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- PDB-5qb3: OXA-48 IN COMPLEX WITH COMPOUND 40 -

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Basic information

Entry
Database: PDB / ID: 5qb3
TitleOXA-48 IN COMPLEX WITH COMPOUND 40
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-AVM / 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: Advisory / Database references / Structure summary
Category: database_2 / pdbx_deposit_group / pdbx_unobs_or_zero_occ_atoms
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)114,63212
Polymers112,9084
Non-polymers1,7258
Water18,5191028
1
A: Beta-lactamase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,6453
Polymers28,2271
Non-polymers4182
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Beta-lactamase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,6092
Polymers28,2271
Non-polymers3821
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Beta-lactamase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,6713
Polymers28,2271
Non-polymers4442
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: Beta-lactamase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,7074
Polymers28,2271
Non-polymers4803
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)89.486, 108.304, 124.569
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 91 or resid 93...
21(chain B and (resid 25 through 91 or resid 93...
31(chain C and (resid 25 through 91 or resid 93...
41(chain D and (resid 25 through 91 or resid 93...

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
11TRPTRPGLNGLN(chain A and (resid 25 through 91 or resid 93...AA25 - 913 - 69
12PHEPHEALAALA(chain A and (resid 25 through 91 or resid 93...AA93 - 10371 - 81
13TRPTRPALAALA(chain A and (resid 25 through 91 or resid 93...AA105 - 11483 - 92
14LYSLYSLYSLYS(chain A and (resid 25 through 91 or resid 93...AA116 - 13794 - 115
15LEULEUILEILE(chain A and (resid 25 through 91 or resid 93...AA139 - 149117 - 127
16GLYGLYILEILE(chain A and (resid 25 through 91 or resid 93...AA151 - 170129 - 148
17PHEPHETRPTRP(chain A and (resid 25 through 91 or resid 93...AA172 - 225150 - 203
18GLUGLUASNASN(chain A and (resid 25 through 91 or resid 93...AA227 - 231205 - 209
19TRPTRPPROPRO(chain A and (resid 25 through 91 or resid 93...AA233 - 265211 - 243
21TRPTRPGLNGLN(chain B and (resid 25 through 91 or resid 93...BB25 - 913 - 69
22PHEPHEALAALA(chain B and (resid 25 through 91 or resid 93...BB93 - 10371 - 81
23TRPTRPALAALA(chain B and (resid 25 through 91 or resid 93...BB105 - 11483 - 92
24LYSLYSLYSLYS(chain B and (resid 25 through 91 or resid 93...BB116 - 13794 - 115
25LEULEUILEILE(chain B and (resid 25 through 91 or resid 93...BB139 - 149117 - 127
26GLYGLYILEILE(chain B and (resid 25 through 91 or resid 93...BB151 - 170129 - 148
27PHEPHETRPTRP(chain B and (resid 25 through 91 or resid 93...BB172 - 225150 - 203
28GLUGLUASNASN(chain B and (resid 25 through 91 or resid 93...BB227 - 231205 - 209
29TRPTRPPROPRO(chain B and (resid 25 through 91 or resid 93...BB233 - 265211 - 243
31TRPTRPGLNGLN(chain C and (resid 25 through 91 or resid 93...CC25 - 913 - 69
32PHEPHEALAALA(chain C and (resid 25 through 91 or resid 93...CC93 - 10371 - 81
33TRPTRPALAALA(chain C and (resid 25 through 91 or resid 93...CC105 - 11483 - 92
34LYSLYSLYSLYS(chain C and (resid 25 through 91 or resid 93...CC116 - 13794 - 115
35LEULEUILEILE(chain C and (resid 25 through 91 or resid 93...CC139 - 149117 - 127
36GLYGLYILEILE(chain C and (resid 25 through 91 or resid 93...CC151 - 170129 - 148
37PHEPHETRPTRP(chain C and (resid 25 through 91 or resid 93...CC172 - 225150 - 203
38GLUGLUASNASN(chain C and (resid 25 through 91 or resid 93...CC227 - 231205 - 209
39TRPTRPPROPRO(chain C and (resid 25 through 91 or resid 93...CC233 - 265211 - 243
41TRPTRPGLNGLN(chain D and (resid 25 through 91 or resid 93...DD25 - 913 - 69
42PHEPHEALAALA(chain D and (resid 25 through 91 or resid 93...DD93 - 10371 - 81
43TRPTRPALAALA(chain D and (resid 25 through 91 or resid 93...DD105 - 11483 - 92
44LYSLYSLYSLYS(chain D and (resid 25 through 91 or resid 93...DD116 - 13794 - 115
45LEULEUILEILE(chain D and (resid 25 through 91 or resid 93...DD139 - 149117 - 127
46GLYGLYILEILE(chain D and (resid 25 through 91 or resid 93...DD151 - 170129 - 148
47PHEPHETRPTRP(chain D and (resid 25 through 91 or resid 93...DD172 - 225150 - 203
48GLUGLUASNASN(chain D and (resid 25 through 91 or resid 93...DD227 - 231205 - 209
49TRPTRPPROPRO(chain D and (resid 25 through 91 or resid 93...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-AVM / 3-(3-acetamidophenyl)-5-quinolin-7-yl-benzoic acid


