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- PDB-4ua9: CTX-M-14 Class A Beta-Lactamase in Complex with a Boronic Acid Ac... -

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Basic information

Entry
Database: PDB / ID: 4ua9
TitleCTX-M-14 Class A Beta-Lactamase in Complex with a Boronic Acid Acylation Transition State Analog at Sub-Angstrom Resolution
ComponentsBeta-lactamase CTX-M-14
KeywordsHYDROLASE / CTX-M-14 / Class A Beta-Lactamase / Boronic Acid / Acylation Transition State
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-CB4 / PHOSPHATE ION / Beta-lactamase
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 0.84 Å
AuthorsNichols, D.A. / Chen, Y.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)AI103158 United States
CitationJournal: J.Am.Chem.Soc. / Year: 2015
Title: Ligand-Induced Proton Transfer and Low-Barrier Hydrogen Bond Revealed by X-ray Crystallography.
Authors: Nichols, D.A. / Hargis, J.C. / Sanishvili, R. / Jaishankar, P. / Defrees, K. / Smith, E.W. / Wang, K.K. / Prati, F. / Renslo, A.R. / Woodcock, H.L. / Chen, Y.
History
DepositionAug 8, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 24, 2015Provider: repository / Type: Initial release
Revision 1.1Jul 15, 2015Group: Database references
Revision 1.2Sep 27, 2017Group: Advisory / Author supporting evidence ...Advisory / Author supporting evidence / Derived calculations / Other / Refinement description / Source and taxonomy
Category: entity_src_gen / pdbx_audit_support ...entity_src_gen / pdbx_audit_support / pdbx_database_status / pdbx_struct_oper_list / pdbx_validate_close_contact / software
Item: _entity_src_gen.pdbx_alt_source_flag / _pdbx_audit_support.funding_organization ..._entity_src_gen.pdbx_alt_source_flag / _pdbx_audit_support.funding_organization / _pdbx_database_status.pdb_format_compatible / _pdbx_struct_oper_list.symmetry_operation / _software.classification
Revision 2.0Dec 11, 2019Group: Author supporting evidence / Polymer sequence / Category: entity_poly / pdbx_audit_support
Item: _entity_poly.pdbx_seq_one_letter_code_can / _pdbx_audit_support.funding_organization
Revision 2.1Sep 27, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / refine_hist
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _refine_hist.number_atoms_total

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Beta-lactamase CTX-M-14
B: Beta-lactamase CTX-M-14
hetero molecules


Theoretical massNumber of molelcules
Total (without water)57,1029
Polymers55,9672
Non-polymers1,1357
Water16,322906
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A: Beta-lactamase CTX-M-14
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,5044
Polymers27,9841
Non-polymers5203
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Beta-lactamase CTX-M-14
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,5995
Polymers27,9841
Non-polymers6154
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)45.074, 106.632, 47.684
Angle α, β, γ (deg.)90.00, 102.18, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Beta-lactamase CTX-M-14


Mass: 27983.516 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: CTX-M-14 / Plasmid: PET-9a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: H6UQI0
#2: Chemical ChemComp-CB4 / PINACOL[[2-AMINO-ALPHA-(1-CARBOXY-1-METHYLETHOXYIMINO)-4-THIAZOLEACETYL]AMINO]METHANEBORONATE


Mass: 330.125 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H15BN4O6S
#3: Chemical
ChemComp-PO4 / PHOSPHATE ION / Phosphate


Mass: 94.971 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: PO4
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 906 / Source method: isolated from a natural source / Formula: H2O

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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 Å3/Da / Density % sol: 38.5 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8.3 / Details: 1.0M Potassium Phosphate / PH range: 8.3

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-B / Wavelength: 0.75142 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Aug 7, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.75142 Å / Relative weight: 1
ReflectionResolution: 0.84→50 Å / Num. obs: 408001 / % possible obs: 99.6 % / Redundancy: 4.9 % / Rmerge(I) obs: 0.072 / Net I/σ(I): 23.3

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Processing

Software
NameClassification
SHELXLrefinement
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2P74

2p74


Resolution: 0.84→20 Å / Num. parameters: 50364 / Num. restraintsaints: 69171 / Cross valid method: FREE R-VALUE / σ(F): 0 / Stereochemistry target values: ENGH AND HUBER / Details: ANISOTROPIC REFINEMENT REDUCED FREE R (NO CUTOFF)
RfactorNum. reflection% reflectionSelection details
Rfree0.1313 12752 3.1 %RANDOM
Rwork0.1223 ---
obs0.1223 407969 96.1 %-
Refine analyzeNum. disordered residues: 202 / Occupancy sum hydrogen: 3826 / Occupancy sum non hydrogen: 4815.3
Refinement stepCycle: 1 / Resolution: 0.84→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3907 0 69 906 4882
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONs_bond_d0.014
X-RAY DIFFRACTIONs_angle_d0.031
X-RAY DIFFRACTIONs_similar_dist0
X-RAY DIFFRACTIONs_from_restr_planes0.039
X-RAY DIFFRACTIONs_zero_chiral_vol0.1
X-RAY DIFFRACTIONs_non_zero_chiral_vol0.1
X-RAY DIFFRACTIONs_anti_bump_dis_restr0.086
X-RAY DIFFRACTIONs_rigid_bond_adp_cmpnt0.005
X-RAY DIFFRACTIONs_similar_adp_cmpnt0.025
X-RAY DIFFRACTIONs_approx_iso_adps0.043

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