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- PDB-6pwl: ADC-7 in complex with boronic acid transition state inhibitor LP06 -

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Basic information

Entry
Database: PDB / ID: 6pwl
TitleADC-7 in complex with boronic acid transition state inhibitor LP06
ComponentsBeta-lactamase
KeywordsHYDROLASE / inhibitor / Beta-lactamase / BATSI / ADC-7.
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/transpeptidase-like
Similarity search - Domain/homology
GLYCINE / Chem-LP0 / Beta-lactamase
Similarity search - Component
Biological speciesAcinetobacter baumannii (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.67 Å
AuthorsCurtis, B.C. / Powers, R.A. / Wallar, B.J.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Human Genome Research Institute (NIH/NHGRI)R01 AI072219 United States
CitationJournal: Antimicrob.Agents Chemother. / Year: 2020
Title: Structural Insights into Inhibition of the Acinetobacter-Derived Cephalosporinase ADC-7 by Ceftazidime and Its Boronic Acid Transition State Analog.
Authors: Curtis, B.N. / Smolen, K.A. / Barlow, S.J. / Caselli, E. / Prati, F. / Taracila, M.A. / Bonomo, R.A. / Wallar, B.J. / Powers, R.A.
History
DepositionJul 23, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 21, 2020Provider: repository / Type: Initial release
Revision 1.1Dec 2, 2020Group: Database references / Category: citation / Item: _citation.journal_volume / _citation.title
Revision 1.2Oct 11, 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
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.3Nov 6, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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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
C: Beta-lactamase
D: Beta-lactamase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)164,9499
Polymers163,2344
Non-polymers1,7155
Water9,818545
1
A: Beta-lactamase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,2192
Polymers40,8081
Non-polymers4101
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Beta-lactamase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,2192
Polymers40,8081
Non-polymers4101
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: Beta-lactamase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,2943
Polymers40,8081
Non-polymers4852
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
4
D: Beta-lactamase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,2192
Polymers40,8081
Non-polymers4101
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)87.735, 81.279, 105.117
Angle α, β, γ (deg.)90.000, 112.990, 90.000
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11B
21A
12B
22C
13B
23D
14A
24C
15A
25D
16C
26D

NCS domain segments:
Dom-IDComponent-IDEns-IDRefine codeAuth asym-IDAuth seq-ID
1010B4 - 358
2010A4 - 358
1020B4 - 356
2020C4 - 356
1030B4 - 358
2030D4 - 358
1040A3 - 356
2040C3 - 356
1050A3 - 358
2050D3 - 358
1060C3 - 357
2060D3 - 357

NCS ensembles :
ID
1
2
3
4
5
6

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Components

#1: Protein
Beta-lactamase


Mass: 40808.496 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Acinetobacter baumannii (bacteria) / Plasmid: pET28a / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q6DRA1, beta-lactamase
#2: Chemical
ChemComp-LP0 / (7Z)-7-(2-amino-1,3-thiazol-4-yl)-1,1,3-trihydroxy-10,10-dimethyl-1,6-dioxo-2,9-dioxa-5,8-diaza-1lambda~5~-phospha-3-boraundec-7-en-11-oic acid


Mass: 410.105 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C10H16BN4O9PS / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-GLY / GLYCINE


Type: peptide linking / Mass: 75.067 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H5NO2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 545 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
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: 2.11 Å3/Da / Density % sol: 41.81 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 5
Details: ADC-7 (3.5mg/mL) in 25% w/v polyethylene glycol (PEG) 1500, 0.1 M succinate/ phosphate/ glycine

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-D / Wavelength: 0.97851 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Jul 10, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97851 Å / Relative weight: 1
ReflectionResolution: 1.67→96.77 Å / Num. obs: 109985 / % possible obs: 80.766 % / Redundancy: 3.9 % / CC1/2: 0.998 / Rmerge(I) obs: 0.061 / Rpim(I) all: 0.035 / Net I/σ(I): 11.4
Reflection shellResolution: 1.676→1.857 Å / Redundancy: 3.9 % / Rmerge(I) obs: 0.741 / Num. unique obs: 5500 / CC1/2: 0.646 / Rpim(I) all: 0.436 / % possible all: 67.7

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Processing

Software
NameVersionClassification
REFMAC5.8.0253refinement
PDB_EXTRACT3.25data extraction
Cootmodel building
XSCALEdata scaling
PHASERphasing
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4U0T

4u0t


Resolution: 1.67→96.77 Å / Cor.coef. Fo:Fc: 0.948 / Cor.coef. Fo:Fc free: 0.927 / SU B: 3.65 / SU ML: 0.118 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.193 / ESU R Free: 0.169
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2626 5463 5 %RANDOM
Rwork0.2221 ---
obs0.2242 104531 69.94 %-
Solvent computationIon probe radii: 0.7 Å / Shrinkage radii: 0.7 Å / VDW probe radii: 1 Å
Displacement parametersBiso max: 120.14 Å2 / Biso mean: 34.15 Å2 / Biso min: 11.04 Å2
Baniso -1Baniso -2Baniso -3
1--0.19 Å20 Å20.07 Å2
2---0.08 Å20 Å2
3---0.15 Å2
Refinement stepCycle: final / Resolution: 1.67→96.77 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11037 0 109 571 11717
Biso mean--55.91 35.69 -
Num. residues----1423
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0050.01311512
X-RAY DIFFRACTIONr_bond_other_d0.0010.01710324
X-RAY DIFFRACTIONr_angle_refined_deg1.4071.66715708
X-RAY DIFFRACTIONr_angle_other_deg1.2531.57824084
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.02151438
X-RAY DIFFRACTIONr_dihedral_angle_2_deg39.94225.029523
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.459151856
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.6431523
X-RAY DIFFRACTIONr_chiral_restr0.0660.21513
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0212917
X-RAY DIFFRACTIONr_gen_planes_other0.0010.022192
Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Weight position: 0.05

Ens-IDDom-IDAuth asym-IDNumberRms dev position (Å)
11B118780.08
12A118780.08
21B114690.08
22C114690.08
31B114010.07
32D114010.07
41A117090.07
42C117090.07
51A115960.07
52D115960.07
61C113250.06
62D113250.06
LS refinement shellResolution: 1.671→1.714 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.342 13 -
Rwork0.276 241 -
all-254 -
obs--2.2 %

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