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- PDB-4tme: Crystal Structure of EutL from Clostridium Perfringens bound to e... -

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Basic information

Entry
Database: PDB / ID: 4tme
TitleCrystal Structure of EutL from Clostridium Perfringens bound to ethanolamine
ComponentsEthanolamine utilization protein EutL
KeywordsTRANSPORT PROTEIN / bacterial microcompartment / Eut / BMC shell protein / ethanolamine / room temperature crystallography
Function / homology
Function and homology information


bacterial microcompartment / cobalamin binding / structural molecule activity / metal ion 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 domain / Bacterial microcompartment domain / CcmK-like superfamily / BMC
Similarity search - Domain/homology
ETHANOLAMINE / Ethanolamine utilization protein EutL / Bacterial microcompartment shell protein EutL
Similarity search - Component
Biological speciesClostridium perfringens E str. JGS1987 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.7 Å
Model detailsbacterial microcompartments (BMC) superfamily
AuthorsThompson, M.C. / Yeates, T.O.
CitationJournal: Protein Sci. / Year: 2015
Title: An allosteric model for control of pore opening by substrate binding in the EutL microcompartment shell protein.
Authors: Thompson, M.C. / Cascio, D. / Leibly, D.J. / Yeates, T.O.
History
DepositionJun 1, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 25, 2015Provider: repository / Type: Initial release
Revision 1.1Jun 10, 2015Group: Database references
Revision 1.2Nov 22, 2017Group: Database references / Derived calculations ...Database references / Derived calculations / Other / Refinement description / Source and taxonomy
Category: citation / entity_src_gen ...citation / entity_src_gen / pdbx_database_status / pdbx_struct_assembly / pdbx_struct_assembly_gen / pdbx_struct_assembly_prop / pdbx_struct_conn_angle / pdbx_struct_oper_list / software
Item: _citation.journal_id_CSD / _entity_src_gen.pdbx_alt_source_flag ..._citation.journal_id_CSD / _entity_src_gen.pdbx_alt_source_flag / _pdbx_database_status.pdb_format_compatible / _pdbx_struct_assembly.oligomeric_details / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_struct_assembly_prop.type / _pdbx_struct_assembly_prop.value / _pdbx_struct_oper_list.symmetry_operation / _software.classification
Revision 2.0Nov 15, 2023Group: Atomic model / Data collection ...Atomic model / Data collection / Database references / Derived calculations / Refinement description
Category: atom_site / chem_comp_atom ...atom_site / chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_conn_angle / refine_hist / struct_conn
Item: _atom_site.auth_atom_id / _atom_site.label_atom_id ..._atom_site.auth_atom_id / _atom_site.label_atom_id / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _refine_hist.number_atoms_total / _refine_hist.pdbx_number_atoms_nucleic_acid / _refine_hist.pdbx_number_atoms_protein / _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_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_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
C: Ethanolamine utilization protein EutL
hetero molecules


Theoretical massNumber of molelcules
Total (without water)71,56311
Polymers71,1503
Non-polymers4128
Water9,440524
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area11170 Å2
ΔGint-99 kcal/mol
Surface area23900 Å2
MethodPISA
Unit cell
Length a, b, c (Å)87.960, 87.960, 251.910
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number96
Space group name H-MP43212

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Components

#1: Protein Ethanolamine utilization protein EutL


Mass: 23716.703 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Clostridium perfringens E str. JGS1987 (bacteria)
Gene: eutL, AC3_1081 / Plasmid: pET22b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)Rosetta / References: UniProt: B1BQ33, UniProt: Q8XLZ0*PLUS
#2: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Na
#3: Chemical
ChemComp-ETA / ETHANOLAMINE


Type: L-peptide COOH carboxy terminus / Mass: 61.083 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C2H7NO
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 524 / 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: 3.42 Å3/Da / Density % sol: 64.08 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 0.1M HEPES buffer, 5% PEG 8000, 8% ethylene glycol, crystals were soaked in 20mM ethanolamine

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 0.9795 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Apr 24, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 1.7→83.043 Å / Num. obs: 109437 / % possible obs: 100 % / Observed criterion σ(I): -3 / Redundancy: 12.5 % / Biso Wilson estimate: 25.31 Å2 / Rmerge F obs: 0.999 / Rmerge(I) obs: 0.088 / Rrim(I) all: 0.092 / Χ2: 1.1 / Net I/σ(I): 17.1 / Num. measured all: 1370706
Reflection shell

