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- PDB-4u0x: Structure of ADC-7 beta-lactamase in complex with boronic acid in... -

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Basic information

Entry
Database: PDB / ID: 4u0x
TitleStructure of ADC-7 beta-lactamase in complex with boronic acid inhibitor S02030
ComponentsADC-7 beta-lactamase
KeywordsHydrolase/Hydrolase inhibitor / beta-lactamase / boronic acid inhibitor / Hydrolase-Hydrolase inhibitor complex
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
PHOSPHATE ION / Chem-ZXM / Beta-lactamase
Similarity search - Component
Biological speciesAcinetobacter baumannii (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.03 Å
AuthorsPowers, R.A. / Wallar, B.J. / Swanson, H.C.
CitationJournal: Biochemistry / Year: 2014
Title: Biochemical and Structural Analysis of Inhibitors Targeting the ADC-7 Cephalosporinase of Acinetobacter baumannii.
Authors: Powers, R.A. / Swanson, H.C. / Taracila, M.A. / Florek, N.W. / Romagnoli, C. / Caselli, E. / Prati, F. / Bonomo, R.A. / Wallar, B.J.
History
DepositionJul 14, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 19, 2014Provider: repository / Type: Initial release
Revision 1.1Dec 24, 2014Group: Database references
Revision 1.2Feb 4, 2015Group: Derived calculations
Revision 1.3Sep 27, 2017Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Source and taxonomy
Category: citation / diffrn_detector ...citation / diffrn_detector / entity_src_gen / pdbx_database_status / pdbx_struct_oper_list
Item: _citation.journal_id_CSD / _diffrn_detector.detector ..._citation.journal_id_CSD / _diffrn_detector.detector / _entity_src_gen.pdbx_alt_source_flag / _pdbx_database_status.pdb_format_compatible / _pdbx_struct_oper_list.symmetry_operation
Revision 1.4Dec 27, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / refine_hist
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _refine_hist.number_atoms_solvent / _refine_hist.number_atoms_total / _refine_hist.pdbx_number_atoms_ligand / _refine_hist.pdbx_number_atoms_nucleic_acid / _refine_hist.pdbx_number_atoms_protein
Revision 1.5Nov 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
B: ADC-7 beta-lactamase
A: ADC-7 beta-lactamase
C: ADC-7 beta-lactamase
D: ADC-7 beta-lactamase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)164,1019
Polymers162,7094
Non-polymers1,3915
Water12,034668
1
B: ADC-7 beta-lactamase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,0012
Polymers40,6771
Non-polymers3241
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
A: ADC-7 beta-lactamase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,0012
Polymers40,6771
Non-polymers3241
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: ADC-7 beta-lactamase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,0963
Polymers40,6771
Non-polymers4192
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
4
D: ADC-7 beta-lactamase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,0012
Polymers40,6771
Non-polymers3241
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)89.272, 81.198, 106.327
Angle α, β, γ (deg.)90.00, 113.08, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
ADC-7 beta-lactamase


Mass: 40677.301 Da / Num. of mol.: 4 / Fragment: UNP residues 24-383
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Acinetobacter baumannii (bacteria) / Plasmid: pET28a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q6DRA1, beta-lactamase
#2: Chemical
ChemComp-ZXM / 1-{(2R)-2-(dihydroxyboranyl)-2-[(thiophen-2-ylacetyl)amino]ethyl}-1H-1,2,3-triazole-4-carboxylic acid


Mass: 324.121 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C11H13BN4O5S
#3: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: PO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 668 / 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

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Sample preparation

CrystalDensity Matthews: 2.22 Å3/Da / Density % sol: 44.5 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 5 / Details: PEG 1500, succinate, phosphate, glycine

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-G / Wavelength: 0.978 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Mar 16, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.978 Å / Relative weight: 1
ReflectionResolution: 2.03→81.198 Å / Num. obs: 91079 / % possible obs: 100 % / Redundancy: 3.9 % / Net I/σ(I): 3.29

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Processing

SoftwareName: REFMAC / Version: 5.7.0029 / Classification: refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.03→50 Å / Cor.coef. Fo:Fc: 0.954 / Cor.coef. Fo:Fc free: 0.918 / SU B: 4.998 / SU ML: 0.138 / Cross valid method: THROUGHOUT / ESU R: 0.214 / ESU R Free: 0.19 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.24758 4563 5 %RANDOM
Rwork0.18529 ---
obs0.18839 86493 99.96 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 33.323 Å2
Baniso -1Baniso -2Baniso -3
1-0.69 Å20 Å21.19 Å2
2---1.9 Å20 Å2
3---0.51 Å2
Refinement stepCycle: 1 / Resolution: 2.03→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11049 0 93 668 11810
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.0211658
X-RAY DIFFRACTIONr_bond_other_d0.0010.0210917
X-RAY DIFFRACTIONr_angle_refined_deg1.841.97215912
X-RAY DIFFRACTIONr_angle_other_deg1.023325158
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.80751468
X-RAY DIFFRACTIONr_dihedral_angle_2_deg40.81725.723505
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.245151908
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.1551524
X-RAY DIFFRACTIONr_chiral_restr0.1070.21752
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.02113480
X-RAY DIFFRACTIONr_gen_planes_other0.0010.022641
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.03→2.078 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.286 333 -
Rwork0.226 6369 -
obs--99.82 %

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