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- PDB-5qat: OXA-48 IN COMPLEX WITH COMPOUND 24 -

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Basic information

Entry
Database: PDB / ID: 5qat
TitleOXA-48 IN COMPLEX WITH COMPOUND 24
ComponentsBeta-lactamase
KeywordsHYDROLASE / Oxacillinase / Inhibitor / Complex / OXA / Antibiotic resistance / beta-lactamase / fragment
Function / homology
Function and homology information


penicillin binding / antibiotic catabolic process / beta-lactamase activity / beta-lactamase / response to antibiotic / metal ion binding
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-[3-(acetyloxymethyl)phenyl]benzoic acid / Beta-lactamase
Similarity search - Component
Biological speciesKlebsiella pneumoniae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 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)114,37015
Polymers112,9084
Non-polymers1,46211
Water16,988943
1
A: Beta-lactamase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,5333
Polymers28,2271
Non-polymers3062
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Beta-lactamase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,4972
Polymers28,2271
Non-polymers2701
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Beta-lactamase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,6575
Polymers28,2271
Non-polymers4304
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: Beta-lactamase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,6835
Polymers28,2271
Non-polymers4564
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)45.135, 125.260, 107.808
Angle α, β, γ (deg.)90.000, 98.540, 90.000
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11(chain A and (resid 24 through 38 or (resid 39...
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 38 or (resid 39...

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
11GLUGLUHISHIS(chain A and (resid 24 through 38 or (resid 39...AA24 - 382 - 16
12LYSLYSLYSLYS(chain A and (resid 24 through 38 or (resid 39...AA3917
13GLUGLUPROPRO(chain A and (resid 24 through 38 or (resid 39...AA24 - 2652 - 243
14GLUGLUPROPRO(chain A and (resid 24 through 38 or (resid 39...AA24 - 2652 - 243
15GLUGLUPROPRO(chain A and (resid 24 through 38 or (resid 39...AA24 - 2652 - 243
16GLUGLUPROPRO(chain A and (resid 24 through 38 or (resid 39...AA24 - 2652 - 243
21GLUGLULYSLYS(chain B and (resid 24 through 39 or resid 41...BB24 - 392 - 17
22GLNGLNVALVAL(chain B and (resid 24 through 39 or resid 41...BB41 - 4319 - 21
23VALVALALAALA(chain B and (resid 24 through 39 or resid 41...BB45 - 10323 - 81
24TRPTRPASNASN(chain B and (resid 24 through 39 or resid 41...BB105 - 10683 - 84
25ASPASPALAALA(chain B and (resid 24 through 39 or resid 41...BB108 - 11486 - 92
26LYSLYSTYRTYR(chain B and (resid 24 through 39 or resid 41...BB116 - 11794 - 95
27VALVALLYSLYS(chain B and (resid 24 through 39 or resid 41...BB119 - 13797 - 115
28LEULEULEULEU(chain B and (resid 24 through 39 or resid 41...BB139117
29ALAALAGLUGLU(chain B and (resid 24 through 39 or resid 41...BB141 - 147119 - 125
210ILEILEALAALA(chain B and (resid 24 through 39 or resid 41...BB149 - 166127 - 144
211GLUGLUILEILE(chain B and (resid 24 through 39 or resid 41...BB168 - 170146 - 148
212PHEPHEASNASN(chain B and (resid 24 through 39 or resid 41...BB172 - 231150 - 209
213TRPTRPPROPRO(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
32GLNGLNVALVAL(chain C and (resid 24 through 39 or resid 41...CC41 - 4319 - 21
33VALVALALAALA(chain C and (resid 24 through 39 or resid 41...CC45 - 10323 - 81
34TRPTRPASNASN(chain C and (resid 24 through 39 or resid 41...CC105 - 10683 - 84
35ASPASPALAALA(chain C and (resid 24 through 39 or resid 41...CC108 - 11486 - 92
36LYSLYSTYRTYR(chain C and (resid 24 through 39 or resid 41...CC116 - 11794 - 95
37VALVALLYSLYS(chain C and (resid 24 through 39 or resid 41...CC119 - 13797 - 115
38LEULEULEULEU(chain C and (resid 24 through 39 or resid 41...CC139117
39ALAALAGLUGLU(chain C and (resid 24 through 39 or resid 41...CC141 - 147119 - 125
310ILEILEALAALA(chain C and (resid 24 through 39 or resid 41...CC149 - 166127 - 144
311GLUGLUILEILE(chain C and (resid 24 through 39 or resid 41...CC168 - 170146 - 148
312PHEPHEASNASN(chain C and (resid 24 through 39 or resid 41...CC172 - 231150 - 209
313TRPTRPPROPRO(chain C and (resid 24 through 39 or resid 41...CC233 - 265211 - 243
41GLUGLUHISHIS(chain D and (resid 24 through 38 or (resid 39...DD24 - 382 - 16
42LYSLYSLYSLYS(chain D and (resid 24 through 38 or (resid 39...DD3917
43LYSLYSPROPRO(chain D and (resid 24 through 38 or (resid 39...DD23 - 2651 - 243
44LYSLYSPROPRO(chain D and (resid 24 through 38 or (resid 39...DD23 - 2651 - 243
45LYSLYSPROPRO(chain D and (resid 24 through 38 or (resid 39...DD23 - 2651 - 243
46LYSLYSPROPRO(chain D and (resid 24 through 38 or (resid 39...DD23 - 2651 - 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-T7O / 3-[3-(acetyloxymethyl)phenyl]benzoic acid


