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- PDB-5qb1: OXA-48 IN COMPLEX WITH COMPOUND 36 -

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Basic information

Entry
Database: PDB / ID: 5qb1
TitleOXA-48 IN COMPLEX WITH COMPOUND 36
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
3,5-bis(3-acetamidophenyl)benzoic acid / Beta-lactamase OXA-48
Similarity search - Component
Biological speciesKlebsiella pneumoniae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 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)114,25216
Polymers112,9084
Non-polymers1,34412
Water14,754819
1
A: Beta-lactamase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,3874
Polymers28,2271
Non-polymers1603
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Beta-lactamase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,8376
Polymers28,2271
Non-polymers6105
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Beta-lactamase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,3513
Polymers28,2271
Non-polymers1242
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: Beta-lactamase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,6773
Polymers28,2271
Non-polymers4502
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)44.962, 125.208, 107.378
Angle α, β, γ (deg.)90.000, 97.820, 90.000
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11(chain A and (resid 24 through 38 or (resid 39...
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 38 or (resid 39...

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
11GLUGLUHISHIS(chain A and (resid 24 through 38 or (resid 39...AA24 - 382 - 16
12LYSLYSLYSLYS(chain A and (resid 24 through 38 or (resid 39...AA3917
13GLUGLUPROPRO(chain A and (resid 24 through 38 or (resid 39...AA24 - 2652 - 243
14GLUGLUPROPRO(chain A and (resid 24 through 38 or (resid 39...AA24 - 2652 - 243
15GLUGLUPROPRO(chain A and (resid 24 through 38 or (resid 39...AA24 - 2652 - 243
16GLUGLUPROPRO(chain A and (resid 24 through 38 or (resid 39...AA24 - 2652 - 243
21GLUGLULYSLYS(chain B and (resid 24 through 39 or resid 41...BB24 - 392 - 17
22GLNGLNVALVAL(chain B and (resid 24 through 39 or resid 41...BB41 - 4319 - 21
23VALVALALAALA(chain B and (resid 24 through 39 or resid 41...BB45 - 10323 - 81
24TRPTRPASNASN(chain B and (resid 24 through 39 or resid 41...BB105 - 10683 - 84
25ASPASPALAALA(chain B and (resid 24 through 39 or resid 41...BB108 - 11486 - 92
26LYSLYSTYRTYR(chain B and (resid 24 through 39 or resid 41...BB116 - 11794 - 95
27VALVALLYSLYS(chain B and (resid 24 through 39 or resid 41...BB119 - 13797 - 115
28LEULEULEULEU(chain B and (resid 24 through 39 or resid 41...BB139117
29ALAALAGLUGLU(chain B and (resid 24 through 39 or resid 41...BB141 - 147119 - 125
210ILEILEALAALA(chain B and (resid 24 through 39 or resid 41...BB149 - 166127 - 144
211GLUGLUILEILE(chain B and (resid 24 through 39 or resid 41...BB168 - 170146 - 148
212PHEPHEASNASN(chain B and (resid 24 through 39 or resid 41...BB172 - 231150 - 209
213TRPTRPPROPRO(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
32GLNGLNVALVAL(chain C and (resid 24 through 39 or resid 41...CC41 - 4319 - 21
33VALVALALAALA(chain C and (resid 24 through 39 or resid 41...CC45 - 10323 - 81
34TRPTRPASNASN(chain C and (resid 24 through 39 or resid 41...CC105 - 10683 - 84
35ASPASPALAALA(chain C and (resid 24 through 39 or resid 41...CC108 - 11486 - 92
36LYSLYSTYRTYR(chain C and (resid 24 through 39 or resid 41...CC116 - 11794 - 95
37VALVALLYSLYS(chain C and (resid 24 through 39 or resid 41...CC119 - 13797 - 115
38LEULEULEULEU(chain C and (resid 24 through 39 or resid 41...CC139117
39ALAALAGLUGLU(chain C and (resid 24 through 39 or resid 41...CC141 - 147119 - 125
310ILEILEALAALA(chain C and (resid 24 through 39 or resid 41...CC149 - 166127 - 144
311GLUGLUILEILE(chain C and (resid 24 through 39 or resid 41...CC168 - 170146 - 148
312PHEPHEASNASN(chain C and (resid 24 through 39 or resid 41...CC172 - 231150 - 209
313TRPTRPPROPRO(chain C and (resid 24 through 39 or resid 41...CC233 - 265211 - 243
41GLUGLUHISHIS(chain D and (resid 24 through 38 or (resid 39...DD24 - 382 - 16
42LYSLYSLYSLYS(chain D and (resid 24 through 38 or (resid 39...DD3917
43GLUGLUPROPRO(chain D and (resid 24 through 38 or (resid 39...DD24 - 2652 - 243
44GLUGLUPROPRO(chain D and (resid 24 through 38 or (resid 39...DD24 - 2652 - 243
45GLUGLUPROPRO(chain D and (resid 24 through 38 or (resid 39...DD24 - 2652 - 243
46GLUGLUPROPRO(chain D and (resid 24 through 38 or (resid 39...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-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#3: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C2H6O2
#4: Chemical ChemComp-F1C / 3,5-bis(3-acetamidophenyl)benzoic acid


