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- PDB-5qal: OXA-48 IN COMPLEX WITH COMPOUND 11b -

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Basic information

Entry
Database: PDB / ID: 5qal
TitleOXA-48 IN COMPLEX WITH COMPOUND 11b
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-(4-aminocarbonylphenyl)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)114,44018
Polymers112,9084
Non-polymers1,53214
Water17,258958
1
A: Beta-lactamase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,5924
Polymers28,2271
Non-polymers3653
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Beta-lactamase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,5303
Polymers28,2271
Non-polymers3032
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Beta-lactamase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,6906
Polymers28,2271
Non-polymers4635
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: Beta-lactamase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,6285
Polymers28,2271
Non-polymers4014
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)85.024, 104.043, 126.849
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 91 or resid 93...
21(chain B and (resid 24 through 91 or resid 93...
31(chain C and (resid 24 through 91 or resid 93...
41(chain D and (resid 24 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
11GLUGLUGLNGLN(chain A and (resid 24 through 91 or resid 93...AA24 - 912 - 69
12PHEPHEALAALA(chain A and (resid 24 through 91 or resid 93...AA93 - 10371 - 81
13TRPTRPALAALA(chain A and (resid 24 through 91 or resid 93...AA105 - 11483 - 92
14LYSLYSTYRTYR(chain A and (resid 24 through 91 or resid 93...AA116 - 11794 - 95
15VALVALLYSLYS(chain A and (resid 24 through 91 or resid 93...AA119 - 13797 - 115
16LEULEUILEILE(chain A and (resid 24 through 91 or resid 93...AA139 - 149117 - 127
17GLYGLYILEILE(chain A and (resid 24 through 91 or resid 93...AA151 - 170129 - 148
18PHEPHEASNASN(chain A and (resid 24 through 91 or resid 93...AA172 - 231150 - 209
19TRPTRPPROPRO(chain A and (resid 24 through 91 or resid 93...AA233 - 265211 - 243
21GLUGLUGLNGLN(chain B and (resid 24 through 91 or resid 93...BB24 - 912 - 69
22PHEPHEALAALA(chain B and (resid 24 through 91 or resid 93...BB93 - 10371 - 81
23TRPTRPALAALA(chain B and (resid 24 through 91 or resid 93...BB105 - 11483 - 92
24LYSLYSTYRTYR(chain B and (resid 24 through 91 or resid 93...BB116 - 11794 - 95
25VALVALLYSLYS(chain B and (resid 24 through 91 or resid 93...BB119 - 13797 - 115
26LEULEUILEILE(chain B and (resid 24 through 91 or resid 93...BB139 - 149117 - 127
27GLYGLYILEILE(chain B and (resid 24 through 91 or resid 93...BB151 - 170129 - 148
28PHEPHEASNASN(chain B and (resid 24 through 91 or resid 93...BB172 - 231150 - 209
29TRPTRPPROPRO(chain B and (resid 24 through 91 or resid 93...BB233 - 265211 - 243
31GLUGLUGLNGLN(chain C and (resid 24 through 91 or resid 93...CC24 - 912 - 69
32PHEPHEALAALA(chain C and (resid 24 through 91 or resid 93...CC93 - 10371 - 81
33TRPTRPALAALA(chain C and (resid 24 through 91 or resid 93...CC105 - 11483 - 92
34LYSLYSTYRTYR(chain C and (resid 24 through 91 or resid 93...CC116 - 11794 - 95
35VALVALLYSLYS(chain C and (resid 24 through 91 or resid 93...CC119 - 13797 - 115
36LEULEUILEILE(chain C and (resid 24 through 91 or resid 93...CC139 - 149117 - 127
37GLYGLYILEILE(chain C and (resid 24 through 91 or resid 93...CC151 - 170129 - 148
38PHEPHEASNASN(chain C and (resid 24 through 91 or resid 93...CC172 - 231150 - 209
39TRPTRPPROPRO(chain C and (resid 24 through 91 or resid 93...CC233 - 265211 - 243
41GLUGLUGLNGLN(chain D and (resid 24 through 91 or resid 93...DD24 - 912 - 69
42PHEPHEALAALA(chain D and (resid 24 through 91 or resid 93...DD93 - 10371 - 81
43TRPTRPALAALA(chain D and (resid 24 through 91 or resid 93...DD105 - 11483 - 92
44LYSLYSTYRTYR(chain D and (resid 24 through 91 or resid 93...DD116 - 11794 - 95
45VALVALLYSLYS(chain D and (resid 24 through 91 or resid 93...DD119 - 13797 - 115
46LEULEUILEILE(chain D and (resid 24 through 91 or resid 93...DD139 - 149117 - 127
47GLYGLYILEILE(chain D and (resid 24 through 91 or resid 93...DD151 - 170129 - 148
48PHEPHEASNASN(chain D and (resid 24 through 91 or resid 93...DD172 - 231150 - 209
49TRPTRPPROPRO(chain D and (resid 24 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-TVZ / 3-(4-aminocarbonylphenyl)benzoic acid


