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- PDB-5qah: OXA-48 IN COMPLEX WITH COMPOUND 9b -

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Basic information

Entry
Database: PDB / ID: 5qah
TitleOXA-48 IN COMPLEX WITH COMPOUND 9b
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-(3-methoxycarbonylphenyl)benzoic acid / Beta-lactamase OXA-48
Similarity search - Component
Biological speciesKlebsiella pneumoniae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.95 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)114,31415
Polymers112,9084
Non-polymers1,40611
Water20,6991149
1
A: Beta-lactamase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,5814
Polymers28,2271
Non-polymers3543
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Beta-lactamase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,5814
Polymers28,2271
Non-polymers3543
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Beta-lactamase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,6074
Polymers28,2271
Non-polymers3803
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: Beta-lactamase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,5453
Polymers28,2271
Non-polymers3182
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)89.908, 108.889, 124.809
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 38 or (resid 39...
21(chain B and (resid 24 through 38 or (resid 39...
31(chain C and (resid 24 through 106 or resid 108...
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
21GLUGLUHISHIS(chain B and (resid 24 through 38 or (resid 39...BB24 - 382 - 16
22LYSLYSLYSLYS(chain B and (resid 24 through 38 or (resid 39...BB3917
23GLUGLUPROPRO(chain B and (resid 24 through 38 or (resid 39...BB24 - 2652 - 243
24GLUGLUPROPRO(chain B and (resid 24 through 38 or (resid 39...BB24 - 2652 - 243
25GLUGLUPROPRO(chain B and (resid 24 through 38 or (resid 39...BB24 - 2652 - 243
26GLUGLUPROPRO(chain B and (resid 24 through 38 or (resid 39...BB24 - 2652 - 243
31GLUGLUASNASN(chain C and (resid 24 through 106 or resid 108...CC24 - 1062 - 84
32ASPASPTYRTYR(chain C and (resid 24 through 106 or resid 108...CC108 - 11786 - 95
33VALVALLEULEU(chain C and (resid 24 through 106 or resid 108...CC119 - 13997 - 117
34ALAALALYSLYS(chain C and (resid 24 through 106 or resid 108...CC141 - 255119 - 233
35VALVALPROPRO(chain C and (resid 24 through 106 or resid 108...CC257 - 265235 - 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-EFX / 3-(3-methoxycarbonylphenyl)benzoic acid


Mass: 256.253 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C15H12O4
#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.: 5 / Source method: obtained synthetically / Formula: C2H6O2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1149 / 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: 2.71 Å3/Da / Density % sol: 54.54 %
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: 0.918409 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jan 13, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.918409 Å / Relative weight: 1
ReflectionResolution: 1.95→43.63 Å / % possible obs: 99.51 % / Redundancy: 4.5 % / Rmerge(I) obs: 0.09984 / Rrim(I) all: 0.11 / Net I/σ(I): 11.23
Reflection shellResolution: 1.95→2.02 Å / % possible obs: 99.49 % / Redundancy: 4.6 % / Rmerge(I) obs: 0.6006 / Num. unique obs: 40881 / Rrim(I) all: 0.68 / Net I/σ(I) obs: 2.34

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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: 1.95→43.63 Å / Cross valid method: THROUGHOUT
RfactorNum. reflection% reflection
Rfree0.2024 1654 -
Rwork0.1743 --
obs-89348 99.51 %
Refinement stepCycle: final / Resolution: 1.95→43.63 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7928 0 172 1149 9249
Biso mean--49.8 40.28 -
Num. residues----968
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0048267
X-RAY DIFFRACTIONf_angle_d0.61811186
X-RAY DIFFRACTIONf_chiral_restr0.0471161
X-RAY DIFFRACTIONf_plane_restr0.0041497
X-RAY DIFFRACTIONf_dihedral_angle_d18.1054881
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A6049X-RAY DIFFRACTION4.407TORSIONAL
12B6049X-RAY DIFFRACTION4.407TORSIONAL
13C6049X-RAY DIFFRACTION4.407TORSIONAL
14D6049X-RAY DIFFRACTION4.407TORSIONAL
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 12

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.95-2.00740.25011360.250871947330100
2.0074-2.07220.24391360.21877238737499
2.0722-2.14630.22641370.203272507387100
2.1463-2.23220.22891360.18487209734599
2.2322-2.33380.21411370.17597251738899
2.3338-2.45680.20671370.168172607397100
2.4568-2.61070.19051370.162472797416100
2.6107-2.81230.17391380.157773197457100
2.8123-3.09520.20561380.163373307468100
3.0952-3.5430.19521390.160973537492100
3.543-4.46320.17561390.15037396753599
4.4632-46.58450.20521440.18467615775999
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)
10.84250.13010.2421.2868-0.31941.6681-0.01680.05930.0659-0.06250.04410.0254-0.2164-0.0809-0.02650.20030.00130.04670.15130.0180.1428130.9851229.858831.8412
20.5717-0.0197-0.1711.3369-0.05351.5736-0.00670.05090.0407-0.11510.03740.01220.01510.0383-0.02360.1311-0.0025-0.03910.16240.00810.14290.0611262.12382.6886
30.5572-0.080.30761.26710.19721.57950.0404-0.0389-0.03930.0812-0.0073-0.03950.0832-0.0196-0.02760.1473-0.0201-0.02810.13320.00990.136990.1063222.6725-2.8278
40.70430.06190.23541.5574-0.29561.51680.00620.02680.05490.01060.06690.0951-0.0843-0.1334-0.04850.1290.0025-0.00220.15730.01870.149686.1643224.638132.0624
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1(chain 'D' and resid 24 through 265)D24 - 265
2X-RAY DIFFRACTION2(chain 'A' and resid 24 through 265)A24 - 265
3X-RAY DIFFRACTION3(chain 'B' and resid 24 through 265)B24 - 265
4X-RAY DIFFRACTION4(chain 'C' and resid 24 through 265)C24 - 265

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