Diffraction-ID: 1 / Rejects: _

Resolution (Å)Highest resolution (Å)Rmerge F obsRmerge(I) obsMean I/σ(I) obsNum. measured obsNum. possibleNum. unique obsRrim(I) all% possible all
1.7-1.740.7191.241.7966620795279501.322100
1.74-1.790.861.0332.6282870778677851.085100
1.79-1.840.9290.8323.87100197754475440.865100
1.84-1.90.9510.6425.0599295736473640.667100
1.9-1.960.9660.4876.5895642714671460.506100
1.96-2.030.9820.3578.5689717690769060.372100
2.03-2.110.9880.26710.9385584668866880.279100
2.11-2.190.9920.20813.8188262643364330.216100
2.19-2.290.9940.17116.1783698617561740.178100
2.29-2.40.9960.1418.6878509595459540.146100
2.4-2.530.9960.1220.8669534565656560.125100
2.53-2.690.9970.10125.6772839532953290.105100
2.69-2.870.9980.08728.7767547505450540.09100
2.87-3.10.9980.07532.0560714471847180.078100
3.1-3.40.9980.06534.352828437343720.068100
3.4-3.80.9990.05939.5951029396739670.061100
3.8-4.390.9990.05341.2743793354235410.056100
4.39-5.380.9990.04841.8635647302230200.0599.9
5.38-7.60.9990.04941.8230501240324030.051100
7.60.9990.0441.8415880143314330.042100

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
XSCALEdata scaling
PDB_EXTRACT3.14data extraction
PHASERphasing
PHENIX(phenix.refine: dev_1525)refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.7→83.043 Å / SU ML: 0.14 / Cross valid method: THROUGHOUT / σ(F): 1.36 / Phase error: 14.96 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1623 5553 5.07 %
Rwork0.147 103869 -
obs0.1478 109422 99.98 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 80.79 Å2 / Biso mean: 31.0407 Å2 / Biso min: 15.44 Å2
Refinement stepCycle: final / Resolution: 1.7→83.043 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4864 0 26 525 5415
Biso mean--26.62 40.43 -
Num. residues----663
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.015245
X-RAY DIFFRACTIONf_angle_d1.247173
X-RAY DIFFRACTIONf_chiral_restr0.054832
X-RAY DIFFRACTIONf_plane_restr0.007958
X-RAY DIFFRACTIONf_dihedral_angle_d12.6791889
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 30 / % reflection obs: 100 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all
1.7-1.71940.31021800.258933783558
1.7194-1.73960.25261830.23434053588
1.7396-1.76080.22941820.215434333615
1.7608-1.78310.21621800.207633803560
1.7831-1.80660.21951840.186334243608
1.8066-1.83130.20031830.170334293612
1.8313-1.85750.19091810.159533913572
1.8575-1.88520.15911840.157434283612
1.8852-1.91470.17841820.166134203602
1.9147-1.94610.17731840.157934293613
1.9461-1.97960.17491820.149734033585
1.9796-2.01560.16311800.150534303610
2.0156-2.05440.17361780.142334233601
2.0544-2.09630.15851770.142734773654
2.0963-2.14190.16181930.144934073600
2.1419-2.19170.16471720.137734403612
2.1917-2.24650.14931860.132634453631
2.2465-2.30730.15821830.138134383621
2.3073-2.37520.141870.130734563643
2.3752-2.45190.16131780.136534553633
2.4519-2.53950.15281840.138134683652
2.5395-2.64120.15562110.134734373648
2.6412-2.76140.15971780.135834913669
2.7614-2.9070.15852000.143234563656
2.907-3.08910.17021670.144135023669
3.0891-3.32760.16951780.158235303708
3.3276-3.66250.17351870.149635453732
3.6625-4.19250.15472020.143135453747
4.1925-5.2820.11861950.122335863781
5.282-83.14240.17462120.164338184030
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.54910.37360.16871.74290.25050.69130.0879-0.115-0.03610.2224-0.0753-0.07170.04080.0366-0.01680.2274-0.0394-0.02310.27010.01590.233-41.9084-3.86175.6046
20.89070.3685-0.04451.1357-0.61231.28630.0009-0.0481-0.0809-0.19360.02150.02140.2213-0.1097-0.02210.2406-0.0144-0.00940.1715-0.00630.2155-56.216-21.894-16.4027
30.91140.1670.87180.77680.12661.6501-0.05830.02470.1004-0.1585-0.05480.0136-0.21070.07670.12440.2458-0.0110.00870.19430.01050.2191-47.33217.3513-21.8703
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain AA1 - 217
2X-RAY DIFFRACTION2chain BB1 - 221
3X-RAY DIFFRACTION3chain CC1 - 225

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