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- PDB-5qa8: OXA-48 IN COMPLEX WITH COMPOUND 4c -

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Basic information

Entry
Database: PDB / ID: 5qa8
TitleOXA-48 IN COMPLEX WITH COMPOUND 4c
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-(4-hydroxyphenyl)benzoic acid / Beta-lactamase OXA-48
Similarity search - Component
Biological speciesKlebsiella pneumoniae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 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 / Category: chem_comp_atom / chem_comp_bond

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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)113,5868
Polymers112,9084
Non-polymers6784
Water6,810378
1
A: Beta-lactamase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,4412
Polymers28,2271
Non-polymers2141
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: 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
3
C: Beta-lactamase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,4412
Polymers28,2271
Non-polymers2141
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: Beta-lactamase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,4412
Polymers28,2271
Non-polymers2141
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)125.014, 88.339, 106.875
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-ID
11
21
31
41

NCS domain segments:
Dom-IDComponent-IDEns-IDSelection details
111(CHAIN A AND (RESID 24 THROUGH 28 OR (RESID 29...
211(CHAIN B AND (RESID 24 THROUGH 36 OR (RESID 37...
311(CHAIN C AND (RESID 24 THROUGH 28 OR (RESID 29...
411(CHAIN D AND (RESID 24 THROUGH 36 OR (RESID 37...

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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-JSX / 3-(4-hydroxyphenyl)benzoic acid


Mass: 214.217 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C13H10O3
#3: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 378 / 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: 2.61 Å3/Da / Density % sol: 52.93 %
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: ID29 / Wavelength: 0.97625 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: May 11, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97625 Å / Relative weight: 1
ReflectionResolution: 2.5→45.72 Å / % possible obs: 95.6 % / Redundancy: 4.8 % / Rmerge(I) obs: 0.1119 / Net I/σ(I): 7.96
Reflection shellResolution: 2.5→2.59 Å / Redundancy: 4.5 % / Rmerge(I) obs: 0.7146

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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: 2.5→45.72 Å / Cross valid method: THROUGHOUT
RfactorNum. reflection% reflection
Rfree0.259 1940 -
Rwork0.206 --
obs-39838 95.6 %
Refinement stepCycle: LAST / Resolution: 2.5→45.72 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7916 0 49 378 8343
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0038317
X-RAY DIFFRACTIONf_angle_d0.58611291
X-RAY DIFFRACTIONf_dihedral_angle_d18.364914
X-RAY DIFFRACTIONf_chiral_restr0.0441184
X-RAY DIFFRACTIONf_plane_restr0.0021504
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDType
11A5923X-RAY DIFFRACTIONPOSITIONAL
12B5923X-RAY DIFFRACTIONPOSITIONAL
13C5923X-RAY DIFFRACTIONPOSITIONAL
14D5923X-RAY DIFFRACTIONPOSITIONAL
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.5-2.56250.34091480.29552673X-RAY DIFFRACTION96
2.5625-2.63180.31811420.28072705X-RAY DIFFRACTION97
2.6318-2.70920.35341160.28572730X-RAY DIFFRACTION97
2.7092-2.79670.33531500.25492711X-RAY DIFFRACTION98
2.7967-2.89660.28681550.24462732X-RAY DIFFRACTION98
2.8966-3.01260.31131640.24372703X-RAY DIFFRACTION97
3.0126-3.14960.31321540.24112639X-RAY DIFFRACTION95
3.1496-3.31560.30751260.23092727X-RAY DIFFRACTION97
3.3156-3.52330.28111360.20722703X-RAY DIFFRACTION96
3.5233-3.79520.25711250.19412716X-RAY DIFFRACTION96
3.7952-4.17690.24451200.17822663X-RAY DIFFRACTION93
4.1769-4.78080.19281530.15432714X-RAY DIFFRACTION95
4.7808-6.02110.18541210.17532716X-RAY DIFFRACTION93
6.0211-45.73050.22191290.18612752X-RAY DIFFRACTION91
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)
11.8902-0.3227-0.52031.2448-0.25291.6198-0.0830.3182-0.0036-0.17270.0052-0.0171-0.1518-0.08910.03030.357-0.00550.02160.443-0.04030.404930.4177-3.7503-11.8596
21.9874-0.0182-0.58220.9399-0.33161.3925-0.10490.2484-0.2919-0.10020.058-0.04810.06520.03690.01160.4674-0.07760.03240.6586-0.03470.547130.217-47.867-6.9661
31.63040.3065-0.3760.9730.12071.60280.010.0309-0.15770.0016-0.0504-0.0408-0.12760.01080.03380.4038-0.0115-0.00670.51090.01130.45482.6524-44.35579.5912
42.01980.318-0.44680.62090.39722.1678-0.04680.05950.01350.0044-0.03880.12210.0178-0.2710.09250.40080.0489-0.01230.4978-0.02630.43472.6334-0.31864.6442
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(CHAIN 'A' AND RESID 24 THROUGH 265)
2X-RAY DIFFRACTION2(CHAIN 'B' AND RESID 25 THROUGH 265)
3X-RAY DIFFRACTION3(CHAIN 'C' AND RESID 25 THROUGH 265)
4X-RAY DIFFRACTION4(CHAIN 'D' AND RESID 25 THROUGH 265)

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