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- PDB-3pag: Crystal structure of the V130D mutant of OXA-24/40 in complex wit... -

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Basic information

Entry
Database: PDB / ID: 3pag
TitleCrystal structure of the V130D mutant of OXA-24/40 in complex with doripenem
ComponentsBeta-lactamase
KeywordsHYDROLASE/ANTIBIOTIC / hydrolase / carbapenemase / HYDROLASE-ANTIBIOTIC complex
Function / homology
Function and homology information


penicillin binding / beta-lactamase activity
Similarity search - Function
Penicillin-binding protein, transpeptidase / Penicillin binding protein transpeptidase domain / Beta-lactamase / DD-peptidase/beta-lactamase superfamily / Beta-lactamase/transpeptidase-like / Prokaryotic membrane lipoprotein lipid attachment site profile. / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Chem-4J6 / Beta-lactamase
Similarity search - Component
Biological speciesAcinetobacter baumannii (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.25 Å
AuthorsPowers, R.A. / Leonard, D.A. / Schneider, K.D.
Citation
Journal: J.Mol.Biol. / Year: 2011
Title: Structures of the Class D Carbapenemase OXA-24 from Acinetobacter baumannii in Complex with Doripenem.
Authors: Schneider, K.D. / Ortega, C.J. / Renck, N.A. / Bonomo, R.A. / Powers, R.A. / Leonard, D.A.
#1: Journal: Biochemistry / Year: 2009
Title: The 1.4 A crystal structure of the class D beta-lactamase OXA-1 complexed with doripenem
Authors: Schneider, K.D. / Karpen, M.E. / Bonomo, R.A. / Leonard, D.A. / Powers, R.A.
History
DepositionOct 19, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 19, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 25, 2015Group: Non-polymer description
Revision 1.3Oct 5, 2016Group: Non-polymer description
Revision 1.4Sep 6, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.5Nov 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

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Assembly

Deposited unit
A: Beta-lactamase
B: Beta-lactamase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)56,80310
Polymers55,3822
Non-polymers1,4218
Water3,531196
1
A: Beta-lactamase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,4025
Polymers27,6911
Non-polymers7114
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Beta-lactamase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,4025
Polymers27,6911
Non-polymers7114
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)102.274, 102.274, 85.449
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number76
Space group name H-MP41

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Components

#1: Protein Beta-lactamase / Beta-lactamase OXA-33 / Betalactamase OXA24 / Carbapenem-hydrolyzing beta-lactamase OXA-40 / ...Beta-lactamase OXA-33 / Betalactamase OXA24 / Carbapenem-hydrolyzing beta-lactamase OXA-40 / Carbapenem-hydrolyzing oxacillinase / Class D beta-lactamase OXA-40 / OXA-24 class D beta-lactamase / Oxa40


Mass: 27690.809 Da / Num. of mol.: 2 / Fragment: UNP residues 32-275 / Mutation: V130D
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Acinetobacter baumannii (bacteria)
Gene: blaOXA-33, bla-OXA-40, blaOXA-24, blaOXA-40, oxa-24, oxa40
Plasmid: pET24a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q8RLA6, beta-lactamase
#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.: 2 / Source method: obtained synthetically / Formula: C15H26N4O6S2
#3: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 196 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY
Nonpolymer details4J6 IN THE STRUCTURE REPRESENTS THE DELTA 2 TAUTOMER, IN WHICH A DOUBLE BOND IS PRESENT BETWEEN ...4J6 IN THE STRUCTURE REPRESENTS THE DELTA 2 TAUTOMER, IN WHICH A DOUBLE BOND IS PRESENT BETWEEN CARBONS 2 AND 3 (ATOMS CAS AND CAZ).

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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: 4.03 Å3/Da / Density % sol: 69.51 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: 100 mM TRIS-HCl, 2.0 M ammonium sulfate, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-D / Wavelength: 1.1 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Jun 5, 2009
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.1 Å / Relative weight: 1
ReflectionResolution: 2.25→50 Å / Num. obs: 41616 / % possible obs: 99 %
Reflection shellResolution: 2.25→2.33 Å / % possible all: 95.5

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Processing

Software
NameVersionClassification
HKL-2000data collection
PHASERphasing
REFMAC5.5.0109refinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2JC7

2jc7


Resolution: 2.25→50 Å / Cor.coef. Fo:Fc: 0.956 / Cor.coef. Fo:Fc free: 0.935 / SU B: 4.934 / SU ML: 0.122 / Cross valid method: THROUGHOUT / ESU R: 0.186 / ESU R Free: 0.174 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.23298 2097 5 %RANDOM
Rwork0.18905 ---
obs0.19127 39512 98.97 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 36.791 Å2
Baniso -1Baniso -2Baniso -3
1--3.16 Å20 Å20 Å2
2---3.16 Å2-0 Å2
3---6.32 Å2
Refinement stepCycle: LAST / Resolution: 2.25→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3874 0 84 196 4154
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0170.0224057
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.6221.9735489
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.6025496
X-RAY DIFFRACTIONr_dihedral_angle_2_deg40.27925.506178
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.39915748
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.3961515
X-RAY DIFFRACTIONr_chiral_restr0.1080.2602
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.0212975
X-RAY DIFFRACTIONr_gen_planes_other
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_it1.0191.52438
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.92423924
X-RAY DIFFRACTIONr_scbond_it2.94231619
X-RAY DIFFRACTIONr_scangle_it4.9484.51561
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.248→2.306 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.385 165 -
Rwork0.311 2746 -
obs--93.39 %

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