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- PDB-4de0: CTX-M-9 class A beta-lactamase complexed with compound 16 -

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Basic information

Entry
Database: PDB / ID: 4de0
TitleCTX-M-9 class A beta-lactamase complexed with compound 16
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 / beta-lactamase activity / 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-0JB / Beta-lactamase
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.12 Å
AuthorsNichols, D.N. / 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 2.0Dec 25, 2019Group: Advisory / Derived calculations / Polymer sequence
Category: entity_poly / pdbx_struct_mod_residue ...entity_poly / pdbx_struct_mod_residue / pdbx_unobs_or_zero_occ_atoms / struct_conn
Item: _entity_poly.pdbx_seq_one_letter_code_can / _pdbx_struct_mod_residue.parent_comp_id / _struct_conn.pdbx_leaving_atom_flag
Revision 2.1Sep 13, 2023Group: Advisory / Data collection ...Advisory / 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_unobs_or_zero_occ_atoms / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 2.2Nov 6, 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)56,6005
Polymers55,9112
Non-polymers6893
Water13,223734
1
A: Beta-lactamase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,2612
Polymers27,9551
Non-polymers3051
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Beta-lactamase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,3393
Polymers27,9551
Non-polymers3832
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)45.192, 106.565, 47.669
Angle α, β, γ (deg.)90.000, 101.720, 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-0JB / N-[3-(1H-tetrazol-5-yl)phenyl]-1H-benzimidazole-7-carboxamide


Mass: 305.294 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C15H11N7O
#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.: 734 / 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: 2.01 Å3/Da / Density % sol: 38.81 %
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: APS / Beamline: 23-ID-B / Wavelength: 0.67019 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Feb 26, 2011 / Details: mirrors
RadiationMonochromator: Double crystal / Protocol: SINGLE WAVELENGTH / Scattering type: x-ray
Radiation wavelengthWavelength: 0.67019 Å / Relative weight: 1
ReflectionResolution: 1.12→50 Å / Num. all: 169565 / Num. obs: 158174 / % possible obs: 93.3 % / Observed criterion σ(I): 5 / Redundancy: 3.6 % / Rmerge(I) obs: 0.057 / Χ2: 1.072 / Net I/σ(I): 14.7
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
1.12-1.143.50.48671421.038184
1.14-1.163.50.44572651.021185.7
1.16-1.183.50.40472671.04186.1
1.18-1.213.50.38473071.059186.8
1.21-1.233.50.35674571.073188
1.23-1.263.40.32675571.065189.2
1.26-1.293.40.30376681.081190.4
1.29-1.333.40.27577551.098191.5
1.33-1.373.40.25978311.095192.6
1.37-1.413.40.23679221.088193.8
1.41-1.463.50.20580201.079194.6
1.46-1.523.50.17380831.074195.9
1.52-1.593.50.14782211.09196.8
1.59-1.673.60.12482601.08197.5
1.67-1.783.60.10782971.085198
1.78-1.923.70.08483641.094198.5
1.92-2.113.80.06383801.037198.8
2.11-2.413.90.0584111.005199
2.41-3.043.90.04284641.07199.2
3.04-503.80.03385031.156198.9

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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: 1.12→50 Å / Cor.coef. Fo:Fc: 0.973 / Cor.coef. Fo:Fc free: 0.964 / Occupancy max: 1 / Occupancy min: 0 / SU B: 0.965 / SU ML: 0.021 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.033 / ESU R Free: 0.035 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.1664 7914 5 %RANDOM
Rwork0.1339 ---
obs0.1355 158058 93.11 %-
all-169565 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso max: 155.02 Å2 / Biso mean: 9.5017 Å2 / Biso min: 2 Å2
Baniso -1Baniso -2Baniso -3
1--0.94 Å20 Å2-0.31 Å2
2--0.49 Å20 Å2
3---0.31 Å2
Refinement stepCycle: LAST / Resolution: 1.12→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3909 0 50 734 4693
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0224186
X-RAY DIFFRACTIONr_angle_refined_deg1.4821.985716
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.7595553
X-RAY DIFFRACTIONr_dihedral_angle_2_deg40.32224.424165
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.70415685
X-RAY DIFFRACTIONr_dihedral_angle_4_deg10.9241532
X-RAY DIFFRACTIONr_chiral_restr0.0990.2668
X-RAY DIFFRACTIONr_gen_planes_refined0.0130.0213198
X-RAY DIFFRACTIONr_mcbond_it1.7561.52720
X-RAY DIFFRACTIONr_mcangle_it2.48624383
X-RAY DIFFRACTIONr_scbond_it3.79631466
X-RAY DIFFRACTIONr_scangle_it5.5724.51333
X-RAY DIFFRACTIONr_rigid_bond_restr1.90634186
LS refinement shellResolution: 1.118→1.147 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.194 530 -
Rwork0.163 9880 -
all-10410 -
obs-158058 82.97 %

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