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- PDB-3mpv: Structure of EUTL in the zinc-induced open form -

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Basic information

Entry
Database: PDB / ID: 3mpv
TitleStructure of EUTL in the zinc-induced open form
ComponentsEthanolamine utilization protein eutL
KeywordsMEMBRANE PROTEIN / shell protein / bacterial microcompartment / ethanolamine / carboxysome
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
BETA-MERCAPTOETHANOL / Bacterial microcompartment shell protein EutL
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.6 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 / struct_conn / 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_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _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
B: Ethanolamine utilization protein eutL
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,6728
Polymers47,2672
Non-polymers4056
Water23413
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)71,72415
Polymers70,9013
Non-polymers82312
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_765-y+2,x-y+1,z1
crystal symmetry operation3_675-x+y+1,-x+2,z1
Buried area3740 Å2
ΔGint-428 kcal/mol
Surface area26840 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)71,2939
Polymers70,9013
Non-polymers3926
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_765-y+2,x-y+1,z1
crystal symmetry operation3_675-x+y+1,-x+2,z1
Buried area2090 Å2
ΔGint-215 kcal/mol
Surface area28120 Å2
MethodPISA
Unit cell
Length a, b, c (Å)67.415, 67.415, 79.604
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, eutL, JW2432, yffJ / Plasmid: TOPO101 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 / References: UniProt: P76541
#2: Chemical ChemComp-BME / BETA-MERCAPTOETHANOL


Mass: 78.133 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6OS
#3: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: Zn
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 13 / 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: 2.21 Å3/Da / Density % sol: 44.33 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 2 M NaCl, 100 mM phosphate, 100 mM MES buffer, 5 % PEG 400, 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: 0.979464 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Apr 1, 2009 / Details: Si III mirror
RadiationMonochromator: SI 111 bend crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979464 Å / Relative weight: 1
Reflection twin
Crystal-IDIDOperatorDomain-IDFraction
11H, K, L10.55
11K, H, -L20.45
ReflectionResolution: 2.6→58.43 Å / Num. obs: 11274 / % possible obs: 98.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 2.8 % / Rmerge(I) obs: 0.117 / Net I/σ(I): 1.9

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Processing

Software
NameVersionClassification
ADSCQuantumdata collection
MOLREPphasing
REFMAC5.5refinement
MOSFLMdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 3GFH

3gfh


Resolution: 2.6→58.38 Å / Cor.coef. Fo:Fc: 0.904 / Cor.coef. Fo:Fc free: 0.85 / SU B: 14.419 / SU ML: 0.291 / Cross valid method: THROUGHOUT / ESU R Free: 0.077 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. Data sets for this crystal appeared twinned. refinement was carried out as described in primary citation. The N-terminal methionine as well ...Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. Data sets for this crystal appeared twinned. refinement was carried out as described in primary citation. The N-terminal methionine as well as the residues from 215B (or 216A) on (including the HIS6-tag) were not visible in the density. Likewise, the aas between residues 69 and 83 and 180-183 were also not visible in the density.
RfactorNum. reflection% reflectionSelection details
Rfree0.26672 972 7.9 %RANDOM
Rwork0.22176 ---
obs0.22523 11250 98.39 %-
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: 34.034 Å2
Baniso -1Baniso -2Baniso -3
1--34.58 Å20 Å20 Å2
2---34.58 Å20 Å2
3---69.17 Å2
Refinement stepCycle: LAST / Resolution: 2.6→58.38 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2942 0 9 13 2964
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0230.0222999
X-RAY DIFFRACTIONr_bond_other_d0.0020.022803
X-RAY DIFFRACTIONr_angle_refined_deg2.1711.9714096
X-RAY DIFFRACTIONr_angle_other_deg0.86636483
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.9375394
X-RAY DIFFRACTIONr_dihedral_angle_2_deg39.95724.386114
X-RAY DIFFRACTIONr_dihedral_angle_3_deg22.7815442
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.3451516
X-RAY DIFFRACTIONr_chiral_restr0.1110.2494
X-RAY DIFFRACTIONr_gen_planes_refined0.0150.0213364
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02562
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_it0.8081.51998
X-RAY DIFFRACTIONr_mcbond_other0.1441.5808
X-RAY DIFFRACTIONr_mcangle_it1.4823196
X-RAY DIFFRACTIONr_scbond_it2.2331001
X-RAY DIFFRACTIONr_scangle_it3.6334.5900
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.6→2.667 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.47 74 -
Rwork0.452 789 -
obs--94.42 %

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