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- PDB-5qa6: OXA-48 IN COMPLEX WITH COMPOUND 4a -

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Basic information

Entry
Database: PDB / ID: 5qa6
TitleOXA-48 IN COMPLEX WITH COMPOUND 4a
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-hydroxyphenyl)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. / 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)114,51821
Polymers112,9084
Non-polymers1,61117
Water22,6991260
1
A: Beta-lactamase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,6015
Polymers28,2271
Non-polymers3744
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Beta-lactamase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,7257
Polymers28,2271
Non-polymers4986
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Beta-lactamase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,6275
Polymers28,2271
Non-polymers4004
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: Beta-lactamase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,5654
Polymers28,2271
Non-polymers3383
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)89.008, 108.992, 124.791
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 39 or resid 41...
21(chain B and (resid 24 through 39 or resid 41...
31(chain C and (resid 24 through 39 or resid 41...
41(chain D and (resid 24 through 39 or resid 41...

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
11GLUGLULYSLYS(chain A and (resid 24 through 39 or resid 41...AA24 - 392 - 17
12GLNGLNGLNGLN(chain A and (resid 24 through 39 or resid 41...AA41 - 9119 - 69
13PHEPHEALAALA(chain A and (resid 24 through 39 or resid 41...AA93 - 11471 - 92
14LYSLYSTYRTYR(chain A and (resid 24 through 39 or resid 41...AA116 - 11794 - 95
15VALVALLYSLYS(chain A and (resid 24 through 39 or resid 41...AA119 - 13797 - 115
16LEULEUILEILE(chain A and (resid 24 through 39 or resid 41...AA139 - 170117 - 148
17PHEPHETRPTRP(chain A and (resid 24 through 39 or resid 41...AA172 - 225150 - 203
18GLUGLUASNASN(chain A and (resid 24 through 39 or resid 41...AA227 - 231205 - 209
19TRPTRPPROPRO(chain A and (resid 24 through 39 or resid 41...AA233 - 265211 - 243
21GLUGLULYSLYS(chain B and (resid 24 through 39 or resid 41...BB24 - 392 - 17
22GLNGLNGLNGLN(chain B and (resid 24 through 39 or resid 41...BB41 - 9119 - 69
23PHEPHEALAALA(chain B and (resid 24 through 39 or resid 41...BB93 - 11471 - 92
24LYSLYSTYRTYR(chain B and (resid 24 through 39 or resid 41...BB116 - 11794 - 95
25VALVALLYSLYS(chain B and (resid 24 through 39 or resid 41...BB119 - 13797 - 115
26LEULEUILEILE(chain B and (resid 24 through 39 or resid 41...BB139 - 170117 - 148
27PHEPHETRPTRP(chain B and (resid 24 through 39 or resid 41...BB172 - 225150 - 203
28GLUGLUASNASN(chain B and (resid 24 through 39 or resid 41...BB227 - 231205 - 209
29TRPTRPPROPRO(chain B and (resid 24 through 39 or resid 41...BB233 - 265211 - 243
31GLUGLULYSLYS(chain C and (resid 24 through 39 or resid 41...CC24 - 392 - 17
32GLNGLNGLNGLN(chain C and (resid 24 through 39 or resid 41...CC41 - 9119 - 69
33PHEPHEALAALA(chain C and (resid 24 through 39 or resid 41...CC93 - 11471 - 92
34LYSLYSTYRTYR(chain C and (resid 24 through 39 or resid 41...CC116 - 11794 - 95
35VALVALLYSLYS(chain C and (resid 24 through 39 or resid 41...CC119 - 13797 - 115
36LEULEUILEILE(chain C and (resid 24 through 39 or resid 41...CC139 - 170117 - 148
37PHEPHETRPTRP(chain C and (resid 24 through 39 or resid 41...CC172 - 225150 - 203
38GLUGLUASNASN(chain C and (resid 24 through 39 or resid 41...CC227 - 231205 - 209
39TRPTRPPROPRO(chain C and (resid 24 through 39 or resid 41...CC233 - 265211 - 243
41GLUGLULYSLYS(chain D and (resid 24 through 39 or resid 41...DD24 - 392 - 17
42GLNGLNGLNGLN(chain D and (resid 24 through 39 or resid 41...DD41 - 9119 - 69
43PHEPHEALAALA(chain D and (resid 24 through 39 or resid 41...DD93 - 11471 - 92
44LYSLYSTYRTYR(chain D and (resid 24 through 39 or resid 41...DD116 - 11794 - 95
45VALVALLYSLYS(chain D and (resid 24 through 39 or resid 41...DD119 - 13797 - 115
46LEULEUILEILE(chain D and (resid 24 through 39 or resid 41...DD139 - 170117 - 148
47PHEPHETRPTRP(chain D and (resid 24 through 39 or resid 41...DD172 - 225150 - 203
48GLUGLUASNASN(chain D and (resid 24 through 39 or resid 41...DD227 - 231205 - 209
49TRPTRPPROPRO(chain D and (resid 24 through 39 or resid 41...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-AUV / 3-(2-hydroxyphenyl)benzoic acid


