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- PDB-5qb2: OXA-48 IN COMPLEX WITH COMPOUND 38 -

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Basic information

Entry
Database: PDB / ID: 5qb2
TitleOXA-48 IN COMPLEX WITH COMPOUND 38
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-quinolin-6-yl-5-quinolin-7-yl-benzoic acid / Beta-lactamase
Similarity search - Component
Biological speciesKlebsiella pneumoniae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.75 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)113,91811
Polymers112,9084
Non-polymers1,0107
Water25,0591391
1
A: Beta-lactamase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,7905
Polymers28,2271
Non-polymers5634
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Beta-lactamase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,6393
Polymers28,2271
Non-polymers4122
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: 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
4
D: Beta-lactamase


Theoretical massNumber of molelcules
Total (without water)28,2271
Polymers28,2271
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)90.035, 108.693, 124.094
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
12PHEPHETYRTYR(chain A and (resid 24 through 91 or resid 93...AA93 - 11771 - 95
13VALVALLEULEU(chain A and (resid 24 through 91 or resid 93...AA119 - 13997 - 117
14ALAALAASPASP(chain A and (resid 24 through 91 or resid 93...AA141 - 154119 - 132
15PHEPHEILEILE(chain A and (resid 24 through 91 or resid 93...AA156 - 170134 - 148
16PHEPHEPROPRO(chain A and (resid 24 through 91 or resid 93...AA172 - 265150 - 243
21GLUGLUGLNGLN(chain B and (resid 24 through 91 or resid 93...BB24 - 912 - 69
22PHEPHETYRTYR(chain B and (resid 24 through 91 or resid 93...BB93 - 11771 - 95
23VALVALLEULEU(chain B and (resid 24 through 91 or resid 93...BB119 - 13997 - 117
24ALAALAASPASP(chain B and (resid 24 through 91 or resid 93...BB141 - 154119 - 132
25PHEPHEILEILE(chain B and (resid 24 through 91 or resid 93...BB156 - 170134 - 148
26PHEPHEPROPRO(chain B and (resid 24 through 91 or resid 93...BB172 - 265150 - 243
31GLUGLUGLNGLN(chain C and (resid 24 through 91 or resid 93...CC24 - 912 - 69
32PHEPHETYRTYR(chain C and (resid 24 through 91 or resid 93...CC93 - 11771 - 95
33VALVALLEULEU(chain C and (resid 24 through 91 or resid 93...CC119 - 13997 - 117
34ALAALAASPASP(chain C and (resid 24 through 91 or resid 93...CC141 - 154119 - 132
35PHEPHEILEILE(chain C and (resid 24 through 91 or resid 93...CC156 - 170134 - 148
36PHEPHEPROPRO(chain C and (resid 24 through 91 or resid 93...CC172 - 265150 - 243
41GLUGLUGLNGLN(chain D and (resid 24 through 91 or resid 93...DD24 - 912 - 69
42PHEPHETYRTYR(chain D and (resid 24 through 91 or resid 93...DD93 - 11771 - 95
43VALVALLEULEU(chain D and (resid 24 through 91 or resid 93...DD119 - 13997 - 117
44ALAALAASPASP(chain D and (resid 24 through 91 or resid 93...DD141 - 154119 - 132
45PHEPHEILEILE(chain D and (resid 24 through 91 or resid 93...DD156 - 170134 - 148
46PHEPHEPROPRO(chain D and (resid 24 through 91 or resid 93...DD172 - 265150 - 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-U3M / 3-quinolin-6-yl-5-quinolin-7-yl-benzoic acid


Mass: 376.407 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C25H16N2O2
#3: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C2H6O2
#4: Chemical ChemComp-CL / CHLORIDE ION


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


Mass: 18.015 Da / Num. of mol.: 1391 / 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: BESSY / Beamline: 14.1 / Wavelength: 0.9184 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Mar 15, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9184 Å / Relative weight: 1
ReflectionResolution: 1.75→42.32 Å / % possible obs: 99.74 % / Redundancy: 7.4 % / Rmerge(I) obs: 0.08648 / Rrim(I) all: 0.09 / Net I/σ(I): 14.79
Reflection shellResolution: 1.75→1.81 Å / % possible obs: 99.76 % / Redundancy: 7.6 % / Rmerge(I) obs: 1.003 / Num. unique obs: 93019 / Rrim(I) all: 1.08 / 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: 1.75→42.32 Å / Cross valid method: THROUGHOUT
RfactorNum. reflection% reflection
Rfree0.2084 1379 -
Rwork0.1749 --
obs-122706 99.74 %
Refinement stepCycle: final / Resolution: 1.75→42.32 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7932 0 164 1391 9487
Biso mean--39.13 41.81 -
Num. residues----968
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0078291
X-RAY DIFFRACTIONf_angle_d0.87411233
X-RAY DIFFRACTIONf_chiral_restr0.0551164
X-RAY DIFFRACTIONf_plane_restr0.0061551
X-RAY DIFFRACTIONf_dihedral_angle_d18.8534912
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A6072X-RAY DIFFRACTION6.497TORSIONAL
12B6072X-RAY DIFFRACTION6.497TORSIONAL
13C6072X-RAY DIFFRACTION6.497TORSIONAL
14D6072X-RAY DIFFRACTION6.497TORSIONAL
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 10 / % reflection obs: 100 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all
1.75-1.81260.30491370.27751200812145
1.8126-1.88510.3071360.24881198212118
1.8851-1.97090.2571370.22181205412191
1.9709-2.07480.24481370.18861199112128
2.0748-2.20480.21431370.16691207912216
2.2048-2.3750.22831380.15451208012218
2.375-2.6140.1911370.15021211212249
2.614-2.99220.1951390.15531216012299
2.9922-3.76950.1731390.15491227012409
3.7695-42.33130.1971430.16771257412717
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)
10.6008-0.1123-0.04170.97080.31221.34720.03340.03080.0142-0.0960.0343-0.0262-0.0310.05910.1450.1801-0.00610.0050.20150.00220.179190.217261.4782.5689
20.36010.05430.25150.92340.14881.18590.0353-0.04560.01520.1327-0.0006-0.02150.0126-0.04820.14380.2118-0.0044-0.00280.19150.00290.201490.2049222.2746-2.5538
30.5364-0.01580.16361.244-0.53311.0263-0.00220.02220.0766-0.04790.10830.1353-0.1214-0.13360.01440.21060.00360.01210.22580.02510.199386.301224.173231.9893
40.53070.00760.10381.0468-0.30791.38120.00010.04230.0619-0.03290.0640.0892-0.1907-0.07250.00350.2170.00330.01120.18150.01660.1911131.1931229.365431.7839
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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