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- PDB-3mpy: Structure of EUTM in 2-D protein membrane -

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Basic information

Entry
Database: PDB / ID: 3mpy
TitleStructure of EUTM in 2-D protein membrane
ComponentsEthanolamine utilization protein eutM
KeywordsMEMBRANE PROTEIN / Bacterial microcompartment / shell protein / ethanolamine ammonia lyase / carboxysome
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 / Resolution: 2 Å
AuthorsSagermann, M. / Takenoya, M. / Nikolakakis, K.
Citation
Journal: J.Bacteriol. / Year: 2010
Title: Crystallographic insights into the pore structures and mechanisms of the EutL and EutM shell proteins of the ethanolamine-utilizing microcompartment of Escherichia coli.
Authors: Takenoya, M. / Nikolakakis, K. / Sagermann, M.
#1: Journal: Proc.Natl.Acad.Sci.USA / Year: 2009
Title: Crystal structure of the EutL shell protein of the ethanolamine ammonia lyase microcompartment.
Authors: Sagermann, M. / Ohtaki, A. / Nikolakakis, K.
History
DepositionApr 27, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 22, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Jun 20, 2012Group: Database references
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 / pdbx_struct_special_symmetry / 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

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Assembly

Deposited unit
A: Ethanolamine utilization protein eutM
hetero molecules


Theoretical massNumber of molelcules
Total (without water)10,8993
Polymers10,7061
Non-polymers1922
Water724
1
A: Ethanolamine utilization protein eutM
hetero molecules
x 6


Theoretical massNumber of molelcules
Total (without water)65,39118
Polymers64,2396
Non-polymers1,15312
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-y,x-y,z1
crystal symmetry operation3_555-x+y,-x,z1
crystal symmetry operation4_555-x,-y,z1
crystal symmetry operation5_555y,-x+y,z1
crystal symmetry operation6_555x-y,x,z1
Buried area13250 Å2
ΔGint-256 kcal/mol
Surface area21660 Å2
MethodPISA
Unit cell
Length a, b, c (Å)69.164, 69.164, 28.950
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number168
Space group name H-MP6
Components on special symmetry positions
IDModelComponents
11A-104-

SO4

21A-200-

SO4

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Components

#1: Protein Ethanolamine utilization protein eutM


Mass: 10706.420 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Strain: K12 / Gene: b2457, cchA, eutM, JW2441, yffZ / Plasmid: pET101 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21-AI / References: UniProt: P0ABF4
#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 4 / 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: 1.87 Å3/Da / Density % sol: 34.12 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 4.6
Details: 2 M ammoniumsulfate, 100 mM sodium acetate, pH 4.6, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL7-1 / Wavelength: 0.97946 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jun 11, 2009 / Details: Rh coated flat mirror.
RadiationMonochromator: SI 111 (side scattering I-beam bent single crystal, asymmetric cut 4.9650 deg)
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97946 Å / Relative weight: 1
Reflection twin
Crystal-IDIDOperatorDomain-IDFraction
11H, K, L10.815
11-H-K, K, -L20.185
ReflectionResolution: 2→17.3 Å / Num. obs: 4477 / % possible obs: 81.1 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 11.1 % / Rsym value: 0.078 / Net I/σ(I): 20.1

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Processing

Software
NameVersionClassification
ADSCQuantumdata collection
MOLREPphasing
REFMAC5.5refinement
XDSdata reduction
XSCALEdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 2A1B (RESIDUES 2-90)

2a1b


Resolution: 2→17.29 Å / Cor.coef. Fo:Fc: 0.938 / Cor.coef. Fo:Fc free: 0.904 / SU B: 11.144 / SU ML: 0.242 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.067 / ESU R Free: 0.051 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. DATA SET WAS TWINNED AND REFINEMENT WAS CARRIED OUT ACCORDINGLY WITH THE PROGRAM REFMAC. OCCUPANCIES OF THE SULFATES ARE LESS THAN ONE DUE ...Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. DATA SET WAS TWINNED AND REFINEMENT WAS CARRIED OUT ACCORDINGLY WITH THE PROGRAM REFMAC. OCCUPANCIES OF THE SULFATES ARE LESS THAN ONE DUE TO THEIR SPECIAL POSITIONS. THE N-TERMINAL METHIONINE AND THE HIS-TAGS WERE NOT VISIBLE IN THE DENSITY.
RfactorNum. reflection% reflectionSelection details
Rfree0.28277 192 4.2 %RANDOM
Rwork0.22415 ---
obs0.22641 4392 83.19 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 40.223 Å2
Baniso -1Baniso -2Baniso -3
1--1.11 Å20 Å20 Å2
2---1.11 Å20 Å2
3---2.22 Å2
Refinement stepCycle: LAST / Resolution: 2→17.29 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms678 0 10 4 692
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0260.022691
X-RAY DIFFRACTIONr_bond_other_d0.0010.02680
X-RAY DIFFRACTIONr_angle_refined_deg2.4592.001933
X-RAY DIFFRACTIONr_angle_other_deg0.88431571
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.895595
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.29924.09122
X-RAY DIFFRACTIONr_dihedral_angle_3_deg23.73815119
X-RAY DIFFRACTIONr_dihedral_angle_4_deg8.199155
X-RAY DIFFRACTIONr_chiral_restr0.1290.2113
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.02768
X-RAY DIFFRACTIONr_gen_planes_other00.02121
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_it1.1531.5470
X-RAY DIFFRACTIONr_mcbond_other0.2341.5203
X-RAY DIFFRACTIONr_mcangle_it2.0432742
X-RAY DIFFRACTIONr_scbond_it3.0723221
X-RAY DIFFRACTIONr_scangle_it5.1784.5191
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2→2.051 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.265 16 -
Rwork0.221 394 -
obs--100 %

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