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

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Basic information

Entry
Database: PDB / ID: 3mpw
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
PHOSPHATE ION / Bacterial microcompartment shell protein EutM
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.7 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 1.0May 11, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Sep 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
G: Ethanolamine utilization protein eutM
H: Ethanolamine utilization protein eutM
I: Ethanolamine utilization protein eutM
J: Ethanolamine utilization protein eutM
K: Ethanolamine utilization protein eutM
L: Ethanolamine utilization protein eutM
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)129,80726
Polymers128,47712
Non-polymers1,33014
Water00
1
G: Ethanolamine utilization protein eutM
H: Ethanolamine utilization protein eutM
I: Ethanolamine utilization protein eutM
J: Ethanolamine utilization protein eutM
K: Ethanolamine utilization protein eutM
L: Ethanolamine utilization protein eutM
hetero molecules


Theoretical massNumber of molelcules
Total (without water)64,90313
Polymers64,2396
Non-polymers6657
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area12490 Å2
ΔGint-131 kcal/mol
Surface area21020 Å2
MethodPISA
2
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)64,90313
Polymers64,2396
Non-polymers6657
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area12560 Å2
ΔGint-129 kcal/mol
Surface area21990 Å2
MethodPISA
Unit cell
Length a, b, c (Å)69.949, 149.069, 70.089
Angle α, β, γ (deg.)90.00, 120.01, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
Ethanolamine utilization protein eutM


Mass: 10706.420 Da / Num. of mol.: 12
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Strain: K12 / Gene: b2457, cchA, eutM, JW2441, yffZ / Plasmid: TOPO101 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 / References: UniProt: P0ABF4
#2: Chemical
ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 14 / Source method: obtained synthetically / Formula: PO4

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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: 2.46 Å3/Da / Density % sol: 50.01 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 100 MM SODIUM DIHYDROGEN PHOSPHATE, 100 MM POTASSIUMDIHYDROGENPHOSPHATE, 2 M SODIUM CHLORIDE, pH 6.5, 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 MIRROR / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97946 Å / Relative weight: 1
ReflectionResolution: 2.7→46.98 Å / Num. obs: 25180 / % possible obs: 84.1 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 2.1 % / Rmerge(I) obs: 0.032 / Net I/σ(I): 19.31

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Processing

SoftwareName: REFMAC / Version: 5.5.0066 / Classification: refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 2A1B (residues 2-90)

2a1b


Resolution: 2.7→46.98 Å / Cor.coef. Fo:Fc: 0.914 / Cor.coef. Fo:Fc free: 0.838 / SU B: 20.657 / SU ML: 0.423 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R Free: 0.518 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.33641 1382 5.2 %RANDOM
Rwork0.24783 ---
obs0.2525 25180 100 %-
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: 33.121 Å2
Baniso -1Baniso -2Baniso -3
1--4.19 Å20 Å2-2.29 Å2
2--7.89 Å20 Å2
3----5.98 Å2
Refinement stepCycle: LAST / Resolution: 2.7→46.98 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7844 0 70 0 7914
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0227968
X-RAY DIFFRACTIONr_bond_other_d00.027933
X-RAY DIFFRACTIONr_angle_refined_deg1.4541.99310753
X-RAY DIFFRACTIONr_angle_other_deg0.645318305
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.91551094
X-RAY DIFFRACTIONr_dihedral_angle_2_deg30.57223.571252
X-RAY DIFFRACTIONr_dihedral_angle_3_deg23.132151381
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.5051560
X-RAY DIFFRACTIONr_chiral_restr0.0740.21309
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.028858
X-RAY DIFFRACTIONr_gen_planes_other00.021418
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_it0.4081.55418
X-RAY DIFFRACTIONr_mcbond_other0.0561.52336
X-RAY DIFFRACTIONr_mcangle_it0.75928560
X-RAY DIFFRACTIONr_scbond_it0.95132550
X-RAY DIFFRACTIONr_scangle_it1.6944.52193
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.7→2.77 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.409 109 -
Rwork0.344 1796 -
obs--100 %

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