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- PDB-6c78: Substrate Binding Induces Conformational Changes In A Class A Bet... -

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Basic information

Entry
Database: PDB / ID: 6c78
TitleSubstrate Binding Induces Conformational Changes In A Class A Beta Lactamase That Primes 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
DEUTERATED WATER / Beta-lactamase Toho-1
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodNEUTRON DIFFRACTION / Resolution: 1.75 Å
AuthorsLangan, P.S. / Vandavasi, V.G. / Cooper, S.J. / Weiss, K.L. / Ginell, S.L. / Parks, J.M. / Coates, L.
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 1.1Mar 13, 2024Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / diffrn_source
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _diffrn_source.pdbx_synchrotron_site / _diffrn_source.source

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Beta-lactamase Toho-1


Theoretical massNumber of molelcules
Total (without water)28,0461
Polymers28,0461
Non-polymers00
Water1,820101
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8190 Å2
ΔGint24 kcal/mol
Surface area14090 Å2
MethodPISA
Unit cell
Length a, b, c (Å)73.400, 73.400, 99.390
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 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-DOD / water / Heavy water


Mass: 18.015 Da / Num. of mol.: 101 / Source method: isolated from a natural source / Formula: D2O

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Experimental details

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Experiment

ExperimentMethod: NEUTRON DIFFRACTION / Number of used crystals: 1

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Sample preparation

Crystal growTemperature: 293 K / Method: batch mode / pH: 6.1
Details: 300 MICROLITERS OF A 10 MG/ML PROTEIN CONCENTRATION IN A SOLUTION CONTAINING 2.0 M AMMONIUM SULFATE AND 0.1 M PREPARED IN D2O, PH 6.1, BATCH MODE, TEMPERATURE 293K
PH range: 6.1

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Data collection

DiffractionMean temperature: 293 K
Diffraction sourceSource: SPALLATION SOURCE / Site: ORNL Spallation Neutron Source / Beamline: MANDI / Wavelength: 2-4
DetectorType: Hamamatsu C10158DK / Detector: CMOS / Date: Jan 3, 2016
RadiationProtocol: LAUE / Monochromatic (M) / Laue (L): L / Scattering type: neutron
Radiation wavelength
IDWavelength (Å)Relative weight
121
241
ReflectionResolution: 1.75→14.76 Å / Num. obs: 27135 / % possible obs: 85.5 % / Redundancy: 4.89 % / Rmerge(I) obs: 0.153 / Net I/σ(I): 12.2
Reflection shellResolution: 1.75→1.81 Å / Rmerge(I) obs: 0.229 / Mean I/σ(I) obs: 3.3 / % possible all: 65.4

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Processing

Software
NameClassification
Mantiddata reduction
LaueViewdata scaling
PHENIXrefinement
RefinementResolution: 1.75→14.76 Å / Cross valid method: FREE R-VALUE /
Num. reflection% reflection
obs27135 85.5 %
Refinement stepCycle: 1 /
ProteinNucleic acidLigandSolvent
Num. atoms1952 0 0 101

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