Mass: 270.280 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C16H14O4
#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.: 5 / Source method: obtained synthetically / Formula: C2H6O2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 943 / 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: 53.92 %
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: ID23-1 / Wavelength: 0.984 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Sep 19, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.984 Å / Relative weight: 1
ReflectionResolution: 1.9→54 Å / % possible obs: 99.19 % / Redundancy: 4.1 % / Rmerge(I) obs: 0.104 / Rrim(I) all: 0.12 / Net I/σ(I): 6.74
Reflection shellResolution: 1.9→1.97 Å / % possible obs: 98.96 % / Redundancy: 4.2 % / Rmerge(I) obs: 0.5781 / Num. unique obs: 38865 / Rrim(I) all: 0.66 / Net I/σ(I) obs: 2.02

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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: 1.9→54 Å / Cross valid method: THROUGHOUT
RfactorNum. reflection% reflection
Rfree0.1975 4436 -
Rwork0.1668 --
obs-92294 99.19 %
Refinement stepCycle: final / Resolution: 1.9→54 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7939 0 184 943 9066
Biso mean--49.57 42.92 -
Num. residues----968
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0058420
X-RAY DIFFRACTIONf_angle_d0.73811421
X-RAY DIFFRACTIONf_chiral_restr0.0521188
X-RAY DIFFRACTIONf_plane_restr0.0051539
X-RAY DIFFRACTIONf_dihedral_angle_d18.7454986
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A5755X-RAY DIFFRACTION26.038TORSIONAL
12B5755X-RAY DIFFRACTION26.038TORSIONAL
13C5755X-RAY DIFFRACTION26.038TORSIONAL
14D5755X-RAY DIFFRACTION26.038TORSIONAL
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 30

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.9-1.92160.25051360.23112900303699
1.9216-1.94420.26461640.22752890305499
1.9442-1.96790.27791610.20732902306399
1.9679-1.99280.22881320.20732905303799
1.9928-2.0190.22841450.19862923306899
2.019-2.04670.23731520.18692971312399
2.0467-2.07590.22771300.17982875300599
2.0759-2.10690.21491400.172885302599
2.1069-2.13990.23461690.16852927309699
2.1399-2.17490.17781730.16522862303598
2.1749-2.21250.1931540.15432891304599
2.2125-2.25270.16921540.14732968312299
2.2527-2.2960.20731310.146729133044100
2.296-2.34290.21111340.154129423076100
2.3429-2.39380.19951340.15362973310799
2.3938-2.44950.20831400.15052911305199
2.4495-2.51080.20111340.1482986312099
2.5108-2.57870.181410.14712856299799
2.5787-2.65450.18721730.15372925309899
2.6545-2.74020.20121600.150628863046100
2.7402-2.83820.17951260.154330133139100
2.8382-2.95180.20161350.155329093044100
2.9518-3.08610.18881710.164229373108100
3.0861-3.24880.2191390.16842974311399
3.2488-3.45240.20081280.16042916304499
3.4524-3.71890.1651360.158229873123100
3.7189-4.09310.16791390.154129793118100
4.0931-4.68520.16531610.15312906306799
4.6852-5.90220.18731860.175529423128100
5.9022-62.6640.24911560.21983002315899
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)
10.68780.278-0.35951.2556-0.43281.1882-0.00250.01640.05870.0092-0.0263-0.0489-0.04110.0519-0.00150.1563-0.0001-0.01350.20210.00610.19590.299741.7606152.6948
20.5636-0.1657-0.14611.3140.43041.07410.078-0.13250.10040.3535-0.13240.3109-0.0459-0.0467-0.05250.3689-0.06380.07330.2406-0.06530.26991.440412.3941115.2812
30.7585-0.0339-0.00411.3555-0.1630.90180.03310.0449-0.0815-0.1342-0.0667-0.08880.0791-0.006200.24730.0152-0.0070.20940.00090.19545.407847.0362113.5736
40.6482-0.0086-0.07131.7426-0.46131.0889-0.002-0.068-0.0940.1223-0.0633-0.12310.00940.0553-0.00310.1861-0.0135-0.01450.2290.02720.23470.678913.7895169.282
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 23 through 265)B23 - 265
3X-RAY DIFFRACTION3(chain 'C' and resid 23 through 265)C23 - 265
4X-RAY DIFFRACTION4(chain 'D' and resid 23 through 265)D23 - 265

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