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- PDB-6c7a: Conformational Changes in a Class A Beta lactamase that Prime it ... -

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Basic information

Entry
Database: PDB / ID: 6c7a
TitleConformational Changes in a Class A Beta lactamase that Prime it for Catalysis
ComponentsBeta-lactamase Toho-1
KeywordsHYDROLASE
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 / Resolution: 1.05 Å
AuthorsCoates, L. / Langan, P.S. / Vandavasi, V.G. / Cooper, S.J. / Weiss, K.L. / Ginell, S.L. / Parks, J.M.
CitationJournal: Acs Catalysis / Year: 2018
Title: Substrate Binding Induces Conformational Changes in a Class A Beta-lactamase That Prime It for Catalysis
Authors: Langan, P.S. / Vandavasi, V.G. / Cooper, S.J. / Weiss, K.L. / Ginell, S.L. / Parks, J.M. / Coates, L.
History
DepositionJan 22, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 21, 2018Provider: repository / Type: Initial release
Revision 1.1Jan 23, 2019Group: Data collection / Refinement description / Category: diffrn / pdbx_refine / Item: _diffrn.ambient_temp
Revision 1.2Mar 13, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Beta-lactamase Toho-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,91010
Polymers28,0461
Non-polymers8659
Water8,971498
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)71.825, 71.825, 96.534
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-538-

HOH

21A-714-

HOH

31A-753-

HOH

41A-894-

HOH

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Components

#1: Protein Beta-lactamase Toho-1


Mass: 28045.688 Da / Num. of mol.: 1 / Fragment: residues 32-291
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: bla / Production host: Escherichia coli (E. coli) / References: UniProt: Q47066, beta-lactamase
#2: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 498 / 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: 2.56 Å3/Da / Density % sol: 52.01 %
Crystal growTemperature: 293 K / Method: batch mode / pH: 6.1
Details: 10 mg/ml protein in a solution containing 2.0 M ammonium sulfate and 0.1 M sodium citrate (pH 6.1)

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Data collection

Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.97 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jan 9, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97 Å / Relative weight: 1
ReflectionResolution: 1.05→48.27 Å / Num. obs: 134116 / % possible obs: 99.9 % / Redundancy: 9.2 % / Rmerge(I) obs: 0.075 / Rpim(I) all: 0.02 / Net I/av σ(I): 5.8 / Net I/σ(I): 5.8
Reflection shellResolution: 1.05→1.11 Å / Redundancy: 7.2 % / Rmerge(I) obs: 0.37 / Mean I/σ(I) obs: 2 / Rpim(I) all: 0.149 / % possible all: 99.1

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Processing

Software
NameClassification
SHELXLrefinement
XDSdata reduction
SCALAdata scaling
RefinementResolution: 1.05→48.27 Å / Cross valid method: FREE R-VALUE
RfactorNum. reflection% reflection
Rfree0.15 --
Rwork0.12 --
obs-134116 99.9 %
Refinement stepCycle: LAST / Resolution: 1.05→48.27 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1968 0 45 498 2511

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