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- PDB-8sq8: X-ray crystal structure of Acinetobacter baumanii beta-lactamase ... -

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Basic information

Entry
Database: PDB / ID: 8sq8
TitleX-ray crystal structure of Acinetobacter baumanii beta-lactamase variant OXA-109 in complex with doripenem
ComponentsBeta-lactamase OXA-109
KeywordsHYDROLASE/INHIBITOR / ANTIBIOTIC / Acinetobacter beta-lactamase Complex carbapenem Doripenem / HYDROLASE / HYDROLASE-INHIBITOR / ANTIBIOTIC complex
Function / homology
Function and homology information


penicillin binding / beta-lactamase
Similarity search - Function
: / Penicillin-binding protein, transpeptidase / Penicillin binding protein transpeptidase domain / Beta-lactamase/transpeptidase-like / Prokaryotic membrane lipoprotein lipid attachment site profile.
Similarity search - Domain/homology
Chem-4J6 / BICARBONATE ION / beta-lactamase
Similarity search - Component
Biological speciesAcinetobacter baumannii (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.27 Å
AuthorsPowers, R.A. / Leonard, D.A. / June, C.M. / Szarecka, A. / Wawrzak, Z.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)R01AI072219 United States
CitationJournal: J.Mol.Biol. / Year: 2024
Title: Structural and Dynamic Features of Acinetobacter baumannii OXA-66 beta-Lactamase Explain Its Stability and Evolution of Novel Variants.
Authors: Klamer, Z.L. / June, C.M. / Wawrzak, Z. / Taracila, M.A. / Grey, J.A. / Benn, A.M.I. / Russell, C.P. / Bonomo, R.A. / Powers, R.A. / Leonard, D.A. / Szarecka, A.
History
DepositionMay 4, 2023Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 22, 2024Provider: repository / Type: Initial release
Revision 1.1May 29, 2024Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.title / _citation_author.name

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Beta-lactamase OXA-109
B: Beta-lactamase OXA-109
C: Beta-lactamase OXA-109
D: Beta-lactamase OXA-109
hetero molecules


Theoretical massNumber of molelcules
Total (without water)114,49310
Polymers112,6804
Non-polymers1,8126
Water1,60389
1
A: Beta-lactamase OXA-109
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,5932
Polymers28,1701
Non-polymers4231
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Beta-lactamase OXA-109
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,6543
Polymers28,1701
Non-polymers4842
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Beta-lactamase OXA-109
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,5932
Polymers28,1701
Non-polymers4231
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: Beta-lactamase OXA-109
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,6543
Polymers28,1701
Non-polymers4842
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)70.249, 70.249, 449.106
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number151
Space group name H-MP3112
Space group name HallP312(x,y,z+1/3)
Symmetry operation#1: x,y,z
#2: -y,x-y,z+1/3
#3: -x+y,-x,z+2/3
#4: -y,-x,-z+2/3
#5: -x+y,y,-z+1/3
#6: x,x-y,-z

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Components

#1: Protein
Beta-lactamase OXA-109 / Carbapenem-hydrolyzing oxacillinase


Mass: 28170.109 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Acinetobacter baumannii (bacteria) / Gene: bla-OXA-109, blaOXA-109 / Plasmid: pET 24a / Production host: Escherichia coli (E. coli) / References: UniProt: A8JZR7
#2: Chemical
ChemComp-4J6 / (4R,5S)-5-[(2S,3R)-3-hydroxy-1-oxobutan-2-yl]-4-methyl-3-({(3S,5S)-5-[(sulfamoylamino)methyl]pyrrolidin-3-yl}sulfanyl)-4,5-dihydro-1H-pyrrole-2-carboxylic acid / Doripenem(open form, pyrroline tautomer form 1, SP2 connection to Thio)


Mass: 422.520 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C15H26N4O6S2 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-BCT / BICARBONATE ION


Mass: 61.017 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: CHO3 / Comment: pH buffer*YM
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 89 / 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: 2.84 Å3/Da / Density % sol: 56.67 %
Crystal growTemperature: 296 K / Method: vapor diffusion, hanging drop
Details: 0.09 M HEPES, pH 7.5, 1.26 M Sodium Citrate, 10% v/v glycerol

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-F / Wavelength: 0.9787 Å
DetectorType: RAYONIX MX-300 / Detector: CCD / Date: Jun 30, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9787 Å / Relative weight: 1
ReflectionResolution: 2.27→30 Å / Num. obs: 59493 / % possible obs: 99.62 % / Redundancy: 7.2 % / CC1/2: 1 / Net I/σ(I): 29.81
Reflection shellResolution: 2.27→2.31 Å / Redundancy: 7.9 % / Mean I/σ(I) obs: 2 / Num. unique obs: 2881 / CC1/2: 0.666 / % possible all: 99.95

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Processing

Software
NameVersionClassification
PHENIX1.19.1_4122refinement
HKL-2000data reduction
HKL-2000data scaling
PHASER2.8.3phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.27→29.94 Å / Cross valid method: FREE R-VALUE / σ(F): 25.61 / Phase error: 29.6723
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.248 3016 5.08 %
Rwork0.2111 56371 -
obs0.2325 59387 99.66 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 53.11 Å2
Refinement stepCycle: LAST / Resolution: 2.27→29.94 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7396 0 116 89 7601
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00247671
X-RAY DIFFRACTIONf_angle_d0.679510428
X-RAY DIFFRACTIONf_chiral_restr0.04231171
X-RAY DIFFRACTIONf_plane_restr0.00291333
X-RAY DIFFRACTIONf_dihedral_angle_d9.99311108
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.27-2.310.3681480.35242723X-RAY DIFFRACTION94.35
2.31-2.350.38061510.36752853X-RAY DIFFRACTION94.97
2.35-2.40.3451260.35692772X-RAY DIFFRACTION95.65
2.4-2.440.34981360.35412826X-RAY DIFFRACTION95.41
2.44-2.50.28771560.36132798X-RAY DIFFRACTION94.72
2.5-2.560.34871660.33622783X-RAY DIFFRACTION94.37
2.56-2.620.42451490.32742795X-RAY DIFFRACTION94.94
2.62-2.690.33711520.3232851X-RAY DIFFRACTION94.91
2.69-2.770.36591440.312771X-RAY DIFFRACTION95.03
2.77-2.860.29961610.31042795X-RAY DIFFRACTION94.55
2.86-2.960.32311480.27972829X-RAY DIFFRACTION95.03
2.96-3.080.27351510.27162812X-RAY DIFFRACTION94.87
3.08-3.220.30891740.27212826X-RAY DIFFRACTION94.14
3.22-3.390.24251430.2382811X-RAY DIFFRACTION95.03
3.39-3.60.30991440.22672808X-RAY DIFFRACTION94.32
3.6-3.880.26491470.20262847X-RAY DIFFRACTION94.24
3.88-4.270.23821490.17812772X-RAY DIFFRACTION93.71
4.27-4.880.22721720.15562803X-RAY DIFFRACTION92.36
4.88-6.140.21761510.17642887X-RAY DIFFRACTION94.44
6.15-29.940.19941470.19553010X-RAY DIFFRACTION95.07

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