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- PDB-5qak: OXA-48 IN COMPLEX WITH COMPOUND 14 -

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Basic information

Entry
Database: PDB / ID: 5qak
TitleOXA-48 IN COMPLEX WITH COMPOUND 14
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-[3-(dimethylamino)phenyl]benzoic acid / Beta-lactamase
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 / 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)114,06812
Polymers112,9084
Non-polymers1,1608
Water17,168953
1
A: Beta-lactamase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,5664
Polymers28,2271
Non-polymers3393
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Beta-lactamase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,5664
Polymers28,2271
Non-polymers3393
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Beta-lactamase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,4682
Polymers28,2271
Non-polymers2411
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: Beta-lactamase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,4682
Polymers28,2271
Non-polymers2411
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)88.943, 107.938, 124.947
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 36 or (resid 37...
21(chain B and (resid 24 through 114 or resid 116...
31(chain C and (resid 24 through 36 or (resid 37...
41(chain D and (resid 24 through 114 or resid 116...

NCS domain segments:
Dom-IDComponent-IDEns-IDSelection detailsAuth asym-IDAuth seq-ID
111(chain A and (resid 24 through 36 or (resid 37...A24 - 36
121(chain A and (resid 24 through 36 or (resid 37...A37
131(chain A and (resid 24 through 36 or (resid 37...A24 - 265
141(chain A and (resid 24 through 36 or (resid 37...A24 - 265
151(chain A and (resid 24 through 36 or (resid 37...A24 - 265
161(chain A and (resid 24 through 36 or (resid 37...A24 - 265
211(chain B and (resid 24 through 114 or resid 116...B24 - 114
221(chain B and (resid 24 through 114 or resid 116...B116 - 117
231(chain B and (resid 24 through 114 or resid 116...B119 - 170
241(chain B and (resid 24 through 114 or resid 116...B172 - 181
251(chain B and (resid 24 through 114 or resid 116...B183 - 231
261(chain B and (resid 24 through 114 or resid 116...B233 - 265
271(chain B and (resid 24 through 114 or resid 116...B266
311(chain C and (resid 24 through 36 or (resid 37...C24 - 36
321(chain C and (resid 24 through 36 or (resid 37...C37
331(chain C and (resid 24 through 36 or (resid 37...C24 - 265
341(chain C and (resid 24 through 36 or (resid 37...C24 - 265
351(chain C and (resid 24 through 36 or (resid 37...C24 - 265
361(chain C and (resid 24 through 36 or (resid 37...C24 - 265
411(chain D and (resid 24 through 114 or resid 116...D24 - 114
421(chain D and (resid 24 through 114 or resid 116...D116 - 117
431(chain D and (resid 24 through 114 or resid 116...D119 - 170
441(chain D and (resid 24 through 114 or resid 116...D172 - 181
451(chain D and (resid 24 through 114 or resid 116...D183 - 231
461(chain D and (resid 24 through 114 or resid 116...D233 - 265
471(chain D and (resid 24 through 114 or resid 116...D266

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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-AV4 / 3-[3-(dimethylamino)phenyl]benzoic acid


Mass: 241.285 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C15H15NO2
#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.: 2 / Source method: obtained synthetically / Formula: C2H6O2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 953 / 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: 2.66 Å3/Da / Density % sol: 53.69 %
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: 0.97624 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: May 12, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97624 Å / Relative weight: 1
ReflectionResolution: 1.9→43.28 Å / % possible obs: 99.78 % / Redundancy: 8.8 % / Rmerge(I) obs: 0.09169 / Rrim(I) all: 0.1 / Net I/σ(I): 12.07
Reflection shellResolution: 1.9→1.97 Å / % possible obs: 99.78 % / Redundancy: 9.1 % / Rmerge(I) obs: 0.8395 / Num. unique obs: 85712 / Rrim(I) all: 0.89 / Net I/σ(I) obs: 2.4

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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→43.28 Å / Cross valid method: THROUGHOUT
RfactorNum. reflection% reflection
Rfree0.1897 4796 -
Rwork0.1599 --
obs-95054 99.78 %
Refinement stepCycle: final / Resolution: 1.9→43.28 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7924 0 150 953 9027
Biso mean--62.61 48.29 -
Num. residues----968
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0058252
X-RAY DIFFRACTIONf_angle_d0.70511175
X-RAY DIFFRACTIONf_chiral_restr0.0511163
X-RAY DIFFRACTIONf_plane_restr0.0041499
X-RAY DIFFRACTIONf_dihedral_angle_d18.0134869
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A6093X-RAY DIFFRACTION4.679TORSIONAL
12B6093X-RAY DIFFRACTION4.679TORSIONAL
13C6093X-RAY DIFFRACTION4.679TORSIONAL
14D6093X-RAY DIFFRACTION4.679TORSIONAL
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 (%)
1.9-1.92160.31591670.271929893156100
1.9216-1.94420.24321660.249129653131100
1.9442-1.96790.27691420.241229553097100
1.9679-1.99280.23281790.227529803159100
1.9928-2.0190.25521530.217929973150100
2.019-2.04670.25141450.204129533098100
2.0467-2.07590.25111430.199530053148100
2.0759-2.10690.25041690.188429553124100
2.1069-2.13990.23381800.179929333113100
2.1399-2.17490.20631620.169430023164100
2.1749-2.21240.2021400.159729783118100
2.2124-2.25270.18871770.156329923169100
2.2527-2.2960.20611360.159430013137100
2.296-2.34290.23251540.152929963150100
2.3429-2.39380.19641440.158530033147100
2.3938-2.44950.17951660.148229973163100
2.4495-2.51070.20851580.143829673125100
2.5107-2.57860.18331860.14429653151100
2.5786-2.65450.17011630.147630153178100
2.6545-2.74020.18011810.145129653146100
2.7402-2.83810.19451580.143630273185100
2.8381-2.95170.20331480.145130283176100
2.9517-3.0860.20021540.157930073161100
3.086-3.24870.20841630.162330393202100
3.2487-3.45210.18441540.148930303184100
3.4521-3.71860.1661630.141330393202100
3.7186-4.09260.1691630.132630603223100
4.0926-4.68430.141550.129830843239100
4.6843-5.89980.15961630.150231063269100
5.8998-46.1530.19581640.19783221338599
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)
10.7407-0.0293-0.30151.74160.14731.8059-0.02470.01090.0119-0.09210.03180.0594-0.05490.1267-0.00280.2914-0.0016-0.020.29190.0070.252489.2071260.04942.4517
20.6245-0.11340.28421.85360.10311.9558-0.0069-0.0555-0.01020.17610.0392-0.01690.04080.0093-0.02520.2260.01080.02260.2290.00750.218489.1712220.5931-2.5764
30.84580.16880.09271.7653-0.61421.81740.01110.07960.08530.03320.10090.0881-0.15-0.2991-0.09980.35520.02380.03830.3660.03420.307785.1535222.765432.1496
40.98360.25710.24511.9818-0.68592.18110.00130.04810.0627-0.01440.0599-0.0417-0.1912-0.0911-0.04770.22580.02180.00910.21970.01240.2098129.5582227.817932.0302
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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