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- PDB-4axi: Structure of the Clostridium difficile EutS protein -

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Basic information

Entry
Database: PDB / ID: 4axi
TitleStructure of the Clostridium difficile EutS protein
ComponentsETHANOLAMINE CARBOXYSOME STRUCTURAL PROTEIN
KeywordsSTRUCTURAL PROTEIN / ETHANOLAMINE / BACTERIAL MICROCOMPARTMENT / BMC
Function / homology
Function and homology information


ethanolamine catabolic process / bacterial microcompartment
Similarity search - Function
Bacterial microcompartment shell protein EutS/PduU/CutR / 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 EutS
Similarity search - Component
Biological speciesCLOSTRIDIUM DIFFICILE (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.51 Å
AuthorsPitts, A.C. / Tuck, L.R. / Faulds-Pain, A. / Lewis, R.J. / Marles-Wright, J.
CitationJournal: Plos One / Year: 2012
Title: Structural Insight Into the Clostridium Difficile Ethanolamine Utilisation Microcompartment.
Authors: Pitts, A.C. / Tuck, L.R. / Faulds-Pain, A. / Lewis, R.J. / Marles-Wright, J.
History
DepositionJun 13, 2012Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 27, 2012Provider: repository / Type: Initial release
Revision 1.1Apr 17, 2013Group: Database references
Revision 1.2May 8, 2019Group: Data collection / Derived calculations ...Data collection / Derived calculations / Experimental preparation / Other
Category: database_PDB_rev / database_PDB_rev_record ...database_PDB_rev / database_PDB_rev_record / exptl_crystal_grow / pdbx_database_proc / pdbx_database_status / pdbx_struct_special_symmetry
Item: _exptl_crystal_grow.method / _pdbx_database_status.recvd_author_approval
Revision 1.3Dec 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _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

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Assembly

Deposited unit
A: ETHANOLAMINE CARBOXYSOME STRUCTURAL PROTEIN
B: ETHANOLAMINE CARBOXYSOME STRUCTURAL PROTEIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,1893
Polymers27,0972
Non-polymers921
Water2,702150
1
A: ETHANOLAMINE CARBOXYSOME STRUCTURAL PROTEIN
B: ETHANOLAMINE CARBOXYSOME STRUCTURAL PROTEIN
hetero molecules

A: ETHANOLAMINE CARBOXYSOME STRUCTURAL PROTEIN
B: ETHANOLAMINE CARBOXYSOME STRUCTURAL PROTEIN
hetero molecules

A: ETHANOLAMINE CARBOXYSOME STRUCTURAL PROTEIN
B: ETHANOLAMINE CARBOXYSOME STRUCTURAL PROTEIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)81,5669
Polymers81,2906
Non-polymers2763
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_555-x+y,-x,z1
crystal symmetry operation2_555-y,x-y,z1
Buried area20830 Å2
ΔGint-99.6 kcal/mol
Surface area25200 Å2
MethodPISA
Unit cell
Length a, b, c (Å)123.200, 123.200, 38.720
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number146
Space group name H-MH3
Components on special symmetry positions
IDModelComponents
11A-2007-

HOH

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Components

#1: Protein ETHANOLAMINE CARBOXYSOME STRUCTURAL PROTEIN / EUTS


Mass: 13548.350 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) CLOSTRIDIUM DIFFICILE (bacteria) / Strain: 630 / Production host: ESCHERICHIA COLI B (bacteria) / Strain (production host): B834 / References: UniProt: Q187M0
#2: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 150 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsN-TERMINAL INSERTION OF GLYCINE AFTER INITIATING METHIONINE AND C-TERMINAL HIS-TAG

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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: 46.21 % / Description: NONE
Crystal growMethod: vapor diffusion, hanging drop / pH: 8
Details: PROTEIN IN 200 MM NACL, 50 MM TRIS HCL PH 8.0 HANGING DROP VAPOUR DIFFUSION WITH 100/100 NL PROTEIN: PRECIPITANT OVER 100 UL WELL SOLUTION OF 24% (W/V) PEG 1500, 20% (W/V) GLYCEROL

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Data collection

DiffractionMean temperature: 93 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I02 / Wavelength: 0.9793
DetectorType: ADSC CCD / Detector: CCD / Date: Nov 22, 2009 / Details: MIRRORS
RadiationMonochromator: SINGLE CRYSTAL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9793 Å / Relative weight: 1
ReflectionResolution: 1.51→61.6 Å / Num. obs: 34286 / % possible obs: 99.7 % / Observed criterion σ(I): 2 / Redundancy: 3.8 % / Biso Wilson estimate: 17.64 Å2 / Rmerge(I) obs: 0.06 / Net I/σ(I): 12.4
Reflection shellResolution: 1.51→1.59 Å / Redundancy: 3.8 % / Rmerge(I) obs: 0.5 / Mean I/σ(I) obs: 2.5 / % possible all: 99.9

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Processing

Software
NameVersionClassification
PHENIX(PHENIX.REFINE)refinement
MOSFLMdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3CGI

3cgi


Resolution: 1.51→27.93 Å / SU ML: 0.19 / σ(F): 2.06 / Phase error: 15.73 / Stereochemistry target values: ML
Details: RESIDUE GLU11 ADOPTS MULTIPLE CONFORMATIONS IN BOTH CHAINS AND IS MODELLED IN ALTERNATING CONFORMATIONS OWING TO STEREOCHEMICAL CONSTRAINTS.
RfactorNum. reflection% reflection
Rfree0.1804 1727 5 %
Rwork0.1395 --
obs0.1417 34282 99.66 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 53.965 Å2 / ksol: 0.387 e/Å3
Displacement parametersBiso mean: 20.06 Å2
Baniso -1Baniso -2Baniso -3
1-3.9018 Å20 Å20 Å2
2--3.9018 Å20 Å2
3---6.5484 Å2
Refinement stepCycle: LAST / Resolution: 1.51→27.93 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1732 0 6 150 1888
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0161804
X-RAY DIFFRACTIONf_angle_d1.6792457
X-RAY DIFFRACTIONf_dihedral_angle_d12.923678
X-RAY DIFFRACTIONf_chiral_restr0.099311
X-RAY DIFFRACTIONf_plane_restr0.007313
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.51-1.5640.29721670.2313244X-RAY DIFFRACTION100
1.564-1.62660.2351610.17383297X-RAY DIFFRACTION100
1.6266-1.70060.20431790.14663255X-RAY DIFFRACTION100
1.7006-1.79030.1941840.11833252X-RAY DIFFRACTION100
1.7903-1.90240.17181520.11193295X-RAY DIFFRACTION100
1.9024-2.04920.15881760.10833281X-RAY DIFFRACTION100
2.0492-2.25540.1751790.11283233X-RAY DIFFRACTION100
2.2554-2.58150.13971710.11783279X-RAY DIFFRACTION100
2.5815-3.25170.18051520.13443269X-RAY DIFFRACTION100
3.2517-27.93480.18492060.16613150X-RAY DIFFRACTION98

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