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- PDB-7pse: Crystal Structure of a Class D Carbapenemase_K73ALY Complexed wit... -

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Basic information

Entry
Database: PDB / ID: 7pse
TitleCrystal Structure of a Class D Carbapenemase_K73ALY Complexed with Oxacillin
ComponentsBeta-lactamase
KeywordsHYDROLASE / OXA / Oxacillin / K73ALY
Function / homology
Function and homology information


penicillin binding / antibiotic catabolic process / cell wall organization / beta-lactamase activity / beta-lactamase / response to antibiotic
Similarity search - Function
Beta-lactamase, class-D active site / Beta-lactamase class-D active site. / Penicillin-binding protein, transpeptidase / Penicillin binding protein transpeptidase domain / Beta-lactamase/transpeptidase-like
Similarity search - Domain/homology
1-BUTANOL / Chem-1S6 / Beta-lactamase
Similarity search - Component
Biological speciesKlebsiella pneumoniae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.32 Å
AuthorsZhou, Q. / He, Y. / Jin, Y.
Funding support China, 1items
OrganizationGrant numberCountry
National Science Foundation (NSF, China)31400663 China
CitationJournal: Acs Cent.Sci. / Year: 2023
Title: An Ion-Pair Induced Intermediate Complex Captured in Class D Carbapenemase Reveals Chloride Ion as a Janus Effector Modulating Activity
Authors: Zhou, Q. / Catalan, P. / Bell, H. / Baumann, P. / Cooke, R. / Evans, R. / Yang, J. / Zhang, Z. / Zappala, D. / Zhang, Y. / Blackburn, G.M. / He, Y. / Jin, Y.
History
DepositionSep 23, 2021Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 5, 2022Provider: repository / Type: Initial release
Revision 2.0Nov 15, 2023Group: Atomic model / Data collection / Refinement description
Category: atom_site / chem_comp_atom ...atom_site / chem_comp_atom / chem_comp_bond / struct_ncs_dom_lim
Item: _atom_site.auth_atom_id / _atom_site.label_atom_id ..._atom_site.auth_atom_id / _atom_site.label_atom_id / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id
Revision 2.1Jan 31, 2024Group: Refinement description / Category: pdbx_initial_refinement_model
Revision 2.2Mar 6, 2024Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.title / _citation.year

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
AAA: Beta-lactamase
BBB: Beta-lactamase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)61,6439
Polymers60,5042
Non-polymers1,1397
Water1,15364
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3000 Å2
ΔGint5 kcal/mol
Surface area19820 Å2
MethodPISA
Unit cell
Length a, b, c (Å)44.830, 105.480, 124.960
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP22121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11AAA
21BBB

NCS domain segments:

Ens-ID: 1 / Beg auth comp-ID: GLU / Beg label comp-ID: GLU / End auth comp-ID: PRO / End label comp-ID: PRO / Auth seq-ID: 24 - 265 / Label seq-ID: 19 - 260

Dom-IDComponent-IDAuth asym-IDLabel asym-ID
11AAAA
22BBBB

NCS ensembles : (Details: Local NCS retraints between domains: 1 2)

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Components

#1: Protein Beta-lactamase


Mass: 30252.156 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Klebsiella pneumoniae (bacteria) / Gene: blaOXA / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0A482LRD5, beta-lactamase
#2: Chemical ChemComp-1S6 / (2R,4S)-5,5-dimethyl-2-[(1R)-1-{[(5-methyl-3-phenyl-1,2-oxazol-4-yl)carbonyl]amino}-2-oxoethyl]-1,3-thiazolidine-4-carb oxylic acid / Oxacillin, bound form


Mass: 403.452 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C19H21N3O5S / Feature type: SUBJECT OF INVESTIGATION / Comment: antibiotic*YM
#3: Chemical
ChemComp-1BO / 1-BUTANOL / BUTAN-1-OL


Mass: 74.122 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C4H10O
#4: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 64 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 2.44 Å3/Da / Density % sol: 49.62 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 0.1M HEPES pH 7.5, 11.6% PEG8000, 8% 1-BuOH, mixed with the 10 mg/mL protein stock at 1:1 ratio.

