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- PDB-2xr0: Room temperature X-ray structure of the perdeuterated Toho-1 R274... -

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Basic information

Entry
Database: PDB / ID: 2xr0
TitleRoom temperature X-ray structure of the perdeuterated Toho-1 R274N R276N double mutant beta-lactamase
ComponentsTOHO-1 BETA-LACTAMASE
KeywordsHYDROLASE / EXTENDED-SPECTRUM BETA-LACTAMASES / ESBLS / CTX-M-TYPE ESBLS
Function / homology
Function and homology information


beta-lactam antibiotic catabolic process / beta-lactamase activity / beta-lactamase / response to antibiotic
Similarity search - Function
Beta-lactamase, class-A active site / Beta-lactamase class-A active site. / Beta-lactamase class A, catalytic domain / Beta-lactamase enzyme family / Beta-lactamase, class-A / Beta-lactamase / DD-peptidase/beta-lactamase superfamily / Beta-lactamase/transpeptidase-like / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Beta-lactamase Toho-1
Similarity search - Component
Biological speciesESCHERICHIA COLI (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 Å
AuthorsTomanicek, S.J. / Wang, K.K. / Weiss, K.L. / Blakeley, M.P. / Cooper, J. / Chen, Y. / Coates, L.
CitationJournal: FEBS Lett. / Year: 2011
Title: The Active Site Protonation States of Perdeuterated Toho-1 Beta-Lactamase Determined by Neutron Diffraction Support a Role for Glu166 as the General Base in Acylation.
Authors: Tomanicek, S.J. / Wang, K.K. / Weiss, K.L. / Blakeley, M.P. / Cooper, J. / Chen, Y. / Coates, L.
History
DepositionSep 8, 2010Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 22, 2010Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
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: TOHO-1 BETA-LACTAMASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,2794
Polymers27,9911
Non-polymers2883
Water2,774154
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)73.500, 73.500, 99.330
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Space group name H-MP3221

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Components

#1: Protein TOHO-1 BETA-LACTAMASE


Mass: 27990.607 Da / Num. of mol.: 1 / Fragment: RESIDUES 32-291 / Mutation: YES
Source method: isolated from a genetically manipulated source
Details: FULLY PERDEUTERATED / Source: (gene. exp.) ESCHERICHIA COLI (E. coli) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21 / References: UniProt: Q47066, beta-lactamase
#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 154 / Source method: isolated from a natural source / Formula: H2O
Sequence details2XR0 USES A RESIDUE NUMBERING SCHEME IN WHICH RESIDUE POSITION 58, RESIDUE POSITION 239, AND ...2XR0 USES A RESIDUE NUMBERING SCHEME IN WHICH RESIDUE POSITION 58, RESIDUE POSITION 239, AND RESIDUE POSITION 253 HAVE NOT BEEN USED - GIVING A SMALL MISMATCH BETWEEN THE NUMBER OF RESIDUES IN THE DBREF SEQUENCE RANGES BELOW.

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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: 2.77 Å3/Da / Density % sol: 55.55 % / Description: NONE
Crystal growpH: 6.5
Details: 2.0 A AMMONIUM SULFATE, 0.1 M SODIUM CITRATE, PD 5.1. PREPARED IN 99.9% D2O AND MIXED 1:1 WITH PERDEUTERATED PROTEIN PREPARED IN 20 MM NA MES AT PD 6.1 (PH 6.5).

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Data collection

DiffractionMean temperature: 293 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1
DetectorType: MARRESEARCH MX-300 / Detector: CCD / Date: Apr 4, 2010
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.2→29.54 Å / Num. obs: 15962 / % possible obs: 98.6 % / Observed criterion σ(I): 2 / Redundancy: 7.5 % / Biso Wilson estimate: 16.86 Å2 / Rmerge(I) obs: 0.05 / Net I/σ(I): 31.3
Reflection shellResolution: 2.2→2.32 Å / Redundancy: 7.5 % / Rmerge(I) obs: 0.83 / Mean I/σ(I) obs: 22 / % possible all: 97.9

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Processing

Software
NameVersionClassification
PHENIX(PHENIX.REFINE: 1.6.4_486)refinement
MOSFLMdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2WYX

2wyx


Resolution: 2.2→29.54 Å / SU ML: 0.16 / σ(F): 1.43 / Phase error: 16.06 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.173 800 5 %
Rwork0.133 --
obs0.135 15956 98.2 %
Solvent computationShrinkage radii: 0.95 Å / VDW probe radii: 1.2 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 28.96 Å2 / ksol: 0.33 e/Å3
Displacement parametersBiso mean: 19.65 Å2
Baniso -1Baniso -2Baniso -3
1--1.0524 Å20 Å20 Å2
2---1.0524 Å20 Å2
3---2.1047 Å2
Refinement stepCycle: LAST / Resolution: 2.2→29.54 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1964 0 15 154 2133
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0092042
X-RAY DIFFRACTIONf_angle_d1.1222783
X-RAY DIFFRACTIONf_dihedral_angle_d13.134758
X-RAY DIFFRACTIONf_chiral_restr0.07327
X-RAY DIFFRACTIONf_plane_restr0.005361
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.2001-2.33790.19131300.12892457X-RAY DIFFRACTION97
2.3379-2.51830.19541270.13192469X-RAY DIFFRACTION98
2.5183-2.77150.19091310.14132498X-RAY DIFFRACTION98
2.7715-3.17220.19571350.14362517X-RAY DIFFRACTION98
3.1722-3.99510.14911340.12472542X-RAY DIFFRACTION99
3.9951-29.54440.15521430.13052673X-RAY DIFFRACTION99

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