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- PDB-5qa4: OXA-48 IN COMPLEX WITH COMPOUND 3a -

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Basic information

Entry
Database: PDB / ID: 5qa4
TitleOXA-48 IN COMPLEX WITH COMPOUND 3a
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-methylphenyl)benzoic acid / Beta-lactamase OXA-48
Similarity search - Component
Biological speciesKlebsiella pneumoniae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.95 Å
AuthorsLund, B.A.
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_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 / Refinement description / Category: database_2 / refine
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _refine.pdbx_diffrn_id
Revision 1.4Nov 24, 2021Group: Structure summary / Category: pdbx_deposit_group
Item: _pdbx_deposit_group.group_description / _pdbx_deposit_group.group_title
Revision 1.5Nov 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)113,92512
Polymers112,9084
Non-polymers1,0178
Water20,8971160
1
A: Beta-lactamase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,4392
Polymers28,2271
Non-polymers2121
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Beta-lactamase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,5725
Polymers28,2271
Non-polymers3454
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Beta-lactamase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,4753
Polymers28,2271
Non-polymers2482
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: Beta-lactamase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,4392
Polymers28,2271
Non-polymers2121
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)89.099, 108.936, 124.908
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 25 through 36 or resid 38...
21(chain B and (resid 25 through 36 or resid 38...
31(chain C and (resid 25 through 36 or resid 38...
41(chain D and (resid 25 through 36 or resid 38...

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
11TRPTRPTHRTHR(chain A and (resid 25 through 36 or resid 38...AA25 - 363 - 14
12HISHISSERSER(chain A and (resid 25 through 36 or resid 38...AA38 - 4016 - 18
13GLYGLYLEULEU(chain A and (resid 25 through 36 or resid 38...AA42 - 5920 - 37
14ARGARGVALVAL(chain A and (resid 25 through 36 or resid 38...AA61 - 8639 - 64
15ASPASPGLNGLN(chain A and (resid 25 through 36 or resid 38...AA88 - 9166 - 69
16PHEPHEGLYGLY(chain A and (resid 25 through 36 or resid 38...AA93 - 9771 - 75
17THRTHRALAALA(chain A and (resid 25 through 36 or resid 38...AA99 - 11477 - 92
18LYSLYSTYRTYR(chain A and (resid 25 through 36 or resid 38...AA116 - 11794 - 95
19VALVALSERSER(chain A and (resid 25 through 36 or resid 38...AA119 - 13697 - 114
110LEULEULEULEU(chain A and (resid 25 through 36 or resid 38...AA139117
111ALAALAILEILE(chain A and (resid 25 through 36 or resid 38...AA141 - 170119 - 148
112PHEPHETRPTRP(chain A and (resid 25 through 36 or resid 38...AA172 - 225150 - 203
113GLUGLUASNASN(chain A and (resid 25 through 36 or resid 38...AA227 - 231205 - 209
114TRPTRPPROPRO(chain A and (resid 25 through 36 or resid 38...AA233 - 265211 - 243
21TRPTRPTHRTHR(chain B and (resid 25 through 36 or resid 38...BB25 - 363 - 14
22HISHISSERSER(chain B and (resid 25 through 36 or resid 38...BB38 - 4016 - 18
23GLYGLYLEULEU(chain B and (resid 25 through 36 or resid 38...BB42 - 5920 - 37
24ARGARGVALVAL(chain B and (resid 25 through 36 or resid 38...BB61 - 8639 - 64
25ASPASPGLNGLN(chain B and (resid 25 through 36 or resid 38...BB88 - 9166 - 69
26PHEPHEGLYGLY(chain B and (resid 25 through 36 or resid 38...BB93 - 9771 - 75
27THRTHRALAALA(chain B and (resid 25 through 36 or resid 38...BB99 - 11477 - 92
28LYSLYSTYRTYR(chain B and (resid 25 through 36 or resid 38...BB116 - 11794 - 95
29VALVALSERSER(chain B and (resid 25 through 36 or resid 38...BB119 - 13697 - 114
210LEULEULEULEU(chain B and (resid 25 through 36 or resid 38...BB139117
211ALAALAILEILE(chain B and (resid 25 through 36 or resid 38...BB141 - 170119 - 148
212PHEPHETRPTRP(chain B and (resid 25 through 36 or resid 38...BB172 - 225150 - 203
213GLUGLUASNASN(chain B and (resid 25 through 36 or resid 38...BB227 - 231205 - 209
214TRPTRPPROPRO(chain B and (resid 25 through 36 or resid 38...BB233 - 265211 - 243
31TRPTRPTHRTHR(chain C and (resid 25 through 36 or resid 38...CC25 - 363 - 14
32HISHISSERSER(chain C and (resid 25 through 36 or resid 38...CC38 - 4016 - 18
33GLYGLYLEULEU(chain C and (resid 25 through 36 or resid 38...CC42 - 5920 - 37
34ARGARGVALVAL(chain C and (resid 25 through 36 or resid 38...CC61 - 8639 - 64
35ASPASPGLNGLN(chain C and (resid 25 through 36 or resid 38...CC88 - 9166 - 69
36PHEPHEGLYGLY(chain C and (resid 25 through 36 or resid 38...CC93 - 9771 - 75
37THRTHRALAALA(chain C and (resid 25 through 36 or resid 38...CC99 - 11477 - 92
38LYSLYSTYRTYR(chain C and (resid 25 through 36 or resid 38...CC116 - 11794 - 95
39VALVALSERSER(chain C and (resid 25 through 36 or resid 38...CC119 - 13697 - 114
310LEULEULEULEU(chain C and (resid 25 through 36 or resid 38...CC139117
311ALAALAILEILE(chain C and (resid 25 through 36 or resid 38...CC141 - 170119 - 148
312PHEPHETRPTRP(chain C and (resid 25 through 36 or resid 38...CC172 - 225150 - 203
313GLUGLUASNASN(chain C and (resid 25 through 36 or resid 38...CC227 - 231205 - 209
314TRPTRPPROPRO(chain C and (resid 25 through 36 or resid 38...CC233 - 265211 - 243
41TRPTRPTHRTHR(chain D and (resid 25 through 36 or resid 38...DD25 - 363 - 14
42HISHISSERSER(chain D and (resid 25 through 36 or resid 38...DD38 - 4016 - 18
43GLYGLYLEULEU(chain D and (resid 25 through 36 or resid 38...DD42 - 5920 - 37
44ARGARGVALVAL(chain D and (resid 25 through 36 or resid 38...DD61 - 8639 - 64
45ASPASPGLNGLN(chain D and (resid 25 through 36 or resid 38...DD88 - 9166 - 69
46PHEPHEGLYGLY(chain D and (resid 25 through 36 or resid 38...DD93 - 9771 - 75
47THRTHRALAALA(chain D and (resid 25 through 36 or resid 38...DD99 - 11477 - 92
48LYSLYSTYRTYR(chain D and (resid 25 through 36 or resid 38...DD116 - 11794 - 95
49VALVALSERSER(chain D and (resid 25 through 36 or resid 38...DD119 - 13697 - 114
410LEULEULEULEU(chain D and (resid 25 through 36 or resid 38...DD139117
411ALAALAILEILE(chain D and (resid 25 through 36 or resid 38...DD141 - 170119 - 148
412PHEPHETRPTRP(chain D and (resid 25 through 36 or resid 38...DD172 - 225150 - 203
413GLUGLUASNASN(chain D and (resid 25 through 36 or resid 38...DD227 - 231205 - 209
414TRPTRPPROPRO(chain D and (resid 25 through 36 or resid 38...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-TI7 / 3-(2-methylphenyl)benzoic acid


