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- PDB-5qas: OXA-48 IN COMPLEX WITH COMPOUND 23b -

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Basic information

Entry
Database: PDB / ID: 5qas
TitleOXA-48 IN COMPLEX WITH COMPOUND 23b
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 / beta-lactamase activity / 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-[4-(2-acetamidoethyl)phenyl]benzoic acid / Beta-lactamase OXA-48
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)114,16510
Polymers112,9084
Non-polymers1,2576
Water16,304905
1
A: Beta-lactamase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,5723
Polymers28,2271
Non-polymers3452
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Beta-lactamase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,5102
Polymers28,2271
Non-polymers2831
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Beta-lactamase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,5102
Polymers28,2271
Non-polymers2831
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: Beta-lactamase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,5723
Polymers28,2271
Non-polymers3452
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)88.778, 108.080, 124.379
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
12GLNGLNALAALA(chain A and (resid 24 through 39 or resid 41...AA41 - 11419 - 92
13LYSLYSLEULEU(chain A and (resid 24 through 39 or resid 41...AA116 - 13994 - 117
14ALAALAPROPRO(chain A and (resid 24 through 39 or resid 41...AA141 - 265119 - 243
21GLUGLULYSLYS(chain B and (resid 24 through 39 or resid 41...BB24 - 392 - 17
22GLNGLNALAALA(chain B and (resid 24 through 39 or resid 41...BB41 - 11419 - 92
23LYSLYSLEULEU(chain B and (resid 24 through 39 or resid 41...BB116 - 13994 - 117
24ALAALAPROPRO(chain B and (resid 24 through 39 or resid 41...BB141 - 265119 - 243
31GLUGLULYSLYS(chain C and (resid 24 through 39 or resid 41...CC24 - 392 - 17
32GLNGLNALAALA(chain C and (resid 24 through 39 or resid 41...CC41 - 11419 - 92
33LYSLYSLEULEU(chain C and (resid 24 through 39 or resid 41...CC116 - 13994 - 117
34ALAALAPROPRO(chain C and (resid 24 through 39 or resid 41...CC141 - 265119 - 243
41GLUGLULYSLYS(chain D and (resid 24 through 39 or resid 41...DD24 - 392 - 17
42GLNGLNALAALA(chain D and (resid 24 through 39 or resid 41...DD41 - 11419 - 92
43LYSLYSLEULEU(chain D and (resid 24 through 39 or resid 41...DD116 - 13994 - 117
44ALAALAPROPRO(chain D and (resid 24 through 39 or resid 41...DD141 - 265119 - 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-CVF / 3-[4-(2-acetamidoethyl)phenyl]benzoic acid


Mass: 283.322 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C17H17NO3
#3: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6O2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 905 / 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: 2.64 Å3/Da / Density % sol: 53.45 %
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: 0.984003 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Nov 25, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.984003 Å / Relative weight: 1
ReflectionResolution: 1.9→46.16 Å / % possible obs: 99.1 % / Redundancy: 6 % / Rmerge(I) obs: 0.1281 / Rrim(I) all: 0.14 / Net I/σ(I): 7.7
Reflection shellResolution: 1.9→1.97 Å / % possible obs: 97.28 % / Redundancy: 5.8 % / Rmerge(I) obs: 0.543 / Num. unique obs: 53284 / Rrim(I) all: 0.59 / 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→46.16 Å / Cross valid method: THROUGHOUT
RfactorNum. reflection% reflection
Rfree0.2303 4630 -
Rwork0.1906 --
obs-93924 99.1 %
Refinement stepCycle: final / Resolution: 1.9→46.16 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7932 0 168 905 9005
Biso mean--64.55 38.27 -
Num. residues----968
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0048250
X-RAY DIFFRACTIONf_angle_d0.67111162
X-RAY DIFFRACTIONf_chiral_restr0.0481159
X-RAY DIFFRACTIONf_plane_restr0.0041495
X-RAY DIFFRACTIONf_dihedral_angle_d18.1744876
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A6126X-RAY DIFFRACTION4.343TORSIONAL
12B6126X-RAY DIFFRACTION4.343TORSIONAL
13C6126X-RAY DIFFRACTION4.343TORSIONAL
14D6126X-RAY DIFFRACTION4.343TORSIONAL
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 (%)
1.9-1.92160.28621490.26052870301997
1.9216-1.94420.30231410.24692895303697
1.9442-1.96790.2951630.24552912307598
1.9679-1.99280.28871600.23242907306799
1.9928-2.0190.27361390.22292988312799
2.019-2.04670.26541600.21932897305799
2.0467-2.07590.29791630.2182960312399
2.0759-2.10690.26511500.21072956310699
2.1069-2.13990.26371620.19829213083100
2.1399-2.17490.22721790.19692936311599
2.1749-2.21240.24121540.18842907306198
2.2124-2.25270.2231510.17892966311799
2.2527-2.2960.22681330.18162957309099
2.296-2.34290.25361420.189830013143100
2.3429-2.39380.2251430.189629713114100
2.3938-2.44950.21151730.182829663139100
2.4495-2.51070.25621470.178329633110100
2.5107-2.57860.24491330.18130013134100
2.5786-2.65450.2411560.18442980313699
2.6545-2.74010.23991510.17622980313199
2.7401-2.83810.21391440.181430173161100
2.8381-2.95170.21581540.183829823136100
2.9517-3.0860.2351500.19163008315899
3.086-3.24870.24981630.203730063169100
3.2487-3.45210.22911630.19152980314399
3.4521-3.71860.21351750.18983019319499
3.7186-4.09260.20181480.16923021316999
4.0926-4.68430.211420.1593077321999
4.6843-5.89980.19131630.17153074323799
5.8998-46.17420.17931780.19873188336699
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)
10.5817-0.0532-0.0840.86950.17380.7605-0.03570.0270.0446-0.13480.03730.0321-0.07460.0492-00.28980.0038-0.0340.25020.00370.217889.0762260.32252.5255
20.4452-0.05180.13281.06910.18320.98610.0011-0.0211-0.02470.07820.01790.0135-0.0002-0.03370.00020.18720.0054-0.00870.18860.00070.184288.8901220.8939-2.5305
30.4690.04310.06391.0944-0.55010.85820.00040.00820.02540.04180.06170.0399-0.0537-0.13010.0010.2162-0.0003-0.00670.24340.01460.21184.9004223.120831.9685
40.6213-0.01190.03561.1362-0.53281.1409-0.02710.05740.0068-0.11190.06180.0372-0.1372-0.11350.00070.19190.01550.02130.19940.00910.1886129.309228.203931.8713
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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