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- PDB-1iel: Crystal Structure of AmpC beta-lactamase from E. coli in Complex ... -

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Basic information

Entry
Database: PDB / ID: 1iel
TitleCrystal Structure of AmpC beta-lactamase from E. coli in Complex with Ceftazidime
Componentsbeta-lactamase
KeywordsHYDROLASE / cephalosporinase / beta-lactamase / serine hydrolase
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
ACYLATED CEFTAZIDIME / PHOSPHATE ION / Beta-lactamase
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsPowers, R.A. / Caselli, E. / Focia, P.J. / Prati, F. / Shoichet, B.K.
CitationJournal: Biochemistry / Year: 2001
Title: Structures of ceftazidime and its transition-state analogue in complex with AmpC beta-lactamase: implications for resistance mutations and inhibitor design.
Authors: Powers, R.A. / Caselli, E. / Focia, P.J. / Prati, F. / Shoichet, B.K.
History
DepositionApr 10, 2001Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 15, 2001Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Aug 9, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Oct 30, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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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)80,2105
Polymers79,1762
Non-polymers1,0343
Water4,990277
1
A: beta-lactamase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)40,1523
Polymers39,5881
Non-polymers5642
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: beta-lactamase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)40,0572
Polymers39,5881
Non-polymers4691
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)118.490, 77.040, 98.070
Angle α, β, γ (deg.)90.00, 115.76, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein beta-lactamase / AmpC 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) / Plasmid: p0G0295 / Production host: Escherichia coli (E. coli) / Strain (production host): JM109 / References: UniProt: P00811, beta-lactamase
#2: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: PO4
#3: Chemical ChemComp-CAZ / ACYLATED CEFTAZIDIME


Mass: 469.492 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C17H19N5O7S2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 277 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 2.54 Å3/Da / Density % sol: 51.65 %
Crystal growTemperature: 296 K / Method: vapor diffusion, hanging drop / pH: 8.7
Details: 1.7M potassium phosphate, 95uM AmpC, pH 8.7, VAPOR DIFFUSION, HANGING DROP, temperature 296K
Crystal grow
*PLUS
Details: used microseeding, Usher, K.C., (1998) Biochemistry, 37, 16082.
PH range low: 8.7 / PH range high: 8.5
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
11.7 Msodium potassium phosphate1reservoir
210 mg/mlprotein1drop

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL7-1 / Wavelength: 1.08 Å
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Jul 1, 2000
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.08 Å / Relative weight: 1
ReflectionResolution: 2→20 Å / Num. all: 46338 / Num. obs: 152381 / % possible obs: 86.5 % / Observed criterion σ(I): -3 / Redundancy: 3.3 % / Biso Wilson estimate: 19.44 Å2 / Rmerge(I) obs: 0.058 / Net I/σ(I): 14.8
Reflection shellResolution: 2→2.07 Å / Rmerge(I) obs: 0.238 / % possible all: 99.9
Reflection
*PLUS
Lowest resolution: 20 Å / Num. obs: 46338 / Num. measured all: 152381
Reflection shell
*PLUS
% possible obs: 99.9 % / Mean I/σ(I) obs: 6.4

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Processing

Software
NameClassification
CNSrefinement
DENZOdata reduction
SCALEPACKdata scaling
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 1FSY

1fsy


Resolution: 2→20 Å / σ(F): 2 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.226 2167 -random
Rwork0.182 ---
all-42951 --
obs-42951 79.9 %-
Refine analyzeLuzzati coordinate error obs: 0.22 Å / Luzzati d res low obs: 5 Å
Refinement stepCycle: LAST / Resolution: 2→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5490 0 67 277 5834
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.011
X-RAY DIFFRACTIONc_angle_deg1.6
LS refinement shellResolution: 2→2.09 Å
RfactorNum. reflection
Rfree0.246 268
Rwork0.189 -
obs-5382
Software
*PLUS
Name: CNS / Version: 1 / Classification: refinement
Refinement
*PLUS
Lowest resolution: 20 Å / σ(F): 2 / % reflection Rfree: 5 % / Rfactor obs: 0.182
Solvent computation
*PLUS
Displacement parameters
*PLUS
LS refinement shell
*PLUS
Rfactor Rfree: 0.246 / Rfactor Rwork: 0.189

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