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- PDB-5qay: OXA-48 IN COMPLEX WITH COMPOUND 32 -

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Basic information

Entry
Database: PDB / ID: 5qay
TitleOXA-48 IN COMPLEX WITH COMPOUND 32
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-(1-methylpyrrol-2-yl)benzoic acid / Beta-lactamase OXA-48
Similarity search - Component
Biological speciesKlebsiella pneumoniae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.7 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: Advisory / Database references / Structure summary
Category: database_2 / pdbx_deposit_group / pdbx_unobs_or_zero_occ_atoms
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)113,90812
Polymers112,9084
Non-polymers1,0008
Water19,8351101
1
A: Beta-lactamase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,4643
Polymers28,2271
Non-polymers2372
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Beta-lactamase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,5264
Polymers28,2271
Non-polymers2993
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Beta-lactamase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,4282
Polymers28,2271
Non-polymers2011
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: Beta-lactamase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,4903
Polymers28,2271
Non-polymers2632
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)89.722, 108.403, 124.870
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 91 or resid 93...
21(chain B and (resid 24 through 91 or resid 93...
31(chain C and (resid 24 through 91 or resid 93...
41(chain D and (resid 24 through 91 or resid 93...

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
11GLUGLUGLNGLN(chain A and (resid 24 through 91 or resid 93...AA24 - 912 - 69
12PHEPHEALAALA(chain A and (resid 24 through 91 or resid 93...AA93 - 10371 - 81
13TRPTRPALAALA(chain A and (resid 24 through 91 or resid 93...AA105 - 11483 - 92
14LYSLYSLYSLYS(chain A and (resid 24 through 91 or resid 93...AA116 - 13794 - 115
15LEULEUILEILE(chain A and (resid 24 through 91 or resid 93...AA139 - 149117 - 127
16GLYGLYILEILE(chain A and (resid 24 through 91 or resid 93...AA151 - 170129 - 148
17PHEPHETRPTRP(chain A and (resid 24 through 91 or resid 93...AA172 - 225150 - 203
18GLUGLUASNASN(chain A and (resid 24 through 91 or resid 93...AA227 - 231205 - 209
19TRPTRPPROPRO(chain A and (resid 24 through 91 or resid 93...AA233 - 265211 - 243
21GLUGLUGLNGLN(chain B and (resid 24 through 91 or resid 93...BB24 - 912 - 69
22PHEPHEALAALA(chain B and (resid 24 through 91 or resid 93...BB93 - 10371 - 81
23TRPTRPALAALA(chain B and (resid 24 through 91 or resid 93...BB105 - 11483 - 92
24LYSLYSLYSLYS(chain B and (resid 24 through 91 or resid 93...BB116 - 13794 - 115
25LEULEUILEILE(chain B and (resid 24 through 91 or resid 93...BB139 - 149117 - 127
26GLYGLYILEILE(chain B and (resid 24 through 91 or resid 93...BB151 - 170129 - 148
27PHEPHETRPTRP(chain B and (resid 24 through 91 or resid 93...BB172 - 225150 - 203
28GLUGLUASNASN(chain B and (resid 24 through 91 or resid 93...BB227 - 231205 - 209
29TRPTRPPROPRO(chain B and (resid 24 through 91 or resid 93...BB233 - 265211 - 243
31GLUGLUGLNGLN(chain C and (resid 24 through 91 or resid 93...CC24 - 912 - 69
32PHEPHEALAALA(chain C and (resid 24 through 91 or resid 93...CC93 - 10371 - 81
33TRPTRPALAALA(chain C and (resid 24 through 91 or resid 93...CC105 - 11483 - 92
34LYSLYSLYSLYS(chain C and (resid 24 through 91 or resid 93...CC116 - 13794 - 115
35LEULEUILEILE(chain C and (resid 24 through 91 or resid 93...CC139 - 149117 - 127
36GLYGLYILEILE(chain C and (resid 24 through 91 or resid 93...CC151 - 170129 - 148
37PHEPHETRPTRP(chain C and (resid 24 through 91 or resid 93...CC172 - 225150 - 203
38GLUGLUASNASN(chain C and (resid 24 through 91 or resid 93...CC227 - 231205 - 209
39TRPTRPPROPRO(chain C and (resid 24 through 91 or resid 93...CC233 - 265211 - 243
41GLUGLUGLNGLN(chain D and (resid 24 through 91 or resid 93...DD24 - 912 - 69
42PHEPHEALAALA(chain D and (resid 24 through 91 or resid 93...DD93 - 10371 - 81
43TRPTRPALAALA(chain D and (resid 24 through 91 or resid 93...DD105 - 11483 - 92
44LYSLYSLYSLYS(chain D and (resid 24 through 91 or resid 93...DD116 - 13794 - 115
45LEULEUILEILE(chain D and (resid 24 through 91 or resid 93...DD139 - 149117 - 127
46GLYGLYILEILE(chain D and (resid 24 through 91 or resid 93...DD151 - 170129 - 148
47PHEPHETRPTRP(chain D and (resid 24 through 91 or resid 93...DD172 - 225150 - 203
48GLUGLUASNASN(chain D and (resid 24 through 91 or resid 93...DD227 - 231205 - 209
49TRPTRPPROPRO(chain D and (resid 24 through 91 or resid 93...DD233 - 265211 - 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-X6P / 3-(1-methylpyrrol-2-yl)benzoic acid


