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- PDB-4dds: CTX-M-9 class A beta-lactamase complexed with compound 11 -

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Basic information

Entry
Database: PDB / ID: 4dds
TitleCTX-M-9 class A beta-lactamase complexed with compound 11
ComponentsBeta-lactamase
KeywordsHydrolase/hydrolase inhibitor / CTX-M / 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
Chem-0J7 / Beta-lactamase
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.36 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)57,7068
Polymers55,9112
Non-polymers1,7956
Water8,881493
1
A: Beta-lactamase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,9854
Polymers27,9551
Non-polymers1,0303
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Beta-lactamase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,7204
Polymers27,9551
Non-polymers7653
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)45.245, 106.941, 47.681
Angle α, β, γ (deg.)90.000, 100.970, 90.000
Int Tables number4
Space group name H-MP1211

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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 30-291
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-0J7 / 3-(pyrimidin-2-yl)-N-[3-(1H-tetrazol-5-yl)phenyl]benzamide


Mass: 343.342 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C18H13N7O
#3: Chemical ChemComp-DMS / DIMETHYL SULFOXIDE


Mass: 78.133 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6OS / Comment: DMSO, precipitant*YM
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 493 / 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: 2.03 Å3/Da / Density % sol: 39.27 %
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: 1.36→50 Å / Num. all: 95149 / Num. obs: 87996 / % possible obs: 92.5 % / Observed criterion σ(I): 5 / Redundancy: 3.7 % / Rmerge(I) obs: 0.056 / Χ2: 1.191 / Net I/σ(I): 18.2
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
1.36-1.383.40.55236830.94178.2
1.38-1.413.70.49943570.975190.8
1.41-1.443.70.4443140.988191.9
1.44-1.473.70.37443201.018190.5
1.47-1.53.70.32742941.082190.9
1.5-1.533.70.28343311.107191.6
1.53-1.573.70.24943681.13191.4
1.57-1.613.70.20643971.174192.5
1.61-1.663.70.18944091.205193.6
1.66-1.713.70.15244711.222194.2
1.71-1.773.70.13245191.245194.8
1.77-1.853.70.10745361.255195.2
1.85-1.933.70.08645491.316196.1
1.93-2.033.80.06846121.329196.7
2.03-2.163.90.05646301.286196.9
2.16-2.333.90.04946141.322197.4
2.33-2.563.90.04246741.227197.8
2.56-2.933.90.03646821.178198.2
2.93-3.693.90.03247141.201198.5
3.69-503.80.03247661.467198.4

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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: 1.36→25.26 Å / Cor.coef. Fo:Fc: 0.963 / Cor.coef. Fo:Fc free: 0.94 / Occupancy max: 1 / Occupancy min: 0.4 / SU B: 2.065 / SU ML: 0.037 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.073 / ESU R Free: 0.066 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.1986 4395 5 %RANDOM
Rwork0.1558 ---
obs0.1579 87912 93 %-
all-95149 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso max: 128.14 Å2 / Biso mean: 10.6623 Å2 / Biso min: 2.5 Å2
Baniso -1Baniso -2Baniso -3
1--1.27 Å20 Å2-0.73 Å2
2--0.85 Å20 Å2
3---0.15 Å2
Refinement stepCycle: LAST / Resolution: 1.36→25.26 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3888 0 134 493 4515
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0224203
X-RAY DIFFRACTIONr_angle_refined_deg1.382.0035729
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.4645541
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.99424.667165
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.57115675
X-RAY DIFFRACTIONr_dihedral_angle_4_deg12.5561530
X-RAY DIFFRACTIONr_chiral_restr0.0940.2659
X-RAY DIFFRACTIONr_gen_planes_refined0.0120.0213232
X-RAY DIFFRACTIONr_mcbond_it1.1611.52661
X-RAY DIFFRACTIONr_mcangle_it1.84224278
X-RAY DIFFRACTIONr_scbond_it2.92131542
X-RAY DIFFRACTIONr_scangle_it4.4314.51448
X-RAY DIFFRACTIONr_rigid_bond_restr1.26734203
LS refinement shellResolution: 1.363→1.398 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.338 283 -
Rwork0.304 5124 -
all-5407 -
obs-87912 77.7 %

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