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- PDB-5qaw: OXA-48 IN COMPLEX WITH COMPOUND 27 -

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Basic information

Entry
Database: PDB / ID: 5qaw
TitleOXA-48 IN COMPLEX WITH COMPOUND 27
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-naphthalen-2-ylbenzoic acid / Beta-lactamase OXA-48
Similarity search - Component
Biological speciesKlebsiella pneumoniae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 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: 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)113,7249
Polymers112,9084
Non-polymers8165
Water17,042946
1
A: Beta-lactamase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,5113
Polymers28,2271
Non-polymers2842
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Beta-lactamase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,2622
Polymers28,2271
Non-polymers351
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Beta-lactamase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,4752
Polymers28,2271
Non-polymers2481
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: Beta-lactamase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,4752
Polymers28,2271
Non-polymers2481
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)90.501, 109.053, 124.636
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 114 or resid 116 through 265))
21(chain B and (resid 25 through 114 or resid 116 through 265))
31(chain C and (resid 25 through 114 or resid 116 through 265))
41(chain D and (resid 25 through 114 or resid 116 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
11TRPTRPALAALA(chain A and (resid 25 through 114 or resid 116 through 265))AA25 - 1143 - 92
12LYSLYSPROPRO(chain A and (resid 25 through 114 or resid 116 through 265))AA116 - 26594 - 243
21TRPTRPALAALA(chain B and (resid 25 through 114 or resid 116 through 265))BB25 - 1143 - 92
22LYSLYSPROPRO(chain B and (resid 25 through 114 or resid 116 through 265))BB116 - 26594 - 243
31TRPTRPALAALA(chain C and (resid 25 through 114 or resid 116 through 265))CC25 - 1143 - 92
32LYSLYSPROPRO(chain C and (resid 25 through 114 or resid 116 through 265))CC116 - 26594 - 243
41TRPTRPALAALA(chain D and (resid 25 through 114 or resid 116 through 265))DD25 - 1143 - 92
42LYSLYSPROPRO(chain D and (resid 25 through 114 or resid 116 through 265))DD116 - 26594 - 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-TVC / 3-naphthalen-2-ylbenzoic acid


Mass: 248.276 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C17H12O2
#3: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 946 / 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: 2.72 Å3/Da / Density % sol: 54.84 %
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: 0.918409 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Apr 15, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.918409 Å / Relative weight: 1
ReflectionResolution: 2.2→46.7 Å / % possible obs: 99.36 % / Redundancy: 4.4 % / Rmerge(I) obs: 0.1047 / Rrim(I) all: 0.12 / Net I/σ(I): 9.13
Reflection shellResolution: 2.2→2.28 Å / % possible obs: 99.41 % / Redundancy: 4.2 % / Rmerge(I) obs: 0.6804 / Num. unique obs: 26270 / Rrim(I) all: 0.78 / Net I/σ(I) obs: 2.05

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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: 2.2→46.7 Å / Cross valid method: THROUGHOUT
RfactorNum. reflection% reflection
Rfree0.2364 3114 -
Rwork0.1978 --
obs-62872 99.36 %
Refinement stepCycle: final / Resolution: 2.2→46.7 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7923 0 92 946 8961
Biso mean--30.4 39.25 -
Num. residues----967
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0038191
X-RAY DIFFRACTIONf_angle_d0.57611088
X-RAY DIFFRACTIONf_chiral_restr0.0451156
X-RAY DIFFRACTIONf_plane_restr0.0031488
X-RAY DIFFRACTIONf_dihedral_angle_d17.9914838
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A6150X-RAY DIFFRACTION4.472TORSIONAL
12B6150X-RAY DIFFRACTION4.472TORSIONAL
13C6150X-RAY DIFFRACTION4.472TORSIONAL
14D6150X-RAY DIFFRACTION4.472TORSIONAL
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 22

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.2-2.23440.30961180.32232692281099
2.2344-2.2710.36581480.31192709285799
2.271-2.31020.33511410.29162633277499
2.3102-2.35220.32491390.283426852824100
2.3522-2.39740.30031340.277627122846100
2.3974-2.44630.28311460.247327042850100
2.4463-2.49950.27921490.23922645279499
2.4995-2.55770.29631290.22132695282499
2.5577-2.62160.27691510.220827112862100
2.6216-2.69250.25971340.21422680281499
2.6925-2.77170.28391280.20612718284699
2.7717-2.86120.24871520.19612692284499
2.8612-2.96340.23891350.200427122847100
2.9634-3.08210.25811430.20022691283499
3.0821-3.22230.24951480.199527192867100
3.2223-3.39210.24051510.19072696284799
3.3921-3.60460.22871310.174127442875100
3.6046-3.88280.18891670.153727202887100
3.8828-4.27330.1761430.1527502893100
4.2733-4.89110.19351450.13472768291399
4.8911-6.160.19441430.16872788293199
6.16-46.71510.21031390.20962893303298
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)
10.77470.0156-0.19821.42840.2012.03340.04440.03960.0558-0.06360.0207-0.0079-0.04060.1779-0.05450.3230.0255-0.00030.23640.00030.198290.6191262.59132.672
20.6123-0.02880.5291.56010.33441.747-0.007-0.063-0.03310.19590.0636-0.00960.0044-0.0865-0.03810.3840.01290.01710.22290.00930.213190.7405223.0286-2.6404
30.64120.10920.22621.4687-0.32771.66380.02880.03360.1027-0.07530.06830.1172-0.2886-0.2068-0.09660.48620.02950.03420.3140.02260.275686.7346225.183532.123
40.9324-0.07450.1551.22-0.54882.19460.01670.04490.06130.00710.0453-0.0333-0.2296-0.0602-0.03310.36810.00250.02270.21280.00650.2183131.8316230.171631.9139
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 25 through 265)C25 - 265
4X-RAY DIFFRACTION4(chain 'D' and resid 24 through 265)D24 - 265

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