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.97627 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jul 7, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97627 Å / Relative weight: 1
ReflectionResolution: 2.32→53.76 Å / Num. obs: 26329 / % possible obs: 99.3 % / Redundancy: 10.9 % / CC1/2: 0.996 / Net I/σ(I): 7
Reflection shellResolution: 2.32→2.4 Å / Mean I/σ(I) obs: 1 / Num. unique obs: 2438 / CC1/2: 0.566

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Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
SADABSdata reduction
Aimlessdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4S2P

4s2p


Resolution: 2.32→53.76 Å / Cor.coef. Fo:Fc: 0.938 / Cor.coef. Fo:Fc free: 0.898 / SU B: 15.429 / SU ML: 0.321 / Cross valid method: FREE R-VALUE / ESU R: 0.384 / ESU R Free: 0.276
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.2886 1266 4.817 %
Rwork0.2352 25014 -
all0.238 --
obs-26280 99.215 %
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT
Displacement parametersBiso mean: 46.938 Å2
Baniso -1Baniso -2Baniso -3
1-4.801 Å20 Å20 Å2
2---0.452 Å20 Å2
3----4.349 Å2
Refinement stepCycle: LAST / Resolution: 2.32→53.76 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3958 0 77 64 4099
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0134133
X-RAY DIFFRACTIONr_bond_other_d0.0010.0183872
X-RAY DIFFRACTIONr_angle_refined_deg1.5291.6395592
X-RAY DIFFRACTIONr_angle_other_deg1.1951.5868869
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.1535480
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.75422.743237
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.29515705
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.3311524
X-RAY DIFFRACTIONr_chiral_restr0.0640.2517
X-RAY DIFFRACTIONr_chiral_restr_other0.1250.22
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.024702
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021026
X-RAY DIFFRACTIONr_nbd_refined0.2140.2883
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1790.23868
X-RAY DIFFRACTIONr_nbtor_refined0.1660.21961
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0780.21968
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1280.2122
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.1220.212
X-RAY DIFFRACTIONr_nbd_other0.1890.234
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.1790.23
X-RAY DIFFRACTIONr_mcbond_it3.9564.8411933
X-RAY DIFFRACTIONr_mcbond_other3.9574.8411930
X-RAY DIFFRACTIONr_mcangle_it6.1287.2432408
X-RAY DIFFRACTIONr_mcangle_other6.1287.2452408
X-RAY DIFFRACTIONr_scbond_it3.6145.1222200
X-RAY DIFFRACTIONr_scbond_other3.6135.1222201
X-RAY DIFFRACTIONr_scangle_it5.7657.5463184
X-RAY DIFFRACTIONr_scangle_other5.7647.5463185
X-RAY DIFFRACTIONr_lrange_it8.52854.5794710
X-RAY DIFFRACTIONr_lrange_other8.52854.5854709
X-RAY DIFFRACTIONr_ncsr_local_group_10.0740.058270
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDRefine-IDTypeRms dev position (Å)Weight position
11AAAX-RAY DIFFRACTIONLocal ncs0.074240.05009
12BBBX-RAY DIFFRACTIONLocal ncs0.074240.05009
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.32-2.380.395960.3851725X-RAY DIFFRACTION94.4502
2.38-2.4450.3741030.381733X-RAY DIFFRACTION97.504
2.445-2.5160.349810.3521720X-RAY DIFFRACTION98.2007
2.516-2.5940.355710.3131668X-RAY DIFFRACTION99.4282
2.594-2.6790.369810.3021642X-RAY DIFFRACTION99.942
2.679-2.7730.329880.2981595X-RAY DIFFRACTION100
2.773-2.8770.362590.2911534X-RAY DIFFRACTION100
2.877-2.9950.335770.2821494X-RAY DIFFRACTION100
2.995-3.1280.394730.2621401X-RAY DIFFRACTION99.8645
3.128-3.280.29780.2411365X-RAY DIFFRACTION100
3.28-3.4580.308570.2231317X-RAY DIFFRACTION100
3.458-3.6670.311640.2181216X-RAY DIFFRACTION100
3.667-3.920.231510.1891167X-RAY DIFFRACTION99.918
3.92-4.2340.233640.1641083X-RAY DIFFRACTION99.8259
4.234-4.6380.218570.164998X-RAY DIFFRACTION99.9053
4.638-5.1840.23480.174923X-RAY DIFFRACTION100
5.184-5.9840.205430.164812X-RAY DIFFRACTION100
5.984-7.3250.236310.175720X-RAY DIFFRACTION100
7.325-10.3420.24270.188559X-RAY DIFFRACTION100

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