DIFFRACTIONr_chiral_restr0.0530.2255
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.0211760
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02287
X-RAY DIFFRACTIONr_mcbond_it1.04821047
X-RAY DIFFRACTIONr_mcbond_other0.1572419
X-RAY DIFFRACTIONr_mcangle_it1.83331673
X-RAY DIFFRACTIONr_scbond_it1.1312508
X-RAY DIFFRACTIONr_scangle_it1.8693454
LS refinement shellResolution: 2.3→2.362 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.314 37 -
Rwork0.228 618 -
all-655 -
obs--91.99 %
Refinement TLS params.Method: refined / Origin x: -15.2049 Å / Origin y: 23.2503 Å / Origin z: 17.8471 Å
111213212223313233
T0.0049 Å20.001 Å2-0.0078 Å2-0.0293 Å20.004 Å2--0.0255 Å2
L0.3498 °2-0.3583 °2-0.0885 °2-2.5156 °20.5042 °2--0.3849 °2
S-0.0341 Å °-0.0313 Å °0.0179 Å °0.0286 Å °0.0199 Å °-0.0182 Å °0.0009 Å °-0.0405 Å °0.0143 Å °

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