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- PDB-4axo: Structure of the Clostridium difficile EutQ protein -

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Basic information

Entry
Database: PDB / ID: 4axo
TitleStructure of the Clostridium difficile EutQ protein
ComponentsETHANOLAMINE UTILIZATION PROTEIN
KeywordsSTRUCTURAL PROTEIN / BACTERIAL MICROCOMPARTMENT / BMC
Function / homology
Function and homology information


acetate kinase / ethanolamine catabolic process / acetate kinase activity / bacterial microcompartment
Similarity search - Function
Acetate kinase EutQ / Ethanolamine utilisation protein EutQ / RmlC-like cupin domain superfamily / Jelly Rolls / RmlC-like jelly roll fold / Jelly Rolls / Sandwich / Mainly Beta
Similarity search - Domain/homology
Biological speciesCLOSTRIDIUM DIFFICILE (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1 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 1.1Jan 9, 2013Group: Database references
Revision 1.2May 8, 2019Group: Data collection / 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
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 / pdbx_struct_conn_angle / struct_conn / 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 / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.value / _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.ptnr1_symmetry / _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 / _struct_conn.ptnr2_symmetry / _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
B: ETHANOLAMINE UTILIZATION PROTEIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,2953
Polymers34,2702
Non-polymers241
Water6,593366
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3520 Å2
ΔGint-29.9 kcal/mol
Surface area12380 Å2
MethodPISA
Unit cell
Length a, b, c (Å)82.332, 66.578, 58.950
Angle α, β, γ (deg.)90.00, 117.54, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11B-2071-

HOH

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Components

#1: Protein ETHANOLAMINE UTILIZATION PROTEIN / EUTQ


Mass: 17135.225 Da / Num. of mol.: 2 / Fragment: RESIDUES 17-157
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: Q187N7
#2: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 366 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsN-TERMINAL TRUNCATION, START AT RESIDUE 17. METHIONINE AND GLYCINE FROM EXPRESSION VECTOR AT N- ...N-TERMINAL TRUNCATION, START AT RESIDUE 17. METHIONINE AND GLYCINE FROM EXPRESSION VECTOR AT N-TERMINUS, 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: 2.12 Å3/Da / Density % sol: 42.05 % / Description: NONE
Crystal growMethod: vapor diffusion, hanging drop / pH: 4.5
Details: PROTEIN IN 150 MM NACL, 50 MM TRIS.HCL PH 8.0 AT 8 MG/ML. HANGING DROP VAPOUR DIFFUSION, 1/1 UL DROPS OVER 1ML OF PRECIPITANT: 100 MM SODIUM ACETATE PH 4.5, 35 % (W/V) PEG 6000, 200 MM MGCL2. ...Details: PROTEIN IN 150 MM NACL, 50 MM TRIS.HCL PH 8.0 AT 8 MG/ML. HANGING DROP VAPOUR DIFFUSION, 1/1 UL DROPS OVER 1ML OF PRECIPITANT: 100 MM SODIUM ACETATE PH 4.5, 35 % (W/V) PEG 6000, 200 MM MGCL2. CRYPROTECTED WITH WELL SOLUTION SUPPLEMENTED WITH 20 % (V/V) PEG 300

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Data collection

DiffractionMean temperature: 93 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.8266
DetectorType: ADSC CCD / Detector: CCD / Date: Jul 30, 2011 / Details: MIRRORS
RadiationMonochromator: SINGLE CRYSTAL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.8266 Å / Relative weight: 1
ReflectionResolution: 1→43.15 Å / Num. obs: 148309 / % possible obs: 97.9 % / Observed criterion σ(I): 2 / Redundancy: 2.3 % / Biso Wilson estimate: 9.8 Å2 / Rmerge(I) obs: 0.06 / Net I/σ(I): 11.5
Reflection shellResolution: 1→1.05 Å / Redundancy: 2 % / Rmerge(I) obs: 0.36 / Mean I/σ(I) obs: 2.4 / % possible all: 99.4

