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- PDB-5qae: OXA-48 IN COMPLEX WITH COMPOUND 8b -

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Basic information

Entry
Database: PDB / ID: 5qae
TitleOXA-48 IN COMPLEX WITH COMPOUND 8b
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-fluorophenyl)benzoic acid / Beta-lactamase
Similarity search - Component
Biological speciesKlebsiella pneumoniae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 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)113,96812
Polymers112,9084
Non-polymers1,0608
Water14,592810
1
A: Beta-lactamase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,4793
Polymers28,2271
Non-polymers2522
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Beta-lactamase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,5414
Polymers28,2271
Non-polymers3143
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Beta-lactamase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,5053
Polymers28,2271
Non-polymers2782
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: Beta-lactamase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,4432
Polymers28,2271
Non-polymers2161
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)90.302, 109.463, 125.187
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 36 or (resid 37...
21chain B
31(chain C and (resid 24 through 36 or (resid 37...
41(chain D and (resid 24 through 36 or (resid 37...

NCS domain segments:

Ens-ID: 1 / Beg auth comp-ID: GLU / Beg label comp-ID: GLU

Dom-IDComponent-IDEnd auth comp-IDEnd label comp-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11THRTHR(chain A and (resid 24 through 36 or (resid 37...AA24 - 362 - 14
12GLUGLU(chain A and (resid 24 through 36 or (resid 37...AA3715
13PROPRO(chain A and (resid 24 through 36 or (resid 37...AA24 - 2652 - 243
14PROPRO(chain A and (resid 24 through 36 or (resid 37...AA24 - 2652 - 243
15PROPRO(chain A and (resid 24 through 36 or (resid 37...AA24 - 2652 - 243
16PROPRO(chain A and (resid 24 through 36 or (resid 37...AA24 - 2652 - 243
21PROPROchain BBB24 - 2652 - 243
31THRTHR(chain C and (resid 24 through 36 or (resid 37...CC24 - 362 - 14
32GLUGLU(chain C and (resid 24 through 36 or (resid 37...CC3715
33PROPRO(chain C and (resid 24 through 36 or (resid 37...CC24 - 2652 - 243
34PROPRO(chain C and (resid 24 through 36 or (resid 37...CC24 - 2652 - 243
35PROPRO(chain C and (resid 24 through 36 or (resid 37...CC24 - 2652 - 243
36PROPRO(chain C and (resid 24 through 36 or (resid 37...CC24 - 2652 - 243
41THRTHR(chain D and (resid 24 through 36 or (resid 37...DD24 - 362 - 14
42GLUGLU(chain D and (resid 24 through 36 or (resid 37...DD3715
43PROPRO(chain D and (resid 24 through 36 or (resid 37...DD24 - 2652 - 243
44PROPRO(chain D and (resid 24 through 36 or (resid 37...DD24 - 2652 - 243
45PROPRO(chain D and (resid 24 through 36 or (resid 37...DD24 - 2652 - 243
46PROPRO(chain D and (resid 24 through 36 or (resid 37...DD24 - 2652 - 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-Q4G / 3-(3-fluorophenyl)benzoic acid


Mass: 216.208 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C13H9FO2
#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.: 810 / 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: 2.74 Å3/Da / Density % sol: 55.11 %
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: 0.87258 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: 0.87258 Å / Relative weight: 1
ReflectionResolution: 2.1→46.81 Å / % possible obs: 99.47 % / Redundancy: 4.8 % / Rmerge(I) obs: 0.1558 / Rrim(I) all: 0.18 / Net I/σ(I): 7.48
Reflection shellResolution: 2.1→2.17 Å / % possible obs: 99.75 % / Redundancy: 5 % / Rmerge(I) obs: 0.7621 / Num. unique obs: 36305 / Rrim(I) all: 0.85 / Net I/σ(I) obs: 2.03

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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: 2.1→46.81 Å / Cross valid method: THROUGHOUT
RfactorNum. reflection% reflection
Rfree0.2397 1399 -
Rwork0.1888 --
obs-72640 99.47 %
Refinement stepCycle: final / Resolution: 2.1→46.81 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7928 0 118 810 8856
Biso mean--39.32 37.69 -
Num. residues----968
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0048198
X-RAY DIFFRACTIONf_angle_d0.65611091
X-RAY DIFFRACTIONf_chiral_restr0.0471156
X-RAY DIFFRACTIONf_plane_restr0.0041483
X-RAY DIFFRACTIONf_dihedral_angle_d18.5924835
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A6210X-RAY DIFFRACTION6.089TORSIONAL
12B6210X-RAY DIFFRACTION6.089TORSIONAL
13C6210X-RAY DIFFRACTION6.089TORSIONAL
14D6210X-RAY DIFFRACTION6.089TORSIONAL
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 (%)
2.1-2.17510.33171380.267670497187100
2.1751-2.26210.31421390.2527013715299
2.2621-2.36510.27461380.238670687206100
2.3651-2.48980.2671390.224570867225100
2.4898-2.64580.25651390.21570477186100
2.6458-2.850.25541390.19747101724099
2.85-3.13680.25461400.190771207260100
3.1368-3.59050.24891400.171971417281100
3.5905-4.52310.18381420.14097179732199
4.5231-46.81720.19281450.16647433757899
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)
10.5997-0.0123-0.21641.17090.06261.17660.0110.04860.029-0.171-0.0007-0.0343-0.02290.0681-0.01230.27660.00060.08060.20930.00880.170790.5251263.44462.6331
20.613-0.01720.45411.46170.0771.3410.0463-0.0257-0.0186-0.0014-0.0199-0.00060.0224-0.0152-0.03350.2184-0.030.0770.16930.00370.156790.4702223.7558-2.6706
30.55370.03470.31141.3939-0.30961.29770.023-0.00580.0523-0.02940.03190.083-0.0324-0.1101-0.05170.1608-0.01360.08340.1960.02050.185786.3993225.837532.1916
40.95390.18830.09961.4162-0.41911.3036-0.00880.05110.05890.00820.04610.0293-0.2073-0.1081-0.02240.36670.0165-0.04620.20250.01810.1747131.5592231.166932.0868
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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