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- PDB-5qad: OXA-48 IN COMPLEX WITH COMPOUND 8a -

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Basic information

Entry
Database: PDB / ID: 5qad
TitleOXA-48 IN COMPLEX WITH COMPOUND 8a
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
3-(2-fluorophenyl)benzoic acid / Beta-lactamase OXA-48
Similarity search - Component
Biological speciesKlebsiella pneumoniae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.75 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)115,45736
Polymers112,9084
Non-polymers2,55032
Water20,8971160
1
A: Beta-lactamase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,94010
Polymers28,2271
Non-polymers7139
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Beta-lactamase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,8519
Polymers28,2271
Non-polymers6248
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Beta-lactamase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,8519
Polymers28,2271
Non-polymers6248
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: Beta-lactamase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,8168
Polymers28,2271
Non-polymers5897
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)88.919, 108.895, 124.888
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
11(chain A and (resid 24 through 43 or resid 45...
21(chain B and (resid 24 through 43 or resid 45...
31(chain C and (resid 24 through 43 or resid 45...
41(chain D and (resid 24 through 43 or resid 45...

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
11GLUGLUVALVAL(chain A and (resid 24 through 43 or resid 45...AA24 - 432 - 21
12VALVALGLNGLN(chain A and (resid 24 through 43 or resid 45...AA45 - 9123 - 69
13PHEPHEALAALA(chain A and (resid 24 through 43 or resid 45...AA93 - 10371 - 81
14TRPTRPALAALA(chain A and (resid 24 through 43 or resid 45...AA105 - 11483 - 92
15LYSLYSTYRTYR(chain A and (resid 24 through 43 or resid 45...AA116 - 11794 - 95
16VALVALLYSLYS(chain A and (resid 24 through 43 or resid 45...AA119 - 13797 - 115
17LEULEULEULEU(chain A and (resid 24 through 43 or resid 45...AA139117
18ALAALAALAALA(chain A and (resid 24 through 43 or resid 45...AA141 - 166119 - 144
19GLUGLUILEILE(chain A and (resid 24 through 43 or resid 45...AA168 - 170146 - 148
110PHEPHETRPTRP(chain A and (resid 24 through 43 or resid 45...AA172 - 225150 - 203
111GLUGLUASNASN(chain A and (resid 24 through 43 or resid 45...AA227 - 231205 - 209
112TRPTRPPROPRO(chain A and (resid 24 through 43 or resid 45...AA233 - 265211 - 243
21GLUGLUVALVAL(chain B and (resid 24 through 43 or resid 45...BB24 - 432 - 21
22VALVALGLNGLN(chain B and (resid 24 through 43 or resid 45...BB45 - 9123 - 69
23PHEPHEALAALA(chain B and (resid 24 through 43 or resid 45...BB93 - 10371 - 81
24TRPTRPALAALA(chain B and (resid 24 through 43 or resid 45...BB105 - 11483 - 92
25LYSLYSTYRTYR(chain B and (resid 24 through 43 or resid 45...BB116 - 11794 - 95
26VALVALLYSLYS(chain B and (resid 24 through 43 or resid 45...BB119 - 13797 - 115
27LEULEULEULEU(chain B and (resid 24 through 43 or resid 45...BB139117
28ALAALAALAALA(chain B and (resid 24 through 43 or resid 45...BB141 - 166119 - 144
29GLUGLUILEILE(chain B and (resid 24 through 43 or resid 45...BB168 - 170146 - 148
210PHEPHETRPTRP(chain B and (resid 24 through 43 or resid 45...BB172 - 225150 - 203
211GLUGLUASNASN(chain B and (resid 24 through 43 or resid 45...BB227 - 231205 - 209
212TRPTRPPROPRO(chain B and (resid 24 through 43 or resid 45...BB233 - 265211 - 243
31GLUGLUVALVAL(chain C and (resid 24 through 43 or resid 45...CC24 - 432 - 21
32VALVALGLNGLN(chain C and (resid 24 through 43 or resid 45...CC45 - 9123 - 69
33PHEPHEALAALA(chain C and (resid 24 through 43 or resid 45...CC93 - 10371 - 81
34TRPTRPALAALA(chain C and (resid 24 through 43 or resid 45...CC105 - 11483 - 92
35LYSLYSTYRTYR(chain C and (resid 24 through 43 or resid 45...CC116 - 11794 - 95
36VALVALLYSLYS(chain C and (resid 24 through 43 or resid 45...CC119 - 13797 - 115
37LEULEULEULEU(chain C and (resid 24 through 43 or resid 45...CC139117
38ALAALAALAALA(chain C and (resid 24 through 43 or resid 45...CC141 - 166119 - 144
39GLUGLUILEILE(chain C and (resid 24 through 43 or resid 45...CC168 - 170146 - 148
310PHEPHETRPTRP(chain C and (resid 24 through 43 or resid 45...CC172 - 225150 - 203
311GLUGLUASNASN(chain C and (resid 24 through 43 or resid 45...CC227 - 231205 - 209
312TRPTRPPROPRO(chain C and (resid 24 through 43 or resid 45...CC233 - 265211 - 243
41GLUGLUVALVAL(chain D and (resid 24 through 43 or resid 45...DD24 - 432 - 21
42VALVALGLNGLN(chain D and (resid 24 through 43 or resid 45...DD45 - 9123 - 69
43PHEPHEALAALA(chain D and (resid 24 through 43 or resid 45...DD93 - 10371 - 81
44TRPTRPALAALA(chain D and (resid 24 through 43 or resid 45...DD105 - 11483 - 92
45LYSLYSTYRTYR(chain D and (resid 24 through 43 or resid 45...DD116 - 11794 - 95
46VALVALLYSLYS(chain D and (resid 24 through 43 or resid 45...DD119 - 13797 - 115
47LEULEULEULEU(chain D and (resid 24 through 43 or resid 45...DD139117
48ALAALAALAALA(chain D and (resid 24 through 43 or resid 45...DD141 - 166119 - 144
49GLUGLUILEILE(chain D and (resid 24 through 43 or resid 45...DD168 - 170146 - 148
410PHEPHETRPTRP(chain D and (resid 24 through 43 or resid 45...DD172 - 225150 - 203
411GLUGLUASNASN(chain D and (resid 24 through 43 or resid 45...DD227 - 231205 - 209
412TRPTRPPROPRO(chain D and (resid 24 through 43 or resid 45...DD233 - 265211 - 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-WVV / 3-(2-fluorophenyl)benzoic acid