Mass: 241.242 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C14H11NO3
#3: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 8 / 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.: 958 / 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: 2.48 Å3/Da / Density % sol: 50.5 %
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→45.68 Å / % possible obs: 99.33 % / Redundancy: 4.7 % / Rmerge(I) obs: 0.1501 / Rrim(I) all: 0.17 / Net I/σ(I): 7.67
Reflection shellResolution: 1.95→2.02 Å / % possible obs: 99.77 % / Redundancy: 4.9 % / Rmerge(I) obs: 0.7637 / Num. unique obs: 39564 / Rrim(I) all: 0.86 / 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: 1.95→45.68 Å / Cross valid method: THROUGHOUT
RfactorNum. reflection% reflection
Rfree0.1947 1739 -
Rwork0.1697 --
obs-82037 99.33 %
Refinement stepCycle: final / Resolution: 1.95→45.68 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7932 0 194 958 9084
Biso mean--65.83 33.94 -
Num. residues----967
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0058381
X-RAY DIFFRACTIONf_angle_d0.73611355
X-RAY DIFFRACTIONf_chiral_restr0.0511181
X-RAY DIFFRACTIONf_plane_restr0.0041526
X-RAY DIFFRACTIONf_dihedral_angle_d18.0414957
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A5934X-RAY DIFFRACTION4.896TORSIONAL
12B5934X-RAY DIFFRACTION4.896TORSIONAL
13C5934X-RAY DIFFRACTION4.896TORSIONAL
14D5934X-RAY DIFFRACTION4.896TORSIONAL
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 (%)
1.95-2.00740.27151450.24566536798100
2.0074-2.07220.22951420.212266166758100
2.0722-2.14620.2141440.193466296773100
2.1462-2.23220.21591440.183466316775100
2.2322-2.33380.21711430.17756645678899
2.3338-2.45680.22871440.17186640678499
2.4568-2.61070.23871450.16236662680799
2.6107-2.81230.20021440.15816695683999
2.8123-3.09520.18161450.1536676682199
3.0952-3.5430.17641440.14796729687399
3.543-4.46330.13811470.14616741688899
4.4633-48.14580.20191510.19046976712799
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)
10.7886-0.1353-0.16120.9465-0.19951.09610.0129-0.0064-0.051-0.06150.01770.02390.0726-0.0499-0.02060.1292-0.0109-0.01380.12010.01190.1288-2.6716-13.498530.9774
20.8605-0.1503-0.08331.1515-0.07561.24850.0418-0.0533-0.04580.0388-0.03340.06210.0245-0.063-0.00410.1334-0.0193-0.01250.1450.01780.13439.6957-4.696330.6669
30.5786-0.034-0.21670.6152-0.03251.1007-0.0162-0.00930.0003-0.00280.0236-0.0190.00450.0047-0.00950.1128-0.0042-0.00720.1229-0.00170.12852.443-11.199465.5914
41.00370.0448-0.24541.2038-0.01961.20720.02690.11530.0182-0.1492-0.0051-0.0527-0.07630.056-0.02640.16670.0107-0.00060.1475-0.00850.132445.5588-1.889565.7099
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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