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- PDB-3qnb: Crystal Structure of an Engineered OXA-10 Variant with Carbapenem... -

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Basic information

Entry
Database: PDB / ID: 3qnb
TitleCrystal Structure of an Engineered OXA-10 Variant with Carbapenemase Activity, OXA-10loop24
ComponentsOxacillinase
KeywordsHYDROLASE / antibiotic resistance / hydrolysis of amide bond of beta-lactam compounds
Function / homology
Function and homology information


penicillin binding / antibiotic catabolic process / cell wall organization / beta-lactamase activity / beta-lactamase / response to antibiotic / metal ion binding
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 / DD-peptidase/beta-lactamase superfamily / Beta-lactamase/transpeptidase-like / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.95 Å
AuthorsDe Luca, F. / Benvenuti, M. / Carboni, F. / Pozzi, C. / Rossolini, G.M. / Mangani, S. / Docquier, J.D.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2011
Title: Evolution to carbapenem-hydrolyzing activity in noncarbapenemase class D {beta}-lactamase OXA-10 by rational protein design.
Authors: De Luca, F. / Benvenuti, M. / Carboni, F. / Pozzi, C. / Rossolini, G.M. / Mangani, S. / Docquier, J.D.
History
DepositionFeb 8, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 2, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 24, 2013Group: Database references
Revision 1.2Jul 26, 2017Group: Refinement description / Source and taxonomy / Category: entity_src_gen / software
Revision 1.3Nov 8, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 1.4May 30, 2018Group: Data collection / Derived calculations / Category: pdbx_struct_assembly_gen / Item: _pdbx_struct_assembly_gen.asym_id_list
Revision 1.5Sep 13, 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 1.6Dec 6, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond / Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_2

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Oxacillinase
B: Oxacillinase
C: Oxacillinase
D: Oxacillinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)111,60934
Polymers109,5094
Non-polymers2,10030
Water8,899494
1
A: Oxacillinase
D: Oxacillinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)55,88318
Polymers54,7542
Non-polymers1,12916
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Oxacillinase
C: Oxacillinase
hetero molecules


  • defined by author
  • 55.7 kDa, 2 polymers
Theoretical massNumber of molelcules
Total (without water)55,72516
Polymers54,7542
Non-polymers97114
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)81.330, 81.330, 151.921
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number145
Space group name H-MP32

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Components

#1: Protein
Oxacillinase / OXA-10loop24 / OXA-10 laboratory variant


Mass: 27377.203 Da / Num. of mol.: 4 / Fragment: SEE REMARK 999
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Strain: DH5(alpha) / Gene: blaOXA-10(loop24) / Plasmid: pLB-II-OXA10loop24 / Production host: Escherichia coli (E. coli) / Strain (production host): DH5(alpha) / References: UniProt: Q7BNC2, beta-lactamase
#2: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: SO4
#3: Chemical...
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 23 / Source method: obtained synthetically / Formula: C2H6O2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 494 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsOXA-10LOOP24 IS A LABORATORY VARIANT OF OXACILLINASE WITH ENGINEERED INSERTION WGMGVTPQVG REPLACING ...OXA-10LOOP24 IS A LABORATORY VARIANT OF OXACILLINASE WITH ENGINEERED INSERTION WGMGVTPQVG REPLACING UNP RESIDUES 208-220.

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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: 2.65 Å3/Da / Density % sol: 53.57 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 8
Details: 2.8 M ammonium sulfate, 0.1 M Tris, pH 8.0, VAPOR DIFFUSION, SITTING DROP, temperature 298.0K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-2 / Wavelength: 0.873
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Jul 27, 2009
RadiationMonochromator: Si 111 Crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.873 Å / Relative weight: 1
ReflectionResolution: 1.95→33.43 Å / Num. all: 85904 / Num. obs: 81931 / % possible obs: 99.9 % / Redundancy: 3.2 % / Biso Wilson estimate: 17.7 Å2 / Rmerge(I) obs: 0.086 / Net I/σ(I): 9.2
Reflection shellResolution: 1.95→2.06 Å / Redundancy: 3.1 % / Rmerge(I) obs: 0.323 / Mean I/σ(I) obs: 3.3 / Num. unique all: 11977 / % possible all: 100

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Processing

Software
NameVersionClassification
MAR345MOSAICdata collection
MOLREPphasing
REFMAC5.5.0109refinement
MOSFLMdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1K55

1k55


Resolution: 1.95→25.82 Å / Cor.coef. Fo:Fc: 0.957 / Cor.coef. Fo:Fc free: 0.933 / SU B: 6.07 / SU ML: 0.088 / Cross valid method: THROUGHOUT / ESU R: 0.143 / ESU R Free: 0.136 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.20967 4100 5 %RANDOM
Rwork0.16636 ---
all0.16852 77737 --
obs0.16852 77737 99.95 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 23.631 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.133 Å0.135 Å
Refinement stepCycle: LAST / Resolution: 1.95→25.82 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7690 0 127 494 8311
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0180.0227963
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.6161.95410724
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.5315963
X-RAY DIFFRACTIONr_dihedral_angle_2_deg39.65225.114352
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.658151423
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.9961532
X-RAY DIFFRACTIONr_chiral_restr0.120.21159
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.0215876
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_it1.0331.54799
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.87227744
X-RAY DIFFRACTIONr_scbond_it2.79733164
X-RAY DIFFRACTIONr_scangle_it4.5164.52980
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.95→2.001 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.274 287 -
Rwork0.213 5721 -
obs-5721 99.98 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.34190.2575-0.23690.44330.10890.47690.00910.0831-0.00250.05820.0322-0.0256-0.0172-0.0792-0.04130.092-0.01560.03210.02520.00270.075330.6247-0.4987-26.9712
20.3255-0.22980.22830.45870.11220.41590.0057-0.08990.0053-0.06210.039-0.0290.0164-0.0739-0.04470.08510.0175-0.03080.03110.00360.07630.63020.490327.0578
30.10680.0134-0.04860.09950.2480.9496-0.04550.04150.04160.06160.0634-0.01190.07840.0525-0.01790.08590.0302-0.03920.0521-0.00180.05645.36526.156555.411
40.042-0.02080.04570.15190.30310.9365-0.0289-0.0349-0.039-0.06360.072-0.0134-0.08410.051-0.0430.0858-0.02240.05120.05290.0050.056645.4267-6.0744-55.2863
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A21 - 262
2X-RAY DIFFRACTION2B21 - 262
3X-RAY DIFFRACTION3C21 - 262
4X-RAY DIFFRACTION4D22 - 262

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