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- PDB-4old: Crystal structure of AmpC beta-lactamase in complex with the prod... -

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Basic information

Entry
Database: PDB / ID: 4old
TitleCrystal structure of AmpC beta-lactamase in complex with the product form of (6R,7R)-7-amino-8-oxo-5-thia-1-azabicyclo[4.2.0]oct-2-ene-2-carboxylic acid
ComponentsBeta-lactamase
KeywordsHYDROLASE / AMPC BETA-LACTAMASE / CLASS C / CEPHALOSPORINASE
Function / homology
Function and homology information


antibiotic catabolic process / beta-lactamase activity / beta-lactamase / outer membrane-bounded periplasmic space / response to antibiotic
Similarity search - Function
Beta-lactamase, class-C active site / Beta-lactamase class-C active site. / : / Beta-lactamase-related / Beta-lactamase / Beta-lactamase / DD-peptidase/beta-lactamase superfamily / Beta-lactamase/transpeptidase-like / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Chem-2UZ / PHOSPHATE ION / Beta-lactamase
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.48 Å
AuthorsShoichet, B.K. / Barelier, S.
CitationJournal: J.Am.Chem.Soc. / Year: 2014
Title: Substrate deconstruction and the nonadditivity of enzyme recognition.
Authors: Barelier, S. / Cummings, J.A. / Rauwerdink, A.M. / Hitchcock, D.S. / Farelli, J.D. / Almo, S.C. / Raushel, F.M. / Allen, K.N. / Shoichet, B.K.
History
DepositionJan 23, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 28, 2014Provider: repository / Type: Initial release
Revision 1.1Jun 18, 2014Group: Database references
Revision 1.2Feb 28, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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: Beta-lactamase
B: Beta-lactamase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)79,8977
Polymers79,1762
Non-polymers7215
Water11,115617
1
A: Beta-lactamase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,9964
Polymers39,5881
Non-polymers4083
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Beta-lactamase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,9013
Polymers39,5881
Non-polymers3132
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)118.450, 76.420, 97.880
Angle α, β, γ (deg.)90.000, 115.950, 90.000
Int Tables number5
Space group name H-MC121

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Components

#1: Protein Beta-lactamase / Cephalosporinase


Mass: 39587.922 Da / Num. of mol.: 2 / Fragment: Beta-lactamase
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Strain: K12 / Gene: ampA, ampC, b4150, JW4111 / Plasmid: POGO295 / Production host: Escherichia coli (E. coli) / Strain (production host): JM109 / References: UniProt: P00811, beta-lactamase
#2: Chemical ChemComp-2UZ / (2R)-2-[(R)-amino(carboxy)methyl]-3,6-dihydro-2H-1,3-thiazine-4-carboxylic acid / (6R,7R)-7-amino-8-oxo-5-thia-1-azabicyclo[4.2.0]oct-2-ene-2-carboxylic acid, hydrolyzed form


Mass: 218.230 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C7H10N2O4S
#3: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: PO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 617 / 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: 2.52 Å3/Da / Density % sol: 51.1 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8.6
Details: 1.7 M POTASSIUM PHOSPHATE, pH 8.6, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 80 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.3.1 / Wavelength: 1.115869 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Apr 11, 2012
RadiationMonochromator: Double flat crystal, Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.115869 Å / Relative weight: 1
ReflectionResolution: 1.48→30 Å / Num. all: 130489 / Num. obs: 129353 / % possible obs: 99.1 % / Observed criterion σ(I): -3
Reflection shellResolution: 1.48→1.57 Å / % possible all: 98.7

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Processing

Software
NameVersionClassificationNB
REFMAC5.6.0117refinement
PDB_EXTRACT3.14data extraction
ADSCQuantumdata collection
XDSdata reduction
XDSdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.48→29.34 Å / Cor.coef. Fo:Fc: 0.97 / Cor.coef. Fo:Fc free: 0.963 / SU B: 1.057 / SU ML: 0.041 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.063 / ESU R Free: 0.064 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.1882 4891 3.8 %RANDOM
Rwork0.1643 ---
obs0.1652 129349 99.28 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 91.78 Å2 / Biso mean: 18.983 Å2 / Biso min: 5.62 Å2
Baniso -1Baniso -2Baniso -3
1-0.78 Å20 Å20.35 Å2
2---0.21 Å20 Å2
3----0.26 Å2
Refinement stepCycle: LAST / Resolution: 1.48→29.34 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5491 0 43 617 6151
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0280.025953
X-RAY DIFFRACTIONr_angle_refined_deg2.6311.9558194
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.675763
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.7324.737247
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.88215903
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.891523
X-RAY DIFFRACTIONr_chiral_restr0.1650.2890
X-RAY DIFFRACTIONr_gen_planes_refined0.0150.0224686
LS refinement shellResolution: 1.481→1.519 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.268 368 -
Rwork0.24 8860 -
all-9228 -
obs--98.02 %

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