Mass: 201.221 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C12H11NO2
#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.: 1101 / 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: 2.69 Å3/Da / Density % sol: 54.26 %
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: 0.984003 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: 0.984003 Å / Relative weight: 1
ReflectionResolution: 1.7→43.49 Å / % possible obs: 99.08 % / Redundancy: 5.4 % / Rmerge(I) obs: 0.1081 / Rrim(I) all: 0.12 / Net I/σ(I): 7.7
Reflection shellResolution: 1.7→1.76 Å / % possible obs: 99.71 % / Redundancy: 5.6 % / Rmerge(I) obs: 0.5328 / Num. unique obs: 74789 / Rrim(I) all: 0.59 / Net I/σ(I) obs: 2

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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: 1.7→43.49 Å / Cross valid method: THROUGHOUT
RfactorNum. reflection% reflection
Rfree0.2388 6660 -
Rwork0.1932 --
obs-132873 99.08 %
Refinement stepCycle: final / Resolution: 1.7→43.49 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7932 0 122 1101 9155
Biso mean--55.16 42.72 -
Num. residues----961
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.018424
X-RAY DIFFRACTIONf_angle_d0.99411446
X-RAY DIFFRACTIONf_chiral_restr0.0611200
X-RAY DIFFRACTIONf_plane_restr0.0071536
X-RAY DIFFRACTIONf_dihedral_angle_d18.194988
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A5961X-RAY DIFFRACTION15.505TORSIONAL
12B5961X-RAY DIFFRACTION15.505TORSIONAL
13C5961X-RAY DIFFRACTION15.505TORSIONAL
14D5961X-RAY DIFFRACTION15.505TORSIONAL
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 (%)
1.7-1.71930.33472130.305642294442100
1.7193-1.73950.33252280.290641894417100
1.7395-1.76080.30542270.274142004427100
1.7608-1.78310.2842290.270241584387100
1.7831-1.80650.31882200.279142024422100
1.8065-1.83130.29671970.262742044401100
1.8313-1.85740.2882280.245941714399100
1.8574-1.88510.29292250.246241824407100
1.8851-1.91460.25442390.230841844423100
1.9146-1.9460.26632290.2141834412100
1.946-1.97960.26761990.209742264425100
1.9796-2.01560.24461950.210842404435100
2.0156-2.05430.2412110.20784176438799
2.0543-2.09630.24612430.203741934436100
2.0963-2.14180.24821900.2044244443499
2.1418-2.19170.26072300.19774160439099
2.1917-2.24650.2482190.18624191441099
2.2465-2.30720.22072590.18034173443299
2.3072-2.37510.22832080.1874196440499
2.3751-2.45170.2112150.18484221443699
2.4517-2.53940.21942440.18154175441999
2.5394-2.6410.24982160.18594223443999
2.641-2.76120.2252290.17914197442699
2.7612-2.90680.21992390.17944166440598
2.9068-3.08890.24252300.1834216444698
3.0889-3.32730.23552360.1844171440798
3.3273-3.6620.24082180.17034231444998
3.662-4.19160.22342060.16524245445198
4.1916-5.27980.20682240.16174252447697
5.2798-46.41040.23292160.21894408462497
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)
10.70750.06910.20851.95180.70471.2967-0.0224-0.05830.06830.0970.1384-0.1251-0.06380.1497-0.07480.19040.0030.01210.2211-0.02840.17313.7113-101.6816155.2058
20.7207-0.0940.19571.74970.58851.6544-0.0252-0.01860.06350.02970.0827-0.0667-0.23910.0994-0.04360.2704-0.01250.02890.1969-0.01460.2076-41.0374-96.3775155.3656
30.5646-0.0181-0.18971.66910.33821.87320.00670.01670.017-0.18040.05380.0132-0.05890.0418-0.05270.1699-0.0105-0.01370.19220.00560.1610.0566-118.401127.7318
40.5412-0.0172-0.28831.55060.31951.59470.03910.06190.0259-0.1609-0.0018-0.0254-0.12960.0019-0.030.22990.0065-0.00070.19230.00440.1875-44.7571-113.0575127.7676
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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