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Processing

Software
NameVersionClassification
PHENIX(PHENIX.REFINE)refinement
XDSdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2PYT

2pyt


Resolution: 1→36.503 Å / SU ML: 0.05 / σ(F): 1.34 / Phase error: 11.83 / Stereochemistry target values: ML
Details: LOOP BETWEEN RESIDUES 56 AND 64 IN CHAIN A MODELLED IN TWO CONFORMATIONS WITH 0.55 AND 0.45 OCCUPANCY.
RfactorNum. reflection% reflection
Rfree0.147 7431 5 %
Rwork0.1357 --
obs0.1363 148298 97.76 %
Solvent computationShrinkage radii: 0.6 Å / VDW probe radii: 0.9 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 42.675 Å2 / ksol: 0.431 e/Å3
Displacement parametersBiso mean: 14.74 Å2
Baniso -1Baniso -2Baniso -3
1-1.233 Å20 Å2-0.5928 Å2
2--1.9062 Å20 Å2
3----3.1392 Å2
Refinement stepCycle: LAST / Resolution: 1→36.503 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2100 0 1 366 2467
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0142354
X-RAY DIFFRACTIONf_angle_d1.6013237
X-RAY DIFFRACTIONf_dihedral_angle_d12.433901
X-RAY DIFFRACTIONf_chiral_restr0.098369
X-RAY DIFFRACTIONf_plane_restr0.011415
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1-1.01140.24272520.23364723X-RAY DIFFRACTION99
1.0114-1.02330.22042400.21744774X-RAY DIFFRACTION99
1.0233-1.03580.21372460.19224749X-RAY DIFFRACTION99
1.0358-1.04890.20882550.18514735X-RAY DIFFRACTION99
1.0489-1.06270.18622360.16954805X-RAY DIFFRACTION100
1.0627-1.07730.15932510.15914730X-RAY DIFFRACTION99
1.0773-1.09270.16422560.14694763X-RAY DIFFRACTION99
1.0927-1.1090.1382650.13584747X-RAY DIFFRACTION99
1.109-1.12630.13992390.12684810X-RAY DIFFRACTION99
1.1263-1.14480.12992340.12184715X-RAY DIFFRACTION99
1.1448-1.16450.11732710.11344710X-RAY DIFFRACTION99
1.1645-1.18570.112420.10834759X-RAY DIFFRACTION99
1.1857-1.20850.12692740.11014715X-RAY DIFFRACTION99
1.2085-1.23320.13762270.11164810X-RAY DIFFRACTION99
1.2332-1.260.12352480.10784695X-RAY DIFFRACTION99
1.26-1.28930.11932480.10444736X-RAY DIFFRACTION98
1.2893-1.32150.10742490.1034698X-RAY DIFFRACTION98
1.3215-1.35730.13862490.1024693X-RAY DIFFRACTION98
1.3573-1.39720.12322760.10184630X-RAY DIFFRACTION97
1.3972-1.44230.12752390.10024682X-RAY DIFFRACTION97
1.4423-1.49390.11042260.10174570X-RAY DIFFRACTION96
1.4939-1.55370.12032450.09844598X-RAY DIFFRACTION95
1.5537-1.62440.11462160.10184531X-RAY DIFFRACTION94
1.6244-1.710.12772360.10844480X-RAY DIFFRACTION92
1.71-1.81710.13032350.11734360X-RAY DIFFRACTION91
1.8171-1.95740.13542530.12634468X-RAY DIFFRACTION93
1.9574-2.15440.13522620.12614784X-RAY DIFFRACTION100
2.1544-2.46610.14682620.14664821X-RAY DIFFRACTION99
2.4661-3.10680.17192640.16184767X-RAY DIFFRACTION99
3.1068-36.52710.17332350.16284809X-RAY DIFFRACTION97

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