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- PDB-5qb0: OXA-48 IN COMPLEX WITH COMPOUND 35 -

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Basic information

Entry
Database: PDB / ID: 5qb0
TitleOXA-48 IN COMPLEX WITH COMPOUND 35
ComponentsBeta-lactamase
KeywordsHYDROLASE / Oxacillinase / Inhibitor / Complex / OXA / Antibiotic resistance / beta-lactamase / fragment
Function / homology
Function and homology information


penicillin binding / antibiotic catabolic process / 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
3-pyridin-2-ylbenzoic acid / Beta-lactamase
Similarity search - Component
Biological speciesKlebsiella pneumoniae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.95 Å
AuthorsLund, B.A. / Leiros, H.K.S.
CitationJournal: Eur J Med Chem / Year: 2018
Title: A focused fragment library targeting the antibiotic resistance enzyme - Oxacillinase-48: Synthesis, structural evaluation and inhibitor design.
Authors: Akhter, S. / Lund, B.A. / Ismael, A. / Langer, M. / Isaksson, J. / Christopeit, T. / Leiros, H.S. / Bayer, A.
History
DepositionJul 11, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 10, 2018Provider: repository / Type: Initial release
Revision 1.1Feb 21, 2018Group: Structure summary / Category: pdbx_deposit_group
Item: _pdbx_deposit_group.group_title / _pdbx_deposit_group.group_type
Revision 1.2Mar 14, 2018Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.name
Revision 1.3Nov 17, 2021Group: Database references / Structure summary / Category: database_2 / pdbx_deposit_group
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_deposit_group.group_description
Revision 1.4Nov 15, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)114,14816
Polymers112,9084
Non-polymers1,24012
Water18,6461035
1
A: Beta-lactamase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,4883
Polymers28,2271
Non-polymers2612
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Beta-lactamase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,5865
Polymers28,2271
Non-polymers3594
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Beta-lactamase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,3874
Polymers28,2271
Non-polymers1603
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: Beta-lactamase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,6874
Polymers28,2271
Non-polymers4603
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)89.211, 107.969, 124.987
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-ID
11
21
31
41

NCS domain segments:
Dom-IDComponent-IDEns-IDSelection details
111(CHAIN A AND (RESID 24 THROUGH 39 OR RESID 41...
211(CHAIN B AND (RESID 24 THROUGH 39 OR RESID 41...
311(CHAIN C AND (RESID 24 THROUGH 39 OR RESID 41...
411(CHAIN D AND (RESID 24 THROUGH 39 OR RESID 41...

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Components

#1: Protein
Beta-lactamase


Mass: 28226.951 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Klebsiella pneumoniae (bacteria) / Gene: bla OXA-48, blaOXA-48, KPE71T_00045 / Production host: Escherichia coli (E. coli) / References: UniProt: Q6XEC0, beta-lactamase
#2: Chemical
ChemComp-AVA / 3-pyridin-2-ylbenzoic acid


Mass: 199.205 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C12H9NO2
#3: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C2H6O2
#4: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1035 / Source method: isolated from a natural source / Formula: H2O

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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: 2.67 Å3/Da / Density % sol: 53.86 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 0.1 M HEPES pH 7.5, 8-11% PEG 8000 and 4-8% 1-butanol

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-2 / Wavelength: 0.87261 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Dec 2, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.87261 Å / Relative weight: 1
ReflectionResolution: 1.95→41.23 Å / % possible obs: 99.5 % / Redundancy: 4.4 % / Rmerge(I) obs: 0.1287 / Net I/σ(I): 7.66
Reflection shellResolution: 1.95→2.02 Å / Redundancy: 4.2 % / Rmerge(I) obs: 0.6919

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Processing

Software
NameVersionClassificationNB
PHENIX1.11.1_2575refinement
PDB_EXTRACT3.22data extraction
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY: 5DTK

5dtk


Resolution: 1.95→41.23 Å / Cross valid method: THROUGHOUT
RfactorNum. reflection% reflection
Rfree0.21 1637 -
Rwork0.166 --
obs-88037 99.5 %
Refinement stepCycle: LAST / Resolution: 1.95→41.23 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7932 0 86 1035 9053
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0078393
X-RAY DIFFRACTIONf_angle_d0.8211381
X-RAY DIFFRACTIONf_dihedral_angle_d18.0424969
X-RAY DIFFRACTIONf_chiral_restr0.0551189
X-RAY DIFFRACTIONf_plane_restr0.0051526
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDType
11A5899X-RAY DIFFRACTIONPOSITIONAL
12B5899X-RAY DIFFRACTIONPOSITIONAL
13C5899X-RAY DIFFRACTIONPOSITIONAL
14D5899X-RAY DIFFRACTIONPOSITIONAL
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.95-2.00740.33051350.26967093X-RAY DIFFRACTION100
2.0074-2.07220.28231350.22427140X-RAY DIFFRACTION99
2.0722-2.14620.24521350.19797119X-RAY DIFFRACTION100
2.1462-2.23220.24221360.18727198X-RAY DIFFRACTION100
2.2322-2.33370.22471350.1787122X-RAY DIFFRACTION100
2.3337-2.45680.21641360.16347205X-RAY DIFFRACTION100
2.4568-2.61070.20261340.15457071X-RAY DIFFRACTION98
2.6107-2.81220.19531360.15127182X-RAY DIFFRACTION100
2.8122-3.09510.19171360.15657188X-RAY DIFFRACTION99
3.0951-3.54280.19151380.14637269X-RAY DIFFRACTION100
3.5428-4.46290.16421390.13437302X-RAY DIFFRACTION99
4.4629-43.33380.21081420.16747506X-RAY DIFFRACTION99
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)
10.4936-0.0002-0.35220.79310.02330.6604-0.00540.02580.0046-0.03570.02670.0527-0.0332-0.0552-0.0240.2103-0.0078-0.02080.18630.00320.183689.7083260.19542.6289
20.5052-0.08810.08681.03930.16871.01040.0192-0.02460.00640.03170.0041-0.07980.00570.0997-0.01660.1374-0.01220.00980.163-0.00160.154889.5721220.6784-2.6253
30.67340.21140.07641.3834-0.13561.1044-0.00840.05720.04080.02910.05430.0667-0.0461-0.0735-0.0420.1326-0.00380.01430.17950.02080.159585.3681222.832232.1375
40.80670.20610.2311.2957-0.42341.3373-0.01020.05110.07150.00010.0204-0.0066-0.121-0.12580.00450.15690.02940.00820.15990.01480.1359130.1392227.7531.991
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(CHAIN 'A' AND RESID 24 THROUGH 265)
2X-RAY DIFFRACTION2(CHAIN 'B' AND RESID 24 THROUGH 265)
3X-RAY DIFFRACTION3(CHAIN 'C' AND RESID 24 THROUGH 265)
4X-RAY DIFFRACTION4(CHAIN 'D' AND RESID 24 THROUGH 265)

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