Mass: 216.208 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C13H9FO2
#3: Chemical...
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 26 / 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.: 1160 / 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: 2.68 Å3/Da / Density % sol: 54.06 %
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: 0.87258 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Dec 1, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.87258 Å / Relative weight: 1
ReflectionResolution: 1.75→41.88 Å / % possible obs: 99.81 % / Redundancy: 5.7 % / Rmerge(I) obs: 0.09686 / Rrim(I) all: 0.11 / Net I/σ(I): 10.53
Reflection shellResolution: 1.75→1.81 Å / % possible obs: 99.82 % / Redundancy: 5.8 % / Rmerge(I) obs: 0.7541 / Num. unique obs: 70114 / Rrim(I) all: 0.83 / Net I/σ(I) obs: 2.16

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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: 1.75→41.88 Å / Cross valid method: THROUGHOUT
RfactorNum. reflection% reflection
Rfree0.1842 1421 -
Rwork0.1567 --
obs-122275 99.81 %
Refinement stepCycle: final / Resolution: 1.75→41.88 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7932 0 358 1160 9450
Biso mean--46.43 36.95 -
Num. residues----963
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0038485
X-RAY DIFFRACTIONf_angle_d0.62811475
X-RAY DIFFRACTIONf_chiral_restr0.0491196
X-RAY DIFFRACTIONf_plane_restr0.0031537
X-RAY DIFFRACTIONf_dihedral_angle_d18.2265003
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A5823X-RAY DIFFRACTION4.91TORSIONAL
12B5823X-RAY DIFFRACTION4.91TORSIONAL
13C5823X-RAY DIFFRACTION4.91TORSIONAL
14D5823X-RAY DIFFRACTION4.91TORSIONAL
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 10 / % reflection obs: 100 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all
1.75-1.81250.26861400.25331195212092
1.8125-1.88510.22891410.21931195912100
1.8851-1.97090.22181410.18511198512126
1.9709-2.07480.21541400.16061201812158
2.0748-2.20480.18911410.15311197712118
2.2048-2.3750.13891420.13921205212194
2.375-2.6140.16691420.1391207112213
2.614-2.99220.18061420.14211209512237
2.9922-3.76940.16591440.14631221912363
3.7694-41.89660.19241480.15351252712675
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)
10.46640.0237-0.2760.7472-0.01440.6643-0.0070.03020.0209-0.04550.01680.0601-0.0284-0.0411-0.00690.1319-0.0047-0.01870.13050.00030.1389.3962262.42362.6405
20.42380.06430.1410.99090.07351.01810.0117-0.0094-0.01270.0453-0.0085-0.05210.05430.0545-0.00120.1385-0.00640.01230.149-0.0020.150889.2556222.6218-2.6058
30.59920.15520.18091.2601-0.14171.0237-0.0080.01360.02170.03530.02850.0577-0.0109-0.0609-0.01920.1258-0.00180.01420.15920.0110.151385.0984225.014532.1857
40.80880.13910.181.3725-0.46751.2758-0.01170.04090.0512-0.00020.02570.0306-0.1093-0.12860.00270.11760.02510.00080.13190.01090.1108129.7128229.846632.0092
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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