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- PDB-1ga9: CRYSTAL STRUCTURE OF AMPC BETA-LACTAMASE FROM E. COLI COMPLEXED W... -

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Basic information

Entry
Database: PDB / ID: 1ga9
TitleCRYSTAL STRUCTURE OF AMPC BETA-LACTAMASE FROM E. COLI COMPLEXED WITH NON-BETA-LACTAMASE INHIBITOR (2, 3-(4-BENZENESULFONYL-THIOPHENE-2-SULFONYLAMINO)-PHENYLBORONIC ACID)
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
Chem-ETP / : / PHOSPHATE ION / Beta-lactamase
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å
AuthorsTondi, D. / Powers, R.A. / Caselli, E. / Negri, M.C. / Blazquez, J. / Costi, M.P. / Shoichet, B.K.
CitationJournal: Chem.Biol. / Year: 2001
Title: Structure-based design and in-parallel synthesis of inhibitors of AmpC beta-lactamase.
Authors: Tondi, D. / Powers, R.A. / Caselli, E. / Negri, M.C. / Blazquez, J. / Costi, M.P. / Shoichet, B.K.
History
DepositionNov 29, 2000Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 25, 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 / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Oct 9, 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)80,2517
Polymers79,1762
Non-polymers1,0765
Water5,729318
1
A: BETA-LACTAMASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)40,2014
Polymers39,5881
Non-polymers6133
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: BETA-LACTAMASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)40,0503
Polymers39,5881
Non-polymers4622
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)118.990, 78.060, 97.790
Angle α, β, γ (deg.)90.00, 115.53, 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 / Fragment: BETA-LACTAMASE (RESIDUES 20-377)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Plasmid: POGO295 / 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.: 2 / Source method: obtained synthetically / Formula: PO4
#3: Chemical ChemComp-ETP / 3-(4-BENZENESULFONYL-THIOPHENE-2-SULFONYLAMINO)-PHENYLBORONIC ACID


Mass: 423.291 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C16H14BNO6S3
#4: Chemical ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: K
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 318 / 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: 2.59 Å3/Da / Density % sol: 52.44 %
Crystal growTemperature: 296 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 1.7 M potassium phosphate, 95 uM AmpC, 600 uM compound 2 (ET011), pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 296K
Crystal grow
*PLUS
Temperature: 23 ℃ / Details: used microseeding
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
11.7 Mpotassium phosphate1reservoir
20.095 mMprotein1drop
30.600 mMinhibitor1drop
42 %DMSO1drop
51.7 Mpotassium phosphate1drop

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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: May 16, 2000
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.1→20 Å / Num. all: 42312 / Num. obs: 156406 / % possible obs: 89.8 % / Observed criterion σ(I): -3 / Redundancy: 3.7 % / Biso Wilson estimate: 27.89 Å2 / Rmerge(I) obs: 0.073 / Net I/σ(I): 25.2
Reflection shellResolution: 2.1→2.18 Å / Rmerge(I) obs: 0.179 / Num. unique all: 4984 / % possible all: 96
Reflection
*PLUS
Num. obs: 42312 / Num. measured all: 156406
Reflection shell
*PLUS
% possible obs: 96 %

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Processing

Software
NameClassification
CNSrefinement
DENZOdata reduction
SCALEPACKdata scaling
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 1C3B

1c3b


Resolution: 2.1→20 Å / σ(F): 2 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.249 2050 -random
Rwork0.206 ---
all-40286 --
obs-40286 85.3 %-
Refine analyzeLuzzati coordinate error obs: 0.27 Å / Luzzati d res low obs: 5 Å
Refinement stepCycle: LAST / Resolution: 2.1→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5477 0 65 318 5860
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_angle_deg1.65
X-RAY DIFFRACTIONc_bond_d0.013
LS refinement shellResolution: 2.1→2.2 Å /
RfactorNum. reflection
Rfree0.272 238
Rwork0.455 -
Software
*PLUS
Name: CNS / Version: 0.5 / Classification: refinement
Refinement
*PLUS
Lowest resolution: 20 Å / σ(F): 2 / % reflection Rfree: 5 % / Rfactor obs: 0.206
Solvent computation
*PLUS
Displacement parameters
*PLUS
LS refinement shell
*PLUS
Rfactor Rfree: 0.272 / Rfactor Rwork: 0.455

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