Mass: 214.217 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C13H10O3
#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.: 11 / Source method: obtained synthetically / Formula: C2H6O2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1260 / 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: 54.11 %
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: 0.8726 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: 0.8726 Å / Relative weight: 1
ReflectionResolution: 1.95→41.92 Å / % possible obs: 99.6 % / Redundancy: 4.7 % / Rmerge(I) obs: 0.1256 / Rrim(I) all: 0.14 / Net I/σ(I): 9.12
Reflection shellResolution: 1.95→2.02 Å / % possible obs: 99.74 % / Redundancy: 4.6 % / Rmerge(I) obs: 0.6591 / Num. unique obs: 40332 / Rrim(I) all: 0.74 / Net I/σ(I) obs: 2.15

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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→41.92 Å / Cross valid method: THROUGHOUT
RfactorNum. reflection% reflection
Rfree0.2048 1425 -
Rwork0.1666 --
obs-88629 99.6 %
Refinement stepCycle: final / Resolution: 1.95→41.92 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7932 0 212 1260 9404
Biso mean--48.15 36.97 -
Num. residues----967
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0078382
X-RAY DIFFRACTIONf_angle_d0.8311349
X-RAY DIFFRACTIONf_chiral_restr0.0541181
X-RAY DIFFRACTIONf_plane_restr0.0061522
X-RAY DIFFRACTIONf_dihedral_angle_d18.2924956
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A5935X-RAY DIFFRACTION5.429TORSIONAL
12B5935X-RAY DIFFRACTION5.429TORSIONAL
13C5935X-RAY DIFFRACTION5.429TORSIONAL
14D5935X-RAY DIFFRACTION5.429TORSIONAL
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 10

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.95-2.01970.24751420.240986288770100
2.0197-2.10060.27571410.213886298770100
2.1006-2.19620.23541400.192986248764100
2.1962-2.31190.19241420.180986798821100
2.3119-2.45680.21211410.175886518792100
2.4568-2.64640.23021430.165487098852100
2.6464-2.91270.17741410.153987028843100
2.9127-3.33410.20421430.15458742888599
3.3341-4.20.18371430.13418774891799
4.2-43.56490.18661480.15959063921199
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)
10.5551-0.07710.27571.37470.09791.28420.0116-0.0071-0.00860.0712-0.0078-0.08840.00770.0778-00.1159-0.0137-0.01150.14430.00260.135189.2675222.8333-2.5544
20.64780.07250.21731.6217-0.13831.1977-0.00870.00930.02230.0610.02850.09590.0013-0.0778-0.0050.1191-0.0045-0.00320.1650.01720.156685.2414225.099432.1109
30.93160.24510.30941.529-0.36711.4767-0.02120.04020.0501-0.02250.03180.029-0.1421-0.1466-0.01430.15870.0310.02830.1440.01320.1295129.8636230.053232.0558
40.5148-0.0337-0.2810.78540.00310.84870.01970.04220.042-0.0919-0.00230.0468-0.0847-0.0229-0.01670.22-0.0101-0.0420.171-0.00230.178689.41262.57812.6119
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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