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- PDB-5qai: OXA-48 IN COMPLEX WITH COMPOUND 12a -

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Basic information

Entry
Database: PDB / ID: 5qai
TitleOXA-48 IN COMPLEX WITH COMPOUND 12a
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-methylsulfonylphenyl)benzoic acid / Beta-lactamase
Similarity search - Component
Biological speciesKlebsiella pneumoniae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 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)114,72120
Polymers112,9084
Non-polymers1,81316
Water19,1681064
1
A: Beta-lactamase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,7416
Polymers28,2271
Non-polymers5145
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Beta-lactamase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,6274
Polymers28,2271
Non-polymers4003
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Beta-lactamase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,6274
Polymers28,2271
Non-polymers4003
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: Beta-lactamase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,7256
Polymers28,2271
Non-polymers4985
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)89.255, 108.766, 124.263
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 39 or resid 41...
21(chain B and (resid 24 through 39 or resid 41...
31(chain C and (resid 24 through 39 or resid 41...
41(chain D and (resid 24 through 39 or resid 41...

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
11GLUGLULYSLYS(chain A and (resid 24 through 39 or resid 41...AA24 - 392 - 17
12GLNGLNGLNGLN(chain A and (resid 24 through 39 or resid 41...AA41 - 9119 - 69
13PHEPHEALAALA(chain A and (resid 24 through 39 or resid 41...AA93 - 10371 - 81
14TRPTRPALAALA(chain A and (resid 24 through 39 or resid 41...AA105 - 11483 - 92
15LYSLYSTYRTYR(chain A and (resid 24 through 39 or resid 41...AA116 - 11794 - 95
16VALVALLYSLYS(chain A and (resid 24 through 39 or resid 41...AA119 - 13797 - 115
17LEULEUILEILE(chain A and (resid 24 through 39 or resid 41...AA139 - 170117 - 148
18PHEPHETRPTRP(chain A and (resid 24 through 39 or resid 41...AA172 - 225150 - 203
19GLUGLUASNASN(chain A and (resid 24 through 39 or resid 41...AA227 - 231205 - 209
110TRPTRPPROPRO(chain A and (resid 24 through 39 or resid 41...AA233 - 265211 - 243
21GLUGLULYSLYS(chain B and (resid 24 through 39 or resid 41...BB24 - 392 - 17
22GLNGLNGLNGLN(chain B and (resid 24 through 39 or resid 41...BB41 - 9119 - 69
23PHEPHEALAALA(chain B and (resid 24 through 39 or resid 41...BB93 - 10371 - 81
24TRPTRPALAALA(chain B and (resid 24 through 39 or resid 41...BB105 - 11483 - 92
25LYSLYSTYRTYR(chain B and (resid 24 through 39 or resid 41...BB116 - 11794 - 95
26VALVALLYSLYS(chain B and (resid 24 through 39 or resid 41...BB119 - 13797 - 115
27LEULEUILEILE(chain B and (resid 24 through 39 or resid 41...BB139 - 170117 - 148
28PHEPHETRPTRP(chain B and (resid 24 through 39 or resid 41...BB172 - 225150 - 203
29GLUGLUASNASN(chain B and (resid 24 through 39 or resid 41...BB227 - 231205 - 209
210TRPTRPPROPRO(chain B and (resid 24 through 39 or resid 41...BB233 - 265211 - 243
31GLUGLULYSLYS(chain C and (resid 24 through 39 or resid 41...CC24 - 392 - 17
32GLNGLNGLNGLN(chain C and (resid 24 through 39 or resid 41...CC41 - 9119 - 69
33PHEPHEALAALA(chain C and (resid 24 through 39 or resid 41...CC93 - 10371 - 81
34TRPTRPALAALA(chain C and (resid 24 through 39 or resid 41...CC105 - 11483 - 92
35LYSLYSTYRTYR(chain C and (resid 24 through 39 or resid 41...CC116 - 11794 - 95
36VALVALLYSLYS(chain C and (resid 24 through 39 or resid 41...CC119 - 13797 - 115
37LEULEUILEILE(chain C and (resid 24 through 39 or resid 41...CC139 - 170117 - 148
38PHEPHETRPTRP(chain C and (resid 24 through 39 or resid 41...CC172 - 225150 - 203
39GLUGLUASNASN(chain C and (resid 24 through 39 or resid 41...CC227 - 231205 - 209
310TRPTRPPROPRO(chain C and (resid 24 through 39 or resid 41...CC233 - 265211 - 243
41GLUGLULYSLYS(chain D and (resid 24 through 39 or resid 41...DD24 - 392 - 17
42GLNGLNGLNGLN(chain D and (resid 24 through 39 or resid 41...DD41 - 9119 - 69
43PHEPHEALAALA(chain D and (resid 24 through 39 or resid 41...DD93 - 10371 - 81
44TRPTRPALAALA(chain D and (resid 24 through 39 or resid 41...DD105 - 11483 - 92
45LYSLYSTYRTYR(chain D and (resid 24 through 39 or resid 41...DD116 - 11794 - 95
46VALVALLYSLYS(chain D and (resid 24 through 39 or resid 41...DD119 - 13797 - 115
47LEULEUILEILE(chain D and (resid 24 through 39 or resid 41...DD139 - 170117 - 148
48PHEPHETRPTRP(chain D and (resid 24 through 39 or resid 41...DD172 - 225150 - 203
49GLUGLUASNASN(chain D and (resid 24 through 39 or resid 41...DD227 - 231205 - 209
410TRPTRPPROPRO(chain D and (resid 24 through 39 or resid 41...DD233 - 265211 - 243