Mass: 382.411 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C24H18N2O3
#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.: 2 / Source method: obtained synthetically / Formula: C2H6O2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1028 / 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: 2.67 Å3/Da / Density % sol: 53.99 %
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: 0.9184 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Mar 15, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9184 Å / Relative weight: 1
ReflectionResolution: 2→43.42 Å / % possible obs: 99.43 % / Redundancy: 7.2 % / Rmerge(I) obs: 0.1387 / Rrim(I) all: 0.15 / Net I/σ(I): 9.89
Reflection shellResolution: 2→2.07 Å / % possible obs: 99.56 % / Redundancy: 7.1 % / Rmerge(I) obs: 0.9015 / Num. unique obs: 57425 / Rrim(I) all: 0.97 / Net I/σ(I) obs: 2.01

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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→43.42 Å / Cross valid method: THROUGHOUT
RfactorNum. reflection% reflection
Rfree0.2357 857 -
Rwork0.2091 --
obs-81882 99.43 %
Refinement stepCycle: final / Resolution: 2→43.42 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7896 0 206 1028 9130
Biso mean--49.4 41.84 -
Num. residues----955
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0048461
X-RAY DIFFRACTIONf_angle_d0.6211503
X-RAY DIFFRACTIONf_chiral_restr0.0471197
X-RAY DIFFRACTIONf_plane_restr0.0041606
X-RAY DIFFRACTIONf_dihedral_angle_d18.0235035
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A5943X-RAY DIFFRACTION15.024TORSIONAL
12B5943X-RAY DIFFRACTION15.024TORSIONAL
13C5943X-RAY DIFFRACTION15.024TORSIONAL
14D5943X-RAY DIFFRACTION15.024TORSIONAL
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 6

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2-2.12530.3281410.2817133481348999
2.1253-2.28940.27391420.2339133581350099
2.2894-2.51980.25451390.21171338313522100
2.5198-2.88440.23171430.19171346313606100
2.8844-3.63380.2411450.18421356813713100
3.6338-46.34190.1961460.1753138861403299
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)
10.4402-0.0084-0.02790.92120.50780.9153-0.00450.0272-0.0163-0.09110.03840.0313-0.0591-0.000200.2691-0.00810.02480.21850.01170.201289.6555260.74782.7832
20.33840.00320.20610.79190.31521.01290.0232-0.0635-0.02520.1604-0.01430.02820.0928-0.00670.00180.28440.00370.03230.23110.00270.203189.651221.498-2.807
30.3792-0.16040.16571.1612-0.66470.78790.01350.03680.0021-0.00190.08370.0212-0.0387-0.099200.2504-0.02060.03840.22680.02010.196785.8521223.536432.1744
40.58720.0812-0.01290.8153-0.5091.0983-0.03350.02670.0866-0.00730.0595-0.0154-0.2401-0.08350.00110.290.021-0.02560.20010.00880.1983130.5518228.536132.0626
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1(chain 'A' and resid 25 through 265)A25 - 265
2X-RAY DIFFRACTION2(chain 'B' and resid 25 through 265)B25 - 265
3X-RAY DIFFRACTION3(chain 'C' and resid 25 through 265)C25 - 265
4X-RAY DIFFRACTION4(chain 'D' and resid 25 through 265)D25 - 265

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