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- PDB-9d78: Apo-OXA-58 carbapenemase -

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Open data


ID or keywords:

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Basic information

Entry
Database: PDB / ID: 9d78
TitleApo-OXA-58 carbapenemase
ComponentsBeta-lactamase
KeywordsHYDROLASE/INHIBITOR / beta-lactamase / carbapenemase / antibiotic resistance / apo structure / carboxylated lysine / HYDROLASE / HYDROLASE-INHIBITOR complex
Function / homology
Function and homology information


penicillin binding / antibiotic catabolic process / cell wall organization / beta-lactamase / beta-lactamase activity / response to antibiotic / plasma membrane
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 / Prokaryotic membrane lipoprotein lipid attachment site profile.
Similarity search - Domain/homology
Beta-lactamase OXA-58
Similarity search - Component
Biological speciesAcinetobacter baumannii (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsMaggiolo, A.O. / Smith, C.A. / Toth, M. / Vakulenko, S.B.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)1R01AI155723 United States
CitationJournal: Acs Infect Dis. / Year: 2024
Title: Decarboxylation of the Catalytic Lysine Residue by the C5 alpha-Methyl-Substituted Carbapenem NA-1-157 Leads to Potent Inhibition of the OXA-58 Carbapenemase.
Authors: Toth, M. / Stewart, N.K. / Maggiolo, A.O. / Quan, P. / Khan, M.M.K. / Buynak, J.D. / Smith, C.A. / Vakulenko, S.B.
History
DepositionAug 16, 2024Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 11, 2024Provider: repository / Type: Initial release
Revision 1.1Dec 25, 2024Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID

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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


Theoretical massNumber of molelcules
Total (without water)111,1234
Polymers111,1234
Non-polymers00
Water4,468248
1
A: Beta-lactamase


Theoretical massNumber of molelcules
Total (without water)27,7811
Polymers27,7811
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Beta-lactamase


Theoretical massNumber of molelcules
Total (without water)27,7811
Polymers27,7811
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: Beta-lactamase


Theoretical massNumber of molelcules
Total (without water)27,7811
Polymers27,7811
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
4
D: Beta-lactamase


Theoretical massNumber of molelcules
Total (without water)27,7811
Polymers27,7811
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)37.018, 66.356, 192.128
Angle α, β, γ (deg.)90.00, 91.21, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
Beta-lactamase


Mass: 27780.666 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Acinetobacter baumannii (bacteria)
Gene: blaOXA-58, bla-oxa-58, bla-oxa58, EKS29_04300, GSE42_20550, H0529_21805, P9867_20895
Production host: Escherichia coli (E. coli) / References: UniProt: Q2TR58, beta-lactamase
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 248 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN
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: 2.15 Å3/Da / Density % sol: 43 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop
Details: 0.2 M sodium acetate, 0.1 M Tris-HCl pH 8.5, 30% PEG4000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL12-2 / Wavelength: 0.9795 Å
DetectorType: DECTRIS EIGER2 XE 16M / Detector: PIXEL / Date: May 28, 2024
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 1.9→38.93 Å / Num. obs: 72794 / % possible obs: 99 % / Redundancy: 7.1 % / CC1/2: 0.997 / Rpim(I) all: 0.059 / Rrim(I) all: 0.158 / Net I/σ(I): 8
Reflection shellResolution: 1.9→1.94 Å / Mean I/σ(I) obs: 1.4 / Num. unique obs: 4499 / CC1/2: 0.629 / Rpim(I) all: 0.65

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Processing

Software
NameVersionClassification
REFMAC5.8.0425refinement
XDSdata reduction
Aimlessdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.9→38.93 Å / Cor.coef. Fo:Fc: 0.958 / Cor.coef. Fo:Fc free: 0.941 / SU B: 5.256 / SU ML: 0.14 / Cross valid method: THROUGHOUT / ESU R: 0.174 / ESU R Free: 0.153 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.23296 3599 4.9 %RANDOM
Rwork0.19525 ---
obs0.19709 69128 98.81 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 30.888 Å2
Baniso -1Baniso -2Baniso -3
1--2.24 Å20 Å20.41 Å2
2--3.37 Å20 Å2
3----1.14 Å2
Refinement stepCycle: 1 / Resolution: 1.9→38.93 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7684 0 0 248 7932
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0030.0127853
X-RAY DIFFRACTIONr_bond_other_d0.0010.0167536
X-RAY DIFFRACTIONr_angle_refined_deg1.0121.81610591
X-RAY DIFFRACTIONr_angle_other_deg0.371.76617306
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.1065941
X-RAY DIFFRACTIONr_dihedral_angle_2_deg3.935540
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.16101362
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.0540.21145
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.029213
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021863
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_it1.363.0573823
X-RAY DIFFRACTIONr_mcbond_other1.363.0573823
X-RAY DIFFRACTIONr_mcangle_it2.2785.4944739
X-RAY DIFFRACTIONr_mcangle_other2.2785.4944740
X-RAY DIFFRACTIONr_scbond_it1.6533.3064030
X-RAY DIFFRACTIONr_scbond_other1.6533.3064030
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other2.8375.995853
X-RAY DIFFRACTIONr_long_range_B_refined4.09130.018603
X-RAY DIFFRACTIONr_long_range_B_other4.05829.68572
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.9→1.949 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.323 276 -
Rwork0.333 5117 -
obs--98.27 %

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