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Components

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Protein , 1 types, 4 molecules ABCD

#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

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Non-polymers , 5 types, 1080 molecules

#2: Chemical
ChemComp-VM7 / 3-(3-methylsulfonylphenyl)benzoic acid


Mass: 276.308 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C14H12O4S
#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.: 9 / Source method: obtained synthetically / Formula: C2H6O2
#5: Chemical ChemComp-DMS / DIMETHYL SULFOXIDE


Mass: 78.133 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6OS / Comment: DMSO, precipitant*YM
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1064 / 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: 2.67 Å3/Da / Density % sol: 53.95 %
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 2, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.87258 Å / Relative weight: 1
ReflectionResolution: 1.9→43.5 Å / % possible obs: 99.67 % / Redundancy: 8.6 % / Rmerge(I) obs: 0.1614 / Rrim(I) all: 0.17 / Net I/σ(I): 9.37
Reflection shellResolution: 1.9→1.97 Å / % possible obs: 99.54 % / Redundancy: 8.9 % / Rmerge(I) obs: 0.9131 / Num. unique obs: 83113 / Rrim(I) all: 0.97 / Net I/σ(I) obs: 2.16

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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: 1.9→43.5 Å / Cross valid method: THROUGHOUT
RfactorNum. reflection% reflection
Rfree0.1972 4808 -
Rwork0.1645 --
obs-95424 99.67 %
Refinement stepCycle: final / Resolution: 1.9→43.5 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7932 0 222 1064 9218
Biso mean--73.95 38.13 -
Num. residues----967
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0088398
X-RAY DIFFRACTIONf_angle_d0.80911385
X-RAY DIFFRACTIONf_chiral_restr0.0551188
X-RAY DIFFRACTIONf_plane_restr0.0051528
X-RAY DIFFRACTIONf_dihedral_angle_d17.944961
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A5907X-RAY DIFFRACTION5.558TORSIONAL
12B5907X-RAY DIFFRACTION5.558TORSIONAL
13C5907X-RAY DIFFRACTION5.558TORSIONAL
14D5907X-RAY DIFFRACTION5.558TORSIONAL
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 (%)
1.9-1.92160.29611550.269329343089100
1.9216-1.94420.27941500.25593020317099
1.9442-1.96790.2531490.247229733122100
1.9679-1.99280.29111470.23022978312599
1.9928-2.0190.24721290.216930143143100
2.019-2.04670.25011760.21452960313699
2.0467-2.07590.23741470.21543026317399
2.0759-2.10690.22141690.194229733142100
2.1069-2.13990.21581510.185629873138100
2.1399-2.17490.22631680.18930083176100
2.1749-2.21240.18271540.177229933147100
2.2124-2.25270.2271550.167229883143100
2.2527-2.2960.21881700.162930073177100
2.296-2.34290.22531630.161429953158100
2.3429-2.39380.20561490.170330103159100
2.3938-2.44950.17831840.15929533137100
2.4495-2.51070.2161630.154230323195100
2.5107-2.57860.18371530.148730243177100
2.5786-2.65450.22081390.149230513190100
2.6545-2.74020.17891710.139629773148100
2.7402-2.83810.18731650.142530313196100
2.8381-2.95170.17121560.146630493205100
2.9517-3.0860.18151620.1530133175100
3.086-3.24870.18261530.152830563209100
3.2487-3.45210.18051680.14530413209100
3.4521-3.71860.16311640.144830563220100
3.7186-4.09260.17541810.139430413222100
4.0926-4.68430.14621660.137231003266100
4.6843-5.89990.18011700.16231123282100
5.8999-46.45530.25041820.20683217339999
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)
10.5939-0.0921-0.21111.0070.08061.13590.00540.03350.026-0.10240.00720.048-0.0660.0072-0.01050.14850.0011-0.02760.1387-0.00130.147389.5579262.15492.5641
20.5335-0.08150.21841.06480.1191.26280.0026-0.018-0.01040.03970.003-0.02040.04410.044-0.00460.1096-0.01-0.00130.1253-0.00090.126589.4914222.4083-2.4483
30.62340.18580.06941.5334-0.25491.2647-0.00540.03280.03840.05780.00950.0487-0.0624-0.10360.01190.12090.0040.00620.15360.00960.151985.3185224.802832.0785
40.89010.09750.37351.3288-0.37231.4912-0.00170.04160.0452-0.00240.00810.0246-0.1228-0.10530.00140.15030.01840.02220.16360.010.146130.1911229.596132.0246
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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