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- PDB-5qav: OXA-48 IN COMPLEX WITH COMPOUND 26b -

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Basic information

Entry
Database: PDB / ID: 5qav
TitleOXA-48 IN COMPLEX WITH COMPOUND 26b
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
Chem-L43 / Beta-lactamase OXA-48
Similarity search - Component
Biological speciesKlebsiella pneumoniae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.72 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)114,07017
Polymers112,9084
Non-polymers1,16213
Water16,358908
1
A: Beta-lactamase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,3513
Polymers28,2271
Non-polymers1242
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Beta-lactamase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,2892
Polymers28,2271
Non-polymers621
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Beta-lactamase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,7156
Polymers28,2271
Non-polymers4885
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: Beta-lactamase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,7156
Polymers28,2271
Non-polymers4885
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)90.070, 108.424, 124.555
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 117 or resid 119 through 139 or resid 141 through 265))
21(chain B and (resid 24 through 117 or resid 119 through 139 or resid 141 through 265))
31(chain C and (resid 24 through 117 or resid 119 through 139 or resid 141 through 265))
41(chain D and (resid 24 through 117 or resid 119 through 139 or resid 141 through 265))

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
11GLUGLUTYRTYR(chain A and (resid 24 through 117 or resid 119 through 139 or resid 141 through 265))AA24 - 1172 - 95
12VALVALLEULEU(chain A and (resid 24 through 117 or resid 119 through 139 or resid 141 through 265))AA119 - 13997 - 117
13ALAALAPROPRO(chain A and (resid 24 through 117 or resid 119 through 139 or resid 141 through 265))AA141 - 265119 - 243
21GLUGLUTYRTYR(chain B and (resid 24 through 117 or resid 119 through 139 or resid 141 through 265))BB24 - 1172 - 95
22VALVALLEULEU(chain B and (resid 24 through 117 or resid 119 through 139 or resid 141 through 265))BB119 - 13997 - 117
23ALAALAPROPRO(chain B and (resid 24 through 117 or resid 119 through 139 or resid 141 through 265))BB141 - 265119 - 243
31GLUGLUTYRTYR(chain C and (resid 24 through 117 or resid 119 through 139 or resid 141 through 265))CC24 - 1172 - 95
32VALVALLEULEU(chain C and (resid 24 through 117 or resid 119 through 139 or resid 141 through 265))CC119 - 13997 - 117
33ALAALAPROPRO(chain C and (resid 24 through 117 or resid 119 through 139 or resid 141 through 265))CC141 - 265119 - 243
41GLUGLUTYRTYR(chain D and (resid 24 through 117 or resid 119 through 139 or resid 141 through 265))DD24 - 1172 - 95
42VALVALLEULEU(chain D and (resid 24 through 117 or resid 119 through 139 or resid 141 through 265))DD119 - 13997 - 117
43ALAALAPROPRO(chain D and (resid 24 through 117 or resid 119 through 139 or resid 141 through 265))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-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: C2H6O2
#3: Chemical ChemComp-L43 / 3-[4-(1~{H}-1,2,3,4-tetrazol-5-yl)phenyl]benzoic acid


Mass: 266.255 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C14H10N4O2
#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.: 908 / 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: 54.33 %
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: ID23-1 / Wavelength: 0.97625 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Sep 30, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97625 Å / Relative weight: 1
ReflectionResolution: 1.72→40.89 Å / % possible obs: 98.31 % / Redundancy: 4.3 % / Rmerge(I) obs: 0.06139 / Rrim(I) all: 0.07 / Net I/σ(I): 11.27
Reflection shellResolution: 1.72→1.78 Å / % possible obs: 96.33 % / Redundancy: 4.1 % / Rmerge(I) obs: 0.67 / Num. unique obs: 50045 / Rrim(I) all: 0.77 / Net I/σ(I) obs: 1.8

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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: 1.72→40.89 Å / Cross valid method: THROUGHOUT
RfactorNum. reflection% reflection
Rfree0.2054 6315 -
Rwork0.1794 --
obs-127494 98.31 %
Refinement stepCycle: final / Resolution: 1.72→40.89 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7932 0 150 908 8990
Biso mean--54.69 43.52 -
Num. residues----968
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0058218
X-RAY DIFFRACTIONf_angle_d0.72711107
X-RAY DIFFRACTIONf_chiral_restr0.051158
X-RAY DIFFRACTIONf_plane_restr0.0041471
X-RAY DIFFRACTIONf_dihedral_angle_d18.5754840
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A6151X-RAY DIFFRACTION6.966TORSIONAL
12B6151X-RAY DIFFRACTION6.966TORSIONAL
13C6151X-RAY DIFFRACTION6.966TORSIONAL
14D6151X-RAY DIFFRACTION6.966TORSIONAL
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 (%)
1.72-1.73950.38772110.3393864407595
1.7395-1.760.37051830.31313945412897
1.76-1.78150.30082060.29583941414797
1.7815-1.8040.27462180.27313972419098
1.804-1.82780.31942100.26543995420598
1.8278-1.85280.2592190.25763996421598
1.8528-1.87930.28142260.25324022424898
1.8793-1.90730.282390.2433920415998
1.9073-1.93710.27291850.23693997418298
1.9371-1.96890.22512260.20844025425199
1.9689-2.00280.252270.2024005423299
2.0028-2.03920.22441990.19314031423098
2.0392-2.07850.23542050.19843970417598
2.0785-2.12090.2381990.19064008420798
2.1209-2.1670.24961970.18794060425799
2.167-2.21740.21192160.17564021423799
2.2174-2.27290.20692110.17743999421098
2.2729-2.33430.17832140.16414024423899
2.3343-2.4030.19512100.16754085429599
2.403-2.48050.1992050.15754085429099
2.4805-2.56920.18242200.15824048426899
2.5692-2.6720.16592000.16364071427199
2.672-2.79360.20461980.15874047424598
2.7936-2.94090.20212230.17044100432399
2.9409-3.12510.2032110.17214109432099
3.1251-3.36620.21222010.17574130433199
3.3662-3.70480.19852160.16924089430599
3.7048-4.24040.16542130.15044096430998
4.2404-5.34060.15042120.14744197440999
5.3406-40.90150.18812150.18374326454198
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)
10.681-0.0345-0.22461.35050.27291.94740.01340.04810.0321-0.14570.0342-0.0118-0.09220.1378-0.04090.18840.0051-0.01310.22270.00520.183690.201261.01812.536
20.47550.07190.26641.41390.20621.75930.0301-0.0434-0.01340.1110.0006-0.01320.0145-0.0545-0.0310.2028-0.00960.0060.1970.00810.20290.1642221.5855-2.5381
30.66010.06410.27061.8014-0.48691.69290.00760.0130.05620.02380.09270.1098-0.1703-0.2231-0.07290.19170.02120.02210.23440.02020.194886.2067223.740432.1138
40.81370.22190.24491.5246-0.49811.8705-0.01160.06440.0514-0.05530.0620.0662-0.1566-0.0775-0.04780.2343-0.00530.02020.20050.00990.2023131.1471228.970631.9513
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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