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- PDB-5qao: OXA-48 IN COMPLEX WITH COMPOUND 19b -

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Basic information

Entry
Database: PDB / ID: 5qao
TitleOXA-48 IN COMPLEX WITH COMPOUND 19b
ComponentsBeta-lactamase
KeywordsHYDROLASE / Oxacillinase / Inhibitor / Complex / OXA / Antibiotic resistance / beta-lactamase / fragment
Function / homology
Function and homology information


penicillin binding / antibiotic catabolic process / cell wall organization / beta-lactamase activity / beta-lactamase / 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 / DD-peptidase/beta-lactamase superfamily / Beta-lactamase/transpeptidase-like / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Chem-Z8R / Beta-lactamase OXA-48
Similarity search - Component
Biological speciesKlebsiella pneumoniae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 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 / Refinement description
Category: chem_comp_atom / chem_comp_bond / struct_ncs_dom_lim
Item: _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id ..._struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

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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)114,40213
Polymers112,9084
Non-polymers1,4959
Water13,259736
1
A: Beta-lactamase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,5683
Polymers28,2271
Non-polymers3412
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Beta-lactamase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,6464
Polymers28,2271
Non-polymers4193
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Beta-lactamase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,5943
Polymers28,2271
Non-polymers3672
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: Beta-lactamase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,5943
Polymers28,2271
Non-polymers3672
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)88.770, 107.275, 125.312
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11chain A
21chain B
31chain C
41chain D

NCS domain segments:

Component-ID: 1 / Ens-ID: 1 / Beg auth comp-ID: GLU / Beg label comp-ID: GLU / End auth comp-ID: PRO / End label comp-ID: PRO / Auth seq-ID: 24 - 265 / Label seq-ID: 2 - 243

Dom-IDSelection detailsAuth asym-IDLabel asym-ID
1chain AAA
2chain BBB
3chain CCC
4chain DDD

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Components

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Protein , 1 types, 4 molecules ABCD

#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

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Non-polymers , 5 types, 745 molecules

#2: Chemical
ChemComp-Z8R / 3-[4-(methylsulfonylaminomethyl)phenyl]benzoic acid


Mass: 305.349 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C15H15NO4S
#3: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#4: Chemical ChemComp-DMS / DIMETHYL SULFOXIDE


Mass: 78.133 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6OS / Comment: DMSO, precipitant*YM
#5: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6O2
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 736 / 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: 2.64 Å3/Da / Density % sol: 53.45 %
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: ID23-1 / Wavelength: 0.98401 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Sep 19, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98401 Å / Relative weight: 1
ReflectionResolution: 2→62.66 Å / % possible obs: 96.78 % / Redundancy: 4.3 % / Rmerge(I) obs: 0.1512 / Rrim(I) all: 0.17 / Net I/σ(I): 3.8
Reflection shellResolution: 2→2.07 Å / % possible obs: 98.7 % / Redundancy: 4.3 % / Rmerge(I) obs: 0.5944 / Num. unique obs: 34116 / Rrim(I) all: 0.67 / Net I/σ(I) obs: 1.64

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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: 2→62.66 Å / Cross valid method: THROUGHOUT
RfactorNum. reflection% reflection
Rfree0.2116 3908 -
Rwork0.1774 --
obs-78807 96.78 %
Refinement stepCycle: final / Resolution: 2→62.66 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7932 0 172 736 8840
Biso mean--74.57 47.13 -
Num. residues----968
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0038225
X-RAY DIFFRACTIONf_angle_d0.5411131
X-RAY DIFFRACTIONf_chiral_restr0.0441160
X-RAY DIFFRACTIONf_plane_restr0.0031488
X-RAY DIFFRACTIONf_dihedral_angle_d18.0344850
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A6295X-RAY DIFFRACTION5.724TORSIONAL
12B6295X-RAY DIFFRACTION5.724TORSIONAL
13C6295X-RAY DIFFRACTION5.724TORSIONAL
14D6295X-RAY DIFFRACTION5.724TORSIONAL
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 28

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2-2.02440.3281340.2672724285899
2.0244-2.050.29491520.26142679283199
2.05-2.0770.30771440.2452694283898
2.077-2.10550.28691560.23692700285699
2.1055-2.13550.26971240.22352689281399
2.1355-2.16740.2351210.20962699282098
2.1674-2.20130.24171340.21342568270293
2.2013-2.23740.20081390.19362560269994
2.2374-2.2760.24231250.18892717284298
2.276-2.31730.22071260.18452726285299
2.3173-2.36190.22691400.18572667280798
2.3619-2.41010.21551480.18122692284098
2.4101-2.46250.22411500.17822696284698
2.4625-2.51980.24871590.18182649280898
2.5198-2.58280.21011340.18142715284998
2.5828-2.65270.22711290.18822613274295
2.6527-2.73070.20491400.19042550269092
2.7307-2.81890.26971480.17732654280298
2.8189-2.91960.24261310.17492738286998
2.9196-3.03650.23841380.17532693283198
3.0365-3.17470.24651380.17472714285297
3.1747-3.34210.18661510.17392690284198
3.3421-3.55150.19021400.16032527266791
3.5515-3.82560.17531430.14962718286197
3.8256-4.21050.15841310.14352703283497
4.2105-4.81960.18611490.13722717286696
4.8196-6.07140.18851330.17252649278293
6.0714-62.68670.20061500.20592750290093
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)
10.69980.0217-0.25751.21680.29761.4023-0.01820.02870.025-0.04690.03970.0712-0.06490.08680.00020.2994-0.0055-0.03830.31890.00470.294189.0386258.40252.5669
20.4809-0.00190.121.16710.2491.27550.0128-0.0619-0.04280.15070.0450.00350.0625-0.0060.01030.29260.0017-0.02190.28640.00710.294289.0388219.1499-2.5949
30.47880.028-0.02781.1631-0.63291.43140.02230.06850.08450.01350.1040.0485-0.2073-0.280100.40840.03380.00640.39610.03960.35284.926221.207532.1152
40.57350.1283-0.03421.1076-0.65761.6320.0110.04920.07010.00320.0626-0.0412-0.1609-0.0749-00.25960.01460.03510.27540.01540.2821129.2832226.325131.979
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1(chain 'A' and resid 24 through 265)A24 - 265
2X-RAY DIFFRACTION2(chain 'B' and resid 24 through 265)B24 - 265
3X-RAY DIFFRACTION3(chain 'C' and resid 24 through 265)C24 - 265
4X-RAY DIFFRACTION4(chain 'D' and resid 24 through 265)D24 - 265

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