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- PDB-3gfh: Crystal structure of EUTL shell protein of the bacterial ethanola... -

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Basic information

Entry
Database: PDB / ID: 3gfh
TitleCrystal structure of EUTL shell protein of the bacterial ethanolamine micrompartment
ComponentsEthanolamine utilization protein eutL
KeywordsSTRUCTURAL PROTEIN / bacterial mircocompartment / shell protein / ethanolamine
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 / BMC / CcmK-like superfamily / 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 / BMC / CcmK-like superfamily / 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: 2.2 Å
AuthorsSagermann, M. / Nikolakakis, K. / Ohtaki, A.
CitationJournal: 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
DepositionFeb 26, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 21, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Feb 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
Revision 1.3Apr 3, 2024Group: Refinement description / Category: pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Ethanolamine utilization protein eutL
B: Ethanolamine utilization protein eutL
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,6684
Polymers47,2672
Non-polymers4012
Water3,081171
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)71,5036
Polymers70,9013
Non-polymers6023
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_665-y+1,x-y+1,z1
crystal symmetry operation3_565-x+y,-x+1,z1
Buried area7310 Å2
ΔGint-47 kcal/mol
Surface area23250 Å2
MethodPISA
2
B: Ethanolamine utilization protein eutL
hetero molecules

B: Ethanolamine utilization protein eutL
hetero molecules

B: Ethanolamine utilization protein eutL
hetero molecules


Theoretical massNumber of molelcules
Total (without water)71,5036
Polymers70,9013
Non-polymers6023
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_655-y+1,x-y,z1
crystal symmetry operation3_665-x+y+1,-x+1,z1
Buried area7380 Å2
ΔGint-48 kcal/mol
Surface area23080 Å2
MethodPISA
Unit cell
Length a, b, c (Å)67.384, 67.384, 79.661
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number143
Space group name H-MP3

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Components

#1: Protein Ethanolamine utilization protein eutL


Mass: 23633.656 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Strain: K12 / Gene: b2439, EUT-L, eutL, JW2432, yffJ / Plasmid: pET101 / Production host: Escherichia coli (E. coli) / Strain (production host): K12 / References: UniProt: P76541
#2: Chemical ChemComp-HG / MERCURY (II) ION


Mass: 200.590 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Hg
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 171 / 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: 2.29 Å3/Da / Density % sol: 46.27 %
Crystal growTemperature: 298 K / pH: 6.5
Details: 2M Nacl, 100mM phosphate, MES buffer pH6.5, 5% PEG 400, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL9-1 / Wavelength: 0.97946
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Details: SI-MIRRORS
RadiationProtocol: 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, L10.575
11K, H, -L20.425
ReflectionResolution: 1.95→19.95 Å / Num. obs: 51500 / % possible obs: 85.8 % / Observed criterion σ(I): 0 / Biso Wilson estimate: 27.3 Å2 / Rmerge(I) obs: 0.08
Reflection shellResolution: 1.95→2.3 Å / Rmerge(I) obs: 0.278 / Mean I/σ(I) obs: 4.46 / % possible all: 74.3

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Processing

Software
NameVersionClassification
ADSCQuantumdata collection
SOLVEphasing
REFMAC5.5.0066refinement
ANDXDSdata reduction
ANDSCALEITdata scaling
RefinementMethod to determine structure: SAD
Starting model: MODEL WAS DERIVED FROM FITTING INTO A 3.5 A SAD DENSITY DERIVED FROM TWO MERCURY ATOMS.

Resolution: 2.2→19.65 Å / Cor.coef. Fo:Fc: 0.906 / Cor.coef. Fo:Fc free: 0.866 / SU B: 9.162 / SU ML: 0.228 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.034 / ESU R Free: 0.033 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: THE STRUCTURE WAS REFINED AGAINST TWINNED DATA AS PUBLISHED. The data is hemohedral twinning with twinning operators: (h,-h-k,-l) and corresponding twinned fractions: 0.575, 0.425. RESIDUES ...Details: THE STRUCTURE WAS REFINED AGAINST TWINNED DATA AS PUBLISHED. The data is hemohedral twinning with twinning operators: (h,-h-k,-l) and corresponding twinned fractions: 0.575, 0.425. RESIDUES 2-216 COULD BE FITTED RELIABLY INTO THE ELECTRON DENSITY MAP. HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.278 2944 7.8 %RANDOM
Rwork0.223 ---
obs0.223 34866 100 %-
all-41108 --
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: 19.34 Å2
Baniso -1Baniso -2Baniso -3
1--10.85 Å20 Å20 Å2
2---10.85 Å20 Å2
3---21.7 Å2
Refinement stepCycle: LAST / Resolution: 2.2→19.65 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3118 0 2 171 3291
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0210.0223200
X-RAY DIFFRACTIONr_bond_other_d0.0010.022944
X-RAY DIFFRACTIONr_angle_refined_deg2.2891.9694383
X-RAY DIFFRACTIONr_angle_other_deg0.87936820
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.135428
X-RAY DIFFRACTIONr_dihedral_angle_2_deg41.59424.333120
X-RAY DIFFRACTIONr_dihedral_angle_3_deg22.37215456
X-RAY DIFFRACTIONr_dihedral_angle_4_deg25.0121516
X-RAY DIFFRACTIONr_chiral_restr0.1160.2520
X-RAY DIFFRACTIONr_gen_planes_refined0.0120.0213646
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02604
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_it0.9351.52150
X-RAY DIFFRACTIONr_mcbond_other0.1881.5862
X-RAY DIFFRACTIONr_mcangle_it1.60623437
X-RAY DIFFRACTIONr_scbond_it2.63231050
X-RAY DIFFRACTIONr_scangle_it4.1624.5946
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.2→2.26 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.334 215 -
Rwork0.265 2503 -
obs--100 %

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