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- PDB-5a90: 100K Neutron Ligand Free: Exploring the Mechanism of beta-Lactam ... -

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Basic information

Entry
Database: PDB / ID: 5a90
Title100K Neutron Ligand Free: Exploring the Mechanism of beta-Lactam Ring Protonation in the Class A beta-lactamase Acylation Mechanism Using Neutron and X-ray Crystallography
ComponentsBETA-LACTAMASE CTX-M-97
KeywordsHYDROLASE / BETA LACTAMASE / NEUTRON CRYSTALLOGRAPHY
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 CTX-M-97
Similarity search - Component
Biological speciesESCHERICHIA COLI (E. coli)
MethodNEUTRON DIFFRACTION / NUCLEAR REACTOR / Resolution: 1.7 Å
AuthorsVandavasi, V.G. / Weiss, K.L. / Cooper, J.B. / Erskine, P.T. / Tomanicek, S.J. / Ostermann, A. / Schrader, T.E. / Ginell, S.L. / Coates, L.
CitationJournal: J.Med.Chem. / Year: 2016
Title: Exploring the Mechanism of Beta-Lactam Ring Protonation in the Class a Beta-Lactamase Acylation Mechanism Using Neutron and X-Ray Crystallography.
Authors: Vandavasi, V.G. / Weiss, K.L. / Cooper, J.B. / Erskine, P.T. / Tomanicek, S.J. / Ostermann, A. / Schrader, T.E. / Ginell, S.L. / Coates, L.
History
DepositionJul 17, 2015Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 16, 2015Provider: repository / Type: Initial release
Revision 1.1Jan 27, 2016Group: Database references
Revision 1.2Mar 22, 2017Group: Atomic model / Data collection

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: BETA-LACTAMASE CTX-M-97


Theoretical massNumber of molelcules
Total (without water)28,1181
Polymers28,1181
Non-polymers00
Water5,711317
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)73.238, 73.238, 98.534
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Space group name H-MP3221
Components on special symmetry positions
IDModelComponents
11A-2116-

HOH

21A-2294-

HOH

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Components

#1: Protein BETA-LACTAMASE CTX-M-97 / TOHO-1 BETA LACTMASE


Mass: 28117.752 Da / Num. of mol.: 1 / Mutation: YES
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) ESCHERICHIA COLI (E. coli) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21 / References: UniProt: E1ANH6, beta-lactamase
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 317 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: NEUTRON DIFFRACTION

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Sample preparation

CrystalDescription: NONE
Crystal growpH: 6.1 / Details: pH 6.1

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: NUCLEAR REACTOR / Site: FRM II / Beamline: BIODIFF / Wavelength: 2.67
DetectorDetector: IMAGE PLATE
RadiationScattering type: neutron
Radiation wavelengthWavelength: 2.67 Å / Relative weight: 1
ReflectionResolution: 1.7→40 Å / Num. obs: 30302 / % possible obs: 88.4 % / Observed criterion σ(I): 0 / Redundancy: 3.9 % / Rmerge(I) obs: 0.19 / Rsym value: 0.19
Reflection shellResolution: 1.7→1.74 Å / Redundancy: 3.2 % / Rmerge(I) obs: 0.626 / Mean I/σ(I) obs: 1.8 / Rsym value: 0.626 / % possible all: 76.8

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Processing

SoftwareName: PHENIX / Classification: refinement
RefinementStarting model: NONE

Resolution: 1.7→38.908 Å / SU ML: 0.17 / σ(F): 1.33 / Phase error: 20.8 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2265 1524 5 %
Rwork0.1919 --
obs0.1937 30294 88.61 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.7→38.908 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1961 0 0 317 2278
Refine LS restraints
Refine-IDTypeDev idealNumber
NEUTRON DIFFRACTIONf_bond_d0.0063968
NEUTRON DIFFRACTIONf_angle_d0.9587190
NEUTRON DIFFRACTIONf_dihedral_angle_d14.3211090
NEUTRON DIFFRACTIONf_chiral_restr0.044321
NEUTRON DIFFRACTIONf_plane_restr0.005628
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.7002-1.7550.28921400.24882283NEUTRON DIFFRACTION79
1.755-1.81780.29031180.22882365NEUTRON DIFFRACTION82
1.8178-1.89050.2871260.21512447NEUTRON DIFFRACTION83
1.8905-1.97660.23021310.18712461NEUTRON DIFFRACTION85
1.9766-2.08080.19611320.16632489NEUTRON DIFFRACTION86
2.0808-2.21110.20331240.1662568NEUTRON DIFFRACTION88
2.2111-2.38180.18881400.15952626NEUTRON DIFFRACTION90
2.3818-2.62150.20071540.16572683NEUTRON DIFFRACTION91
2.6215-3.00070.24441440.19722752NEUTRON DIFFRACTION93
3.0007-3.78010.22291500.20912972NEUTRON DIFFRACTION99
3.7801-38.91830.22691650.20763124NEUTRON DIFFRACTION100

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