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- PDB-4u6i: Crystal Structure of the EutL Microcompartment Shell Protein from... -

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Basic information

Entry
Database: PDB / ID: 4u6i
TitleCrystal Structure of the EutL Microcompartment Shell Protein from Clostridium Perfringens Bound to Vitamin B12
ComponentsEthanolamine utilization protein EutL
KeywordsTRANSPORT PROTEIN / bacterial microcompartment / Eut / BMC shell protein / cobalamin / vitamin B12
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
COBALAMIN / : / Bacterial microcompartment shell protein EutL
Similarity search - Component
Biological speciesClostridium perfringens (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å
Model detailsbacterial microcompartments (BMC) superfamily
AuthorsThompson, M.C. / Crowley, C.S. / Kopstein, J.S. / Yeates, T.O.
CitationJournal: Acta Crystallogr.,Sect.F / Year: 2014
Title: Structure of a bacterial microcompartment shell protein bound to a cobalamin cofactor.
Authors: Thompson, M.C. / Crowley, C.S. / Kopstein, J. / Bobik, T.A. / Yeates, T.O.
History
DepositionJul 29, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 22, 2014Provider: repository / Type: Initial release
Revision 1.1Dec 24, 2014Group: Database references
Revision 1.2Nov 22, 2017Group: Derived calculations / Other ...Derived calculations / Other / Refinement description / Source and taxonomy
Category: entity_src_gen / pdbx_database_status ...entity_src_gen / pdbx_database_status / pdbx_struct_assembly / pdbx_struct_assembly_gen / pdbx_struct_assembly_prop / pdbx_struct_oper_list / software
Item: _entity_src_gen.pdbx_alt_source_flag / _pdbx_database_status.pdb_format_compatible ..._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 1.3Sep 27, 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 / refine_hist / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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)72,5035
Polymers71,1503
Non-polymers1,3532
Water1,838102
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8610 Å2
ΔGint-72 kcal/mol
Surface area23680 Å2
MethodPISA
Unit cell
Length a, b, c (Å)88.230, 88.230, 252.010
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 (bacteria) / Gene: eutL / Plasmid: pET22b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)Rosetta / References: UniProt: B1RMU6, UniProt: Q8XLZ0*PLUS
#2: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#3: Chemical ChemComp-B12 / COBALAMIN / Vitamin B12


Mass: 1330.356 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C62H89CoN13O14P
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 102 / 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: 3.45 Å3/Da / Density % sol: 64.31 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7 / Details: 0.1M HEPES buffer, 5% PEG 8000, 8% ethylene glycol

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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: 2.1→83.27 Å / Num. obs: 59035 / % possible obs: 99.88 % / Redundancy: 12.5 % / Biso Wilson estimate: 47.06 Å2 / Net I/σ(I): 13.54

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Processing

Software
NameVersionClassification
XSCALEdata scaling
PDB_EXTRACT3.14data extraction
PHENIX(phenix.refine: dev_1555)refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4EDI

4edi


Resolution: 2.1→72.274 Å / SU ML: 0.24 / Cross valid method: THROUGHOUT / σ(F): 3.57 / Phase error: 22.32 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2104 3020 5.12 %
Rwork0.1845 56015 -
obs0.1859 59035 99.88 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 144.5 Å2 / Biso mean: 61.1411 Å2 / Biso min: 36.99 Å2
Refinement stepCycle: final / Resolution: 2.1→72.274 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4738 0 92 102 4932
Biso mean--97.81 54.24 -
Num. residues----650
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0035114
X-RAY DIFFRACTIONf_angle_d0.7316998
X-RAY DIFFRACTIONf_chiral_restr0.041816
X-RAY DIFFRACTIONf_plane_restr0.003947
X-RAY DIFFRACTIONf_dihedral_angle_d11.4921886
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 22

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.1-2.13280.29821420.27824492591100
2.1328-2.16780.30521260.257625082634100
2.1678-2.20520.25171370.250725132650100
2.2052-2.24530.23411400.241624892629100
2.2453-2.28850.25081320.228525002632100
2.2885-2.33520.25381300.21482496262699
2.3352-2.3860.22591320.200625372669100
2.386-2.44150.23171310.202525202651100
2.4415-2.50250.24991200.200325062626100
2.5025-2.57020.24671550.188924812636100
2.5702-2.64580.21271510.186325152666100
2.6458-2.73120.22881360.188725252661100
2.7312-2.82880.28391190.195425532672100
2.8288-2.94210.22631490.196725292678100
2.9421-3.0760.19931250.192725532678100
3.076-3.23820.24881490.20125462695100
3.2382-3.44110.22731150.203525632678100
3.4411-3.70670.24061440.180425792723100
3.7067-4.07970.19021480.167825612709100
4.0797-4.670.15511350.138626322767100
4.67-5.88330.18251610.152526372798100
5.8833-72.31650.19921430.20328232966100
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)
11.4390.75910.47353.1677-0.19712.71090.0848-0.2555-0.0480.6085-0.1988-0.3109-0.08370.27540.00010.53370.026-0.14250.6636-0.00670.5696-42.189-4.1786.112
21.78330.74440.46242.6569-0.81521.9305-0.0364-0.1438-0.2385-0.35890.0911-0.01250.5793-0.207900.62840.0564-0.03380.5076-0.04010.5575-56.458-22.445-15.443
31.77390.43091.18292.2635-0.26783.189-0.20560.17230.2937-0.2288-0.0861-0.0521-0.47350.288800.51340.0023-0.03130.52160.02020.5329-48.7187.447-23.155
40.0162-0.01230.00650.0122-0.01190.0195-0.08950.0494-0.4148-0.19460.04260.4864-0.0013-0.40480.00011.0136-0.0346-0.21631.41780.31261.102-77.6245.166-37.647
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1( CHAIN A AND RESID 1:217 )A1 - 217
2X-RAY DIFFRACTION2( CHAIN B AND RESID 1:217 )B1 - 217
3X-RAY DIFFRACTION3( CHAIN C AND RESID 1:216 )C1 - 216
4X-RAY DIFFRACTION4( CHAIN C AND RESID 301:301 )C301

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