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- PDB-4de3: CTX-M-9 class A beta-lactamase complexed with compound 4 -

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Basic information

Entry
Database: PDB / ID: 4de3
TitleCTX-M-9 class A beta-lactamase complexed with compound 4
ComponentsBeta-lactamase
KeywordsHydrolase/hydrolase inhibitor / CTX-M / beta-lactamase / molecular docking / fragment / Hydrolase-hydrolase inhibitor complex
Function / homology
Function and homology information


beta-lactam antibiotic catabolic process / beta-lactamase activity / beta-lactamase / response to antibiotic
Similarity search - Function
Beta-lactamase, class-A active site / Beta-lactamase class-A active site. / Beta-lactamase class A, catalytic domain / Beta-lactamase enzyme family / Beta-lactamase, class-A / Beta-lactamase / DD-peptidase/beta-lactamase superfamily / Beta-lactamase/transpeptidase-like / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
3-bromo-N-[3-(1H-tetrazol-5-yl)phenyl]benzamide / Beta-lactamase
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.44 Å
AuthorsNichols, D.A. / Chen, Y.
CitationJournal: J.Med.Chem. / Year: 2012
Title: Structure-Based Design of Potent and Ligand-Efficient Inhibitors of CTX-M Class A Beta-Lactamase
Authors: Nichols, D.A. / Jaishankar, P. / Larson, W. / Smith, E. / Liu, G. / Beyrouthy, R. / Bonnet, R. / Renslo, A.R. / Chen, Y.
History
DepositionJan 19, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 28, 2012Provider: repository / Type: Initial release
Revision 2.0Sep 13, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Polymer sequence / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / entity_poly / pdbx_initial_refinement_model / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _entity_poly.pdbx_seq_one_letter_code_can / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 2.1Oct 9, 2024Group: Structure summary / Category: pdbx_entry_details

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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)59,85315
Polymers55,9112
Non-polymers3,94213
Water8,647480
1
A: Beta-lactamase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,0998
Polymers27,9551
Non-polymers2,1437
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Beta-lactamase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,7547
Polymers27,9551
Non-polymers1,7996
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)45.174, 107.188, 47.487
Angle α, β, γ (deg.)90.000, 100.380, 90.000
Int Tables number4
Space group name H-MP1211
DetailsThe biological unit is monomer. There are 2 biological units in the asymmetric unit.

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Components

#1: Protein Beta-lactamase / Beta-lactamase CTX-M / Beta-lactamase CTX-M-9a / Betalactamase CTX-M-9 / CTX-M-9 beta-lactamase / ...Beta-lactamase CTX-M / Beta-lactamase CTX-M-9a / Betalactamase CTX-M-9 / CTX-M-9 beta-lactamase / CTX-M-9 extended-spectrum beta-lactamase


Mass: 27955.463 Da / Num. of mol.: 2 / Fragment: unp residues 29-291
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: blaCTX-M-9, blaCTX-M-9a, blaCTX-M-9b, CTX-M / Plasmid: pET-9a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q9L5C8, beta-lactamase
#2: Chemical
ChemComp-DN8 / 3-bromo-N-[3-(1H-tetrazol-5-yl)phenyl]benzamide


Mass: 344.166 Da / Num. of mol.: 11 / Source method: obtained synthetically / Formula: C14H10BrN5O
#3: Chemical ChemComp-DMS / DIMETHYL SULFOXIDE


Mass: 78.133 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6OS / Comment: DMSO, precipitant*YM
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 480 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationN

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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: 2.02 Å3/Da / Density % sol: 39.19 %
Crystal growTemperature: 292 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: Potassium Phosphate, pH 8.5, vapor diffusion, hanging drop, temperature 292K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X6A / Wavelength: 0.9795 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Jun 21, 2010 / Details: mirrors
RadiationMonochromator: Double crystal / Protocol: SINGLE WAVELENGTH / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 1.44→50 Å / Num. all: 79883 / Num. obs: 75901 / % possible obs: 95 % / Observed criterion σ(I): 5 / Redundancy: 2.5 % / Rmerge(I) obs: 0.063 / Χ2: 1.247 / Net I/σ(I): 12.9
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
1.44-1.462.10.43433061.171183.7
1.46-1.492.10.40535401.158188.3
1.49-1.522.20.36736211.168190.7
1.52-1.552.30.34237101.249193.3
1.55-1.582.40.32137421.262194.3
1.58-1.622.40.28837861.26194.8
1.62-1.662.50.25737641.261194.9
1.66-1.712.50.23338351.317196
1.71-1.762.50.20238381.331195.9
1.76-1.812.60.17738071.337195.7
1.81-1.882.60.14938351.312196
1.88-1.952.60.12338491.35196.8
1.95-2.042.60.10438781.332196.9
2.04-2.152.60.08638801.314196.9
2.15-2.292.60.07838811.268197.6
2.29-2.462.60.0739131.25197.9
2.46-2.712.60.06538951.247197.8
2.71-3.12.60.05739321.197198.2
3.1-3.912.50.04839791.051198.4
3.91-502.50.04839101.036196.1

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Processing

Software
NameVersionClassificationNB
SCALEPACKdata scaling
REFMAC5.5.0109refinement
PDB_EXTRACT3.1data extraction
HKL-2000data collection
HKL-2000data reduction
HKL-2000data scaling
REFMAC5.5.0109phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: pdb entry 3G35

3g35


Resolution: 1.44→50 Å / Cor.coef. Fo:Fc: 0.963 / Cor.coef. Fo:Fc free: 0.945 / Occupancy max: 1 / Occupancy min: 0 / SU B: 2.942 / SU ML: 0.05 / Cross valid method: THROUGHOUT / ESU R: 0.096 / ESU R Free: 0.079 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2062 3811 5 %RANDOM
Rwork0.1628 ---
obs0.165 75828 94.85 %-
all-79883 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso max: 129.37 Å2 / Biso mean: 14.3205 Å2 / Biso min: 6.32 Å2
Baniso -1Baniso -2Baniso -3
1--1.64 Å20 Å20.19 Å2
2--1.48 Å20 Å2
3---0.23 Å2
Refinement stepCycle: LAST / Resolution: 1.44→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3888 0 239 480 4607
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0224303
X-RAY DIFFRACTIONr_angle_refined_deg1.5552.0295869
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.0785545
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.5924.545165
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.95315681
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.1581531
X-RAY DIFFRACTIONr_chiral_restr0.0940.2663
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0213285
X-RAY DIFFRACTIONr_mcbond_it0.8221.52643
X-RAY DIFFRACTIONr_mcangle_it1.34224256
X-RAY DIFFRACTIONr_scbond_it2.19331660
X-RAY DIFFRACTIONr_scangle_it3.3244.51599
X-RAY DIFFRACTIONr_rigid_bond_restr0.71324303
LS refinement shellResolution: 1.441→1.478 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.325 251 -
Rwork0.262 4648 -
all-4899 -
obs-75828 83.2 %

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