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- PDB-5qaa: OXA-48 IN COMPLEX WITH COMPOUND 6a -

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Basic information

Entry
Database: PDB / ID: 5qaa
TitleOXA-48 IN COMPLEX WITH COMPOUND 6a
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-(2-methoxyphenyl)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 1.3Apr 4, 2018Group: Data collection / Category: diffrn_source / Item: _diffrn_source.type
Revision 2.0Apr 11, 2018Group: Atomic model / Data collection ...Atomic model / Data collection / Derived calculations / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / diffrn_source / entity / pdbx_entity_nonpoly
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_atom_id / _atom_site.label_atom_id / _chem_comp.name / _diffrn_source.pdbx_synchrotron_beamline / _entity.pdbx_description / _pdbx_entity_nonpoly.name
Revision 3.0Nov 17, 2021Group: Atomic model / Database references ...Atomic model / Database references / Derived calculations / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / database_2 / entity / pdbx_deposit_group / pdbx_entity_nonpoly
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_atom_id / _atom_site.label_atom_id / _chem_comp.name / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _entity.pdbx_description / _pdbx_deposit_group.group_description / _pdbx_entity_nonpoly.name
Revision 3.1Nov 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)114,76124
Polymers112,9084
Non-polymers1,85320
Water21,6181200
1
A: Beta-lactamase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,6155
Polymers28,2271
Non-polymers3884
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Beta-lactamase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,7397
Polymers28,2271
Non-polymers5126
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Beta-lactamase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,7036
Polymers28,2271
Non-polymers4775
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: Beta-lactamase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,7036
Polymers28,2271
Non-polymers4775
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)90.280, 108.936, 124.109
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 265))
21(chain B and (resid 24 through 117 or resid 119 through 265))
31(chain C and (resid 24 through 117 or resid 119 through 265))
41(chain D and (resid 24 through 117 or resid 119 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 265))AA24 - 1172 - 95
12VALVALPROPRO(chain A and (resid 24 through 117 or resid 119 through 265))AA119 - 26597 - 243
21GLUGLUTYRTYR(chain B and (resid 24 through 117 or resid 119 through 265))BB24 - 1172 - 95
22VALVALPROPRO(chain B and (resid 24 through 117 or resid 119 through 265))BB119 - 26597 - 243
31GLUGLUTYRTYR(chain C and (resid 24 through 117 or resid 119 through 265))CC24 - 1172 - 95
32VALVALPROPRO(chain C and (resid 24 through 117 or resid 119 through 265))CC119 - 26597 - 243
41GLUGLUTYRTYR(chain D and (resid 24 through 117 or resid 119 through 265))DD24 - 1172 - 95
42VALVALPROPRO(chain D and (resid 24 through 117 or resid 119 through 265))DD119 - 26597 - 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-EAJ / 3-(2-methoxyphenyl)benzoic acid


Mass: 228.243 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C14H12O3
#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.: 14 / Source method: obtained synthetically / Formula: C2H6O2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1200 / 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: 2.7 Å3/Da / Density % sol: 54.49 %
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: 0.91841 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jan 13, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.91841 Å / Relative weight: 1
ReflectionResolution: 1.95→43.66 Å / % possible obs: 99.05 % / Redundancy: 4.5 % / Rmerge(I) obs: 0.1146 / Rrim(I) all: 0.13 / Net I/σ(I): 10.13
Reflection shellResolution: 1.95→2.02 Å / % possible obs: 98.65 % / Redundancy: 4.6 % / Rmerge(I) obs: 0.6427 / Num. unique obs: 40597 / Rrim(I) all: 0.73 / Net I/σ(I) obs: 2.32

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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→43.66 Å / Cross valid method: THROUGHOUT
RfactorNum. reflection% reflection
Rfree0.2056 1921 -
Rwork0.1693 --
obs-88890 99.05 %
Refinement stepCycle: final / Resolution: 1.95→43.66 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7932 0 254 1200 9386
Biso mean--65.68 35.46 -
Num. residues----968
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0058249
X-RAY DIFFRACTIONf_angle_d0.69911135
X-RAY DIFFRACTIONf_chiral_restr0.0491157
X-RAY DIFFRACTIONf_plane_restr0.0041486
X-RAY DIFFRACTIONf_dihedral_angle_d18.3434863
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A6191X-RAY DIFFRACTION5.17TORSIONAL
12B6191X-RAY DIFFRACTION5.17TORSIONAL
13C6191X-RAY DIFFRACTION5.17TORSIONAL
14D6191X-RAY DIFFRACTION5.17TORSIONAL
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 14

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.95-1.99880.26551360.26116140627699
1.9988-2.05280.30621350.24276106624199
2.0528-2.11320.26241350.22596117625299
2.1132-2.18140.27711350.216126626199
2.1814-2.25940.24491360.19346165630199
2.2594-2.34980.22331360.18596119625599
2.3498-2.45680.21481360.17346166630299
2.4568-2.58630.20781380.16346226636499
2.5863-2.74830.20911360.1586186632299
2.7483-2.96050.18611380.156862406378100
2.9605-3.25840.19761380.155262416379100
3.2584-3.72970.17381390.14446274641399
3.7297-4.69830.15691400.13046333647399
4.6983-46.65070.19411430.16766531667499
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)
10.59490.010.18691.2346-0.30041.22790.01190.01130.0512-0.02910.06840.0979-0.1168-0.1675-0.04790.13980.01120.00120.15050.0170.13586.4708224.68131.8902
20.6480.09980.08731.0312-0.26341.36390.0120.03730.06360.03450.02270.0378-0.2305-0.0559-0.01780.2393-0.00190.03810.16080.01170.1545131.4942230.053631.7322
30.2731-0.046-0.1731.03940.06441.50890.01290.04910.0125-0.0650.01650.00840.02050.0606-0.02910.1217-0.0026-0.02150.16340.00630.144790.363262.15372.6754
40.45730.01230.21391.01890.12591.13050.0267-0.0289-0.03270.04160.0032-0.02970.0178-0.0131-0.02690.1816-0.0173-0.01450.14420.00520.130690.4619222.6684-2.7074
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1(chain 'C' and resid 24 through 265)C24 - 265
2X-RAY DIFFRACTION2(chain 'D' and resid 24 through 265)D24 - 265
3X-RAY DIFFRACTION3(chain 'A' and resid 24 through 265)A24 - 265
4X-RAY DIFFRACTION4(chain 'B' and resid 24 through 265)B24 - 265

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