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- PDB-5qau: OXA-48 IN COMPLEX WITH COMPOUND 26a -

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Basic information

Entry
Database: PDB / ID: 5qau
TitleOXA-48 IN COMPLEX WITH COMPOUND 26a
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
Chem-V7V / Beta-lactamase
Similarity search - Component
Biological speciesKlebsiella pneumoniae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.75 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)114,07017
Polymers112,9084
Non-polymers1,16213
Water16,556919
1
A: Beta-lactamase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,4495
Polymers28,2271
Non-polymers2224
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Beta-lactamase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,3513
Polymers28,2271
Non-polymers1242
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Beta-lactamase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,6174
Polymers28,2271
Non-polymers3903
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: Beta-lactamase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,6535
Polymers28,2271
Non-polymers4264
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)89.695, 108.732, 124.164
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 117 or resid 119 through 136 or resid 138 through 265))
21(chain B and (resid 24 through 117 or resid 119 through 136 or resid 138 through 265))
31(chain C and (resid 24 through 117 or resid 119 through 136 or resid 138 through 265))
41(chain D and (resid 24 through 117 or resid 119 through 136 or resid 138 through 265))

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
11GLUGLUTYRTYR(chain A and (resid 24 through 117 or resid 119 through 136 or resid 138 through 265))AA24 - 1172 - 95
12VALVALSERSER(chain A and (resid 24 through 117 or resid 119 through 136 or resid 138 through 265))AA119 - 13697 - 114
13METMETPROPRO(chain A and (resid 24 through 117 or resid 119 through 136 or resid 138 through 265))AA138 - 265116 - 243
21GLUGLUTYRTYR(chain B and (resid 24 through 117 or resid 119 through 136 or resid 138 through 265))BB24 - 1172 - 95
22VALVALSERSER(chain B and (resid 24 through 117 or resid 119 through 136 or resid 138 through 265))BB119 - 13697 - 114
23METMETPROPRO(chain B and (resid 24 through 117 or resid 119 through 136 or resid 138 through 265))BB138 - 265116 - 243
31GLUGLUTYRTYR(chain C and (resid 24 through 117 or resid 119 through 136 or resid 138 through 265))CC24 - 1172 - 95
32VALVALSERSER(chain C and (resid 24 through 117 or resid 119 through 136 or resid 138 through 265))CC119 - 13697 - 114
33METMETPROPRO(chain C and (resid 24 through 117 or resid 119 through 136 or resid 138 through 265))CC138 - 265116 - 243
41GLUGLUTYRTYR(chain D and (resid 24 through 117 or resid 119 through 136 or resid 138 through 265))DD24 - 1172 - 95
42VALVALSERSER(chain D and (resid 24 through 117 or resid 119 through 136 or resid 138 through 265))DD119 - 13697 - 114
43METMETPROPRO(chain D and (resid 24 through 117 or resid 119 through 136 or resid 138 through 265))DD138 - 265116 - 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-CL / CHLORIDE ION


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


Mass: 62.068 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: C2H6O2
#4: Chemical ChemComp-V7V / 3-[3-(1~{H}-1,2,3,4-tetrazol-5-yl)phenyl]benzoic acid


Mass: 266.255 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C14H10N4O2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 919 / 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: 54.13 %
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: 0.97625 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Sep 30, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97625 Å / Relative weight: 1
ReflectionResolution: 1.75→40.9 Å / % possible obs: 97.52 % / Redundancy: 4.2 % / Rmerge(I) obs: 0.07357 / Rrim(I) all: 0.08 / Net I/σ(I): 10.15
Reflection shellResolution: 1.75→1.81 Å / % possible obs: 97.7 % / Redundancy: 3.9 % / Rmerge(I) obs: 0.7771 / Num. unique obs: 46442 / Rrim(I) all: 0.89 / Net I/σ(I) obs: 1.6

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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: 1.75→40.9 Å / Cross valid method: THROUGHOUT
RfactorNum. reflection% reflection
Rfree0.213 5936 -
Rwork0.178 --
obs-119605 97.52 %
Refinement stepCycle: final / Resolution: 1.75→40.9 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7932 0 208 919 9059
Biso mean--61.3 40.7 -
Num. residues----968
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0078260
X-RAY DIFFRACTIONf_angle_d0.87911163
X-RAY DIFFRACTIONf_chiral_restr0.0561158
X-RAY DIFFRACTIONf_plane_restr0.0051516
X-RAY DIFFRACTIONf_dihedral_angle_d18.7254882
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A6152X-RAY DIFFRACTION4.34TORSIONAL
12B6152X-RAY DIFFRACTION4.34TORSIONAL
13C6152X-RAY DIFFRACTION4.34TORSIONAL
14D6152X-RAY DIFFRACTION4.34TORSIONAL
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 (%)
1.7501-1.770.41452020.3443653385596
1.77-1.79080.32812220.3173792401499
1.7908-1.81260.33481990.30413756395599
1.8126-1.83560.3351910.29943831402299
1.8356-1.85970.35221910.29613790398198
1.8597-1.88520.30471990.28153760395999
1.8852-1.91210.30162210.26073806402798
1.9121-1.94070.28032150.23123749396498
1.9407-1.9710.30271790.22333789396898
1.971-2.00330.23592020.21293783398598
2.0033-2.03790.27871970.20073780397798
2.0379-2.07490.25061940.19883758395298
2.0749-2.11480.24272270.19683743397098
2.1148-2.1580.22322020.18973792399498
2.158-2.20490.22161930.17463779397298
2.2049-2.25620.20491820.17163806398898
2.2562-2.31260.20041950.15753761395698
2.3126-2.37510.19962030.1593794399798
2.3751-2.4450.23681680.15993798396697
2.445-2.52390.19361810.15313813399498
2.5239-2.61410.18042020.15053794399697
2.6141-2.71880.20371970.15363813401098
2.7188-2.84250.17981930.15193801399498
2.8425-2.99240.19531860.16253834402098
2.9924-3.17980.19572060.16063804401097
3.1798-3.42520.21182020.1663780398297
3.4252-3.76980.17912010.16183803400497
3.7698-4.3150.1692040.15043801400596
4.315-5.43510.16871890.14453827401695
5.4351-46.50880.20011930.19443879407293
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)
10.5405-0.0252-0.20111.2820.26941.7137-0.00230.04620.0193-0.10390.0238-0.02870.01250.1055-0.01870.16990.003-0.01370.20560.00530.177389.8305261.65372.6111
20.5045-0.00380.25291.37930.17521.57410.0343-0.0366-0.01540.1105-0.015-0.01140.0905-0.0498-0.01720.2015-0.01860.00210.19660.00620.202189.7874222.254-2.6416
30.65660.02540.20851.4464-0.44691.385-0.00120.02580.0434-0.02930.08910.1171-0.0718-0.2051-0.07680.22490.00210.01760.25370.02230.220285.8512224.257631.9378
40.62330.12550.13661.3861-0.39621.8994-0.00010.04850.05310.02910.05360.0479-0.2566-0.0761-0.04090.21070.0070.01980.18740.01250.1902130.6194229.624431.7947
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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