Mass: 388.416 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C23H20N2O4
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 819 / 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: 2.65 Å3/Da / Density % sol: 53.62 %
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: 0.97625 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Sep 30, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97625 Å / Relative weight: 1
ReflectionResolution: 1.8→40.87 Å / % possible obs: 94 % / Redundancy: 2.7 % / Rmerge(I) obs: 0.06527 / Rrim(I) all: 0.08 / Net I/σ(I): 9.19
Reflection shellResolution: 1.8→1.86 Å / % possible obs: 97.89 % / Redundancy: 2.8 % / Rmerge(I) obs: 0.4562 / Num. unique obs: 29312 / Rrim(I) all: 0.56 / Net I/σ(I) obs: 2.04

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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: 1.8→40.87 Å / Cross valid method: THROUGHOUT
RfactorNum. reflection% reflection
Rfree0.2014 5086 -
Rwork0.1645 --
obs-102162 94 %
Refinement stepCycle: final / Resolution: 1.8→40.87 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7924 0 178 819 8921
Biso mean--60.93 42.96 -
Num. residues----966
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0078369
X-RAY DIFFRACTIONf_angle_d0.79611343
X-RAY DIFFRACTIONf_chiral_restr0.0521180
X-RAY DIFFRACTIONf_plane_restr0.0051518
X-RAY DIFFRACTIONf_dihedral_angle_d18.114947
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A5766X-RAY DIFFRACTION26.787TORSIONAL
12B5766X-RAY DIFFRACTION26.787TORSIONAL
13C5766X-RAY DIFFRACTION26.787TORSIONAL
14D5766X-RAY DIFFRACTION26.787TORSIONAL
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 (%)
1.8-1.82050.33031710.28943385355698
1.8205-1.84190.27061810.2593320350198
1.8419-1.86430.30611530.25783405355898
1.8643-1.88790.29181810.23353325350698
1.8879-1.91280.25511910.21943301349297
1.9128-1.9390.27991910.21443334352597
1.939-1.96670.25251810.20513358353997
1.9667-1.99610.25151510.1923274342597
1.9961-2.02720.22691610.19493321348295
2.0272-2.06050.22081640.18113306347096
2.0605-2.0960.22781800.17983248342895
2.096-2.13410.21021680.18033250341894
2.1341-2.17520.23621780.16843258343696
2.1752-2.21960.1921650.16483253341895
2.2196-2.26780.21241680.16063267343595
2.2678-2.32060.21371860.16093212339894
2.3206-2.37860.19091650.1663283344894
2.3786-2.44290.21921680.15843214338294
2.4429-2.51480.21371610.15713274343594
2.5148-2.5960.21941550.15793150330593
2.596-2.68880.20681480.15583197334592
2.6888-2.79640.19371610.15963150331191
2.7964-2.92370.18272140.16593146336093
2.9237-3.07780.25171470.16363167331492
3.0778-3.27060.19351750.16483147332291
3.2706-3.5230.17921680.15493106327490
3.523-3.87740.18081600.14963054321489
3.8774-4.43820.16091680.13363130329890
4.4382-5.59040.15381720.13873122329490
5.5904-48.97320.21371540.17813120327488
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)
10.9540.4649-0.62182.0327-0.51481.8322-0.00810.01310.0735-0.0243-0.0326-0.0633-0.03730.08140.03310.1209-0.0016-0.03750.1736-0.00010.16032.149941.4775152.3345
20.8305-0.1426-0.26722.31020.87131.88780.0237-0.16370.12780.5092-0.1370.3640.0764-0.11050.04760.4155-0.04550.08340.2158-0.04970.25662.913312.2985115.115
30.8704-0.1772-0.22052.4047-0.27181.35480.02040.0225-0.0789-0.2313-0.0612-0.14880.06970.03920.04070.24880.0019-0.00570.18290.00150.1766.733847.0034113.3694
40.9998-0.0938-0.35792.1707-0.37551.4206-0.0309-0.0983-0.10190.2036-0.0605-0.17820.02260.12380.05520.1497-0.0072-0.02920.16870.02510.17252.729113.5677168.9825
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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