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- PDB-5qax: OXA-48 IN COMPLEX WITH COMPOUND 28 -

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Basic information

Entry
Database: PDB / ID: 5qax
TitleOXA-48 IN COMPLEX WITH COMPOUND 28
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-quinolin-6-ylbenzoic acid / Beta-lactamase
Similarity search - Component
Biological speciesKlebsiella pneumoniae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.31 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)114,16213
Polymers112,9084
Non-polymers1,2549
Water7,134396
1
A: Beta-lactamase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,6365
Polymers28,2271
Non-polymers4094
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Beta-lactamase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,4762
Polymers28,2271
Non-polymers2491
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Beta-lactamase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,5744
Polymers28,2271
Non-polymers3473
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: Beta-lactamase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,4762
Polymers28,2271
Non-polymers2491
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)64.196, 107.848, 85.150
Angle α, β, γ (deg.)90.000, 103.820, 90.000
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11(chain A and (resid 24 through 114 or resid 116 through 117 or resid 119 through 265))
21(chain B and (resid 24 through 114 or resid 116 through 117 or resid 119 through 265))
31(chain C and (resid 24 through 114 or resid 116 through 117 or resid 119 through 265))
41(chain D and (resid 24 through 114 or resid 116 through 117 or resid 119 through 265))

NCS domain segments:

Ens-ID: 1

Dom-IDComponent-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11GLUGLUALAALA(chain A and (resid 24 through 114 or resid 116 through 117 or resid 119 through 265))AA24 - 1142 - 92
12LYSLYSTYRTYR(chain A and (resid 24 through 114 or resid 116 through 117 or resid 119 through 265))AA116 - 11794 - 95
13VALVALPROPRO(chain A and (resid 24 through 114 or resid 116 through 117 or resid 119 through 265))AA119 - 26597 - 243
21GLUGLUALAALA(chain B and (resid 24 through 114 or resid 116 through 117 or resid 119 through 265))BB24 - 1142 - 92
22LYSLYSTYRTYR(chain B and (resid 24 through 114 or resid 116 through 117 or resid 119 through 265))BB116 - 11794 - 95
23VALVALPROPRO(chain B and (resid 24 through 114 or resid 116 through 117 or resid 119 through 265))BB119 - 26597 - 243
31GLUGLUALAALA(chain C and (resid 24 through 114 or resid 116 through 117 or resid 119 through 265))CC24 - 1142 - 92
32LYSLYSTYRTYR(chain C and (resid 24 through 114 or resid 116 through 117 or resid 119 through 265))CC116 - 11794 - 95
33VALVALPROPRO(chain C and (resid 24 through 114 or resid 116 through 117 or resid 119 through 265))CC119 - 26597 - 243
41GLUGLUALAALA(chain D and (resid 24 through 114 or resid 116 through 117 or resid 119 through 265))DD24 - 1142 - 92
42LYSLYSTYRTYR(chain D and (resid 24 through 114 or resid 116 through 117 or resid 119 through 265))DD116 - 11794 - 95
43VALVALPROPRO(chain D and (resid 24 through 114 or resid 116 through 117 or resid 119 through 265))DD119 - 26597 - 243

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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-Q92 / 3-quinolin-6-ylbenzoic acid


Mass: 249.264 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C16H11NO2
#3: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#4: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C2H6O2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 396 / 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: 2.54 Å3/Da / Density % sol: 51.48 %
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: BESSY / Beamline: 14.1 / Wavelength: 0.918409 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Apr 15, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.918409 Å / Relative weight: 1
ReflectionResolution: 2.31→44.89 Å / % possible obs: 97.87 % / Redundancy: 4.6 % / Rmerge(I) obs: 0.1147 / Rrim(I) all: 0.13 / Net I/σ(I): 9.47
Reflection shellResolution: 2.31→2.4 Å / % possible obs: 87.35 % / Redundancy: 4.4 % / Rmerge(I) obs: 0.5245 / Num. unique obs: 18937 / Rrim(I) all: 0.59 / Net I/σ(I) obs: 2.1

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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: 2.31→44.89 Å / Cross valid method: THROUGHOUT
RfactorNum. reflection% reflection
Rfree0.2092 2370 -
Rwork0.1726 --
obs-48233 97.87 %
Refinement stepCycle: final / Resolution: 2.31→44.89 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7932 0 148 396 8476
Biso mean--57.22 39.38 -
Num. residues----968
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0038264
X-RAY DIFFRACTIONf_angle_d0.59611185
X-RAY DIFFRACTIONf_chiral_restr0.0441161
X-RAY DIFFRACTIONf_plane_restr0.0031522
X-RAY DIFFRACTIONf_dihedral_angle_d18.5534892
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A6168X-RAY DIFFRACTION5.388TORSIONAL
12B6168X-RAY DIFFRACTION5.388TORSIONAL
13C6168X-RAY DIFFRACTION5.388TORSIONAL
14D6168X-RAY DIFFRACTION5.388TORSIONAL
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 17

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.3122-2.35940.30321110.23662159227079
2.3594-2.41070.23721540.219627292883100
2.4107-2.46680.27361520.211527492901100
2.4668-2.52840.26911330.210627162849100
2.5284-2.59680.25571440.19427702914100
2.5968-2.67320.27191350.227632898100
2.6732-2.75950.21681230.190127552878100
2.7595-2.85810.22761430.182627352878100
2.8581-2.97250.2131230.179827442867100
2.9725-3.10770.22891330.189727592892100
3.1077-3.27150.22881450.19992727287299
3.2715-3.47650.1921570.17192713287099
3.4765-3.74480.22071280.16622682281097
3.7448-4.12140.19211470.15422654280197
4.1214-4.71720.17621470.13542703285098
4.7172-5.9410.16841520.14792731288398
5.941-45.17590.18181430.16082775291899
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)
12.02480.27690.23561.4739-0.2020.52430.08-0.1603-0.08950.0726-0.06620.08640.0932-0.0762-0.03060.285-0.05420.01040.30170.01420.1985136.8543-109.317420.9943
22.28670.30930.5591.41020.03070.8813-0.0379-0.18090.24590.04620.0372-0.1881-0.06520.0294-0.01810.2335-0.03530.00230.2805-0.05840.3133165.3176-93.488422.159
32.3213-0.7780.54952.5603-0.30210.95820.1612-0.086-0.6751-0.07590.04180.17830.1771-0.0555-0.14430.28260.0399-0.02470.25050.03190.3807139.3043-116.7422-18.9677
41.5413-0.45070.43462.446-0.01431.5447-0.1882-0.09080.32270.11140.0102-0.318-0.243-0.00910.13150.29550.0508-0.03480.2390.00160.2949139.3409-84.1907-17.7464
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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