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- PDB-1my8: AmpC beta-lactamase in complex with an M.carboxyphenylglycylboron... -

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Basic information

Entry
Database: PDB / ID: 1my8
TitleAmpC beta-lactamase in complex with an M.carboxyphenylglycylboronic acid bearing the cephalothin R1 side chain
Componentsbeta-lactamase
KeywordsHYDROLASE / AmpC / beta-lactamase / cephalosporinase / 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
PHOSPHATE ION / Chem-SM3 / Beta-lactamase
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.72 Å
AuthorsMorandi, F. / Caselli, E. / Morandi, S. / Focia, P.J. / Blazquez, J. / Shoichet, B.K. / Prati, F.
CitationJournal: J.Am.Chem.Soc. / Year: 2003
Title: Nanomolar inhibitors of AmpC beta-lactamase.
Authors: Morandi, F. / Caselli, E. / Morandi, S. / Focia, P.J. / Blazquez, J. / Shoichet, B.K. / Prati, F.
History
DepositionOct 3, 2002Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 4, 2003Provider: repository / Type: Initial release
Revision 1.1Apr 28, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 30, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_initial_refinement_model / pdbx_modification_feature / 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

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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)79,8215
Polymers79,1762
Non-polymers6453
Water10,593588
1
A: beta-lactamase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,9583
Polymers39,5881
Non-polymers3702
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: beta-lactamase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,8632
Polymers39,5881
Non-polymers2751
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)118.205, 76.699, 97.656
Angle α, β, γ (deg.)90.00, 116.31, 90.00
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) / Gene: ampc / Plasmid: POGO295 / Species (production host): Escherichia coli / Production host: Escherichia coli K12 (bacteria) / Strain (production host): K12 / 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-SM3 / (1R)-1-(2-THIENYLACETYLAMINO)-1-PHENYLMETHYLBORONIC ACID


Mass: 275.131 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C13H14BNO3S
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 588 / 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: 2.27 Å3/Da / Density % sol: 45.28 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 8.7
Details: potassium phosphate buffer, pH 8.7, VAPOR DIFFUSION, HANGING DROP, temperature 295K
Crystal grow
*PLUS
Temperature: 23 ℃ / Details: used microseeding
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
11.7 Mpotassium phosphate1reservoirpH8.7
23.8 mg/mlprotein1drop
31.2 %DMSO1drop
41 Mpotassium phosphate1droppH8.7

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 5ID-B / Wavelength: 1 Å
DetectorType: MARRESEARCH / Detector: CCD / Date: Jun 12, 2002
RadiationMonochromator: mirrors / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.72→20 Å / Num. all: 82999 / Num. obs: 82138 / % possible obs: 99 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 4.27 % / Rmerge(I) obs: 0.04 / Net I/σ(I): 29.99
Reflection shellResolution: 1.72→1.76 Å / Rmerge(I) obs: 0.12 / Mean I/σ(I) obs: 11.23 / % possible all: 96
Reflection
*PLUS
% possible obs: 99.2 % / Num. measured all: 350811 / Rmerge(I) obs: 0.04
Reflection shell
*PLUS
% possible obs: 96 % / Rmerge(I) obs: 0.12 / Mean I/σ(I) obs: 11.2

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Processing

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

1fsy


Resolution: 1.72→20 Å / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.1888 2537 3.1 %random
Rwork0.1669 ---
all-82999 --
obs-81560 98.3 %-
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--2.394 Å20 Å2-1.918 Å2
2--0.466 Å20 Å2
3---1.928 Å2
Refinement stepCycle: LAST / Resolution: 1.72→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5606 0 62 588 6256
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONo_bond_d0.013
X-RAY DIFFRACTIONo_angle_deg1.753
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein_top
X-RAY DIFFRACTION2dna-rna_rep.paramdna-rna.top
X-RAY DIFFRACTION3water_rep.paramwater.top
X-RAY DIFFRACTION4ion.paramion.top
X-RAY DIFFRACTION5sm3301.parsm3301.top
Refinement
*PLUS
Rfactor Rfree: 0.189 / Rfactor Rwork: 0.167
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONo_bond_d0.014
X-RAY DIFFRACTIONo_angle_deg1.76
LS refinement shell
*PLUS
Highest resolution: 1.72 Å / Lowest resolution: 1.76 Å

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