Mass: 212.244 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C14H12O2
#3: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Cl
#4: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#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: 54.18 %
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 2, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.87258 Å / Relative weight: 1
ReflectionResolution: 1.95→43.56 Å / % possible obs: 99.57 % / Redundancy: 4.6 % / Rmerge(I) obs: 0.1269 / Rrim(I) all: 0.14 / Net I/σ(I): 8.72
Reflection shellResolution: 1.95→2.02 Å / % possible obs: 99.76 % / Redundancy: 4.7 % / Rmerge(I) obs: 0.6498 / Num. unique obs: 41707 / Rrim(I) all: 0.73 / 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: 1.95→43.56 Å / Cross valid method: THROUGHOUT
RfactorNum. reflection% reflection
Rfree0.2029 1629 -
Rwork0.1664 --
obs-88724 99.57 %
Refinement stepCycle: final / Resolution: 1.95→43.56 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7932 0 121 1160 9213
Biso mean--42.34 38.22 -
Num. residues----966
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0078369
X-RAY DIFFRACTIONf_angle_d0.81211357
X-RAY DIFFRACTIONf_chiral_restr0.0551186
X-RAY DIFFRACTIONf_plane_restr0.0051526
X-RAY DIFFRACTIONf_dihedral_angle_d18.0434956
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A5674X-RAY DIFFRACTION5.275TORSIONAL
12B5674X-RAY DIFFRACTION5.275TORSIONAL
13C5674X-RAY DIFFRACTION5.275TORSIONAL
14D5674X-RAY DIFFRACTION5.275TORSIONAL
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 12

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.95-2.00740.26041330.253871527285100
2.0074-2.07220.29321350.216572047339100
2.0722-2.14620.22261340.196971547288100
2.1462-2.23220.21461350.18572247359100
2.2322-2.33380.22631340.17927144727899
2.3338-2.45680.22111340.17017206734099
2.4568-2.61070.20191360.15772447380100
2.6107-2.81230.171350.150772287363100
2.8123-3.09520.19171360.151672767412100
3.0952-3.5430.19441380.149273207458100
3.543-4.46320.17591370.13657349748699
4.4632-46.48540.20021420.17297589773199
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)
10.359-0.01940.21291.09140.0851.1920.0112-0.0171-0.01480.0262-0.0099-0.04560.03240.04270.00090.1031-0.0126-0.00880.14540.00180.129689.3271222.702-2.6757
20.47910.07660.16111.4066-0.15650.9771-0.02340.01620.03120.07160.04680.0569-0.0249-0.042-0.0150.1234-0.00360.00230.16950.01450.155785.3492225.013932.1814
30.8040.10860.19751.3582-0.36491.1652-0.01240.05550.0383-0.04550.02840.031-0.1101-0.1446-0.01660.17740.01930.01910.17630.01560.1422129.984229.928332.0608
40.3742-0.0043-0.12950.8289-0.01820.73140.00830.03620.0305-0.10050.0120.0427-0.0333-0.012-0.02020.196-0.0064-0.0280.1702-0.00190.158489.399262.52282.6532
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1(chain 'B' and resid 24 through 265)B24 - 265
2X-RAY DIFFRACTION2(chain 'C' and resid 24 through 265)C24 - 265
3X-RAY DIFFRACTION3(chain 'D' and resid 24 through 265)D24 - 265
4X-RAY DIFFRACTION4(chain 'A' and resid 24 through 265)A24 - 265

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