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- PDB-4olg: Crystal structure of AmpC beta-lactamase in complex with covalent... -

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Basic information

Entry
Database: PDB / ID: 4olg
TitleCrystal structure of AmpC beta-lactamase in complex with covalently bound N-formyl 7-aminocephalosporanic acid
ComponentsBeta-lactamase
KeywordsHYDROLASE / AMPC BETA-LACTAMASE / CLASS / 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-2TV / PHOSPHATE ION / Beta-lactamase
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.71 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

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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)79,8715
Polymers79,1762
Non-polymers6963
Water7,620423
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1430 Å2
ΔGint-14 kcal/mol
Surface area27090 Å2
MethodPISA
Unit cell
Length a, b, c (Å)118.660, 77.150, 98.140
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
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-2TV / (2R,5Z)-5-[(acetyloxy)methylidene]-2-[(1R)-1-(formylamino)-2-oxoethyl]-5,6-dihydro-2H-1,3-thiazine-4-carboxylic acid / N-formyl 7-aminocephalosporanic acid, bound form


Mass: 300.288 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C11H12N2O6S
#3: Chemical ChemComp-PO4 / PHOSPHATE ION / Phosphate


Mass: 94.971 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: PO4
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 423 / 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: 2.55 Å3/Da / Density % sol: 51.78 %
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: 1.71→30 Å / Num. all: 85920 / Num. obs: 85387 / % possible obs: 99.4 % / Observed criterion σ(I): -3
Reflection shellResolution: 1.71→1.81 Å / % possible all: 98.8

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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: 1.71→29.41 Å / Cor.coef. Fo:Fc: 0.967 / Cor.coef. Fo:Fc free: 0.952 / SU B: 1.845 / SU ML: 0.062 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.094 / ESU R Free: 0.095 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2001 3140 3.7 %RANDOM
Rwork0.166 ---
obs0.1673 85385 99.52 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso max: 107.28 Å2 / Biso mean: 28.513 Å2 / Biso min: 15.03 Å2
Baniso -1Baniso -2Baniso -3
1-0.62 Å20 Å20.36 Å2
2--0.46 Å20 Å2
3----0.76 Å2
Refinement stepCycle: LAST / Resolution: 1.71→29.41 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5511 0 45 423 5979
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0240.025860
X-RAY DIFFRACTIONr_angle_refined_deg2.3021.9498046
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.4965743
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.08124.758248
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.34315877
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.1671523
X-RAY DIFFRACTIONr_chiral_restr0.1720.2874
X-RAY DIFFRACTIONr_gen_planes_refined0.0140.0214591
LS refinement shellResolution: 1.711→1.756 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.271 210 -
Rwork0.206 5821 -
all-6031 -
obs--97.62 %

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