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- PDB-5qb4: OXA-48 IN COMPLEX WITH SUBSTRATE IMIPENEM -

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Basic information

Entry
Database: PDB / ID: 5qb4
TitleOXA-48 IN COMPLEX WITH SUBSTRATE IMIPENEM
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-IM2 / 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 / Derived calculations / Structure summary
Category: chem_comp / database_2 ...chem_comp / database_2 / entity / pdbx_deposit_group / pdbx_entity_nonpoly
Item: _chem_comp.name / _database_2.pdbx_DOI ..._chem_comp.name / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _entity.pdbx_description / _pdbx_deposit_group.group_description / _pdbx_entity_nonpoly.name
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)114,24611
Polymers112,9084
Non-polymers1,3387
Water14,052780
1
A: Beta-lactamase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,5282
Polymers28,2271
Non-polymers3011
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Beta-lactamase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,5282
Polymers28,2271
Non-polymers3011
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Beta-lactamase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,6264
Polymers28,2271
Non-polymers3993
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: Beta-lactamase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,5643
Polymers28,2271
Non-polymers3372
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)88.790, 107.500, 124.330
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
12GLNGLNLEULEU(chain A and (resid 24 through 39 or resid 41...AA41 - 13919 - 117
13ALAALAASNASN(chain A and (resid 24 through 39 or resid 41...AA141 - 231119 - 209
14TRPTRPPROPRO(chain A and (resid 24 through 39 or resid 41...AA233 - 265211 - 243
21GLUGLULYSLYS(chain B and (resid 24 through 39 or resid 41...BB24 - 392 - 17
22GLNGLNLEULEU(chain B and (resid 24 through 39 or resid 41...BB41 - 13919 - 117
23ALAALAASNASN(chain B and (resid 24 through 39 or resid 41...BB141 - 231119 - 209
24TRPTRPPROPRO(chain B and (resid 24 through 39 or resid 41...BB233 - 265211 - 243
31GLUGLULYSLYS(chain C and (resid 24 through 39 or resid 41...CC24 - 392 - 17
32GLNGLNLEULEU(chain C and (resid 24 through 39 or resid 41...CC41 - 13919 - 117
33ALAALAASNASN(chain C and (resid 24 through 39 or resid 41...CC141 - 231119 - 209
34TRPTRPPROPRO(chain C and (resid 24 through 39 or resid 41...CC233 - 265211 - 243
41GLUGLULYSLYS(chain D and (resid 24 through 39 or resid 41...DD24 - 392 - 17
42GLNGLNLEULEU(chain D and (resid 24 through 39 or resid 41...DD41 - 13919 - 117
43ALAALAASNASN(chain D and (resid 24 through 39 or resid 41...DD141 - 231119 - 209
44TRPTRPPROPRO(chain D and (resid 24 through 39 or resid 41...DD233 - 265211 - 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-IM2 / (5R)-5-[(1S,2R)-1-formyl-2-hydroxypropyl]-3-[(2-{[(E)-iminomethyl]amino}ethyl)sulfanyl]-4,5-dihydro-1H-pyrrole-2-carbox ylic acid / IMIPENEM, open form / N-FORMIMIDOYL-THIENAMYCINE, open form


Mass: 301.362 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C12H19N3O4S / Comment: antibiotic*YM
#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.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 780 / 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: 2.63 Å3/Da / Density % sol: 53.19 %
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: 0.976254 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Oct 1, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.976254 Å / Relative weight: 1
ReflectionResolution: 1.95→43.13 Å / % possible obs: 95.55 % / Redundancy: 4.7 % / Rmerge(I) obs: 0.1019 / Rrim(I) all: 0.11 / Net I/σ(I): 9.13
Reflection shellResolution: 1.95→2.02 Å / % possible obs: 93.89 % / Redundancy: 4.5 % / Rmerge(I) obs: 0.6324 / Num. unique obs: 36743 / Rrim(I) all: 0.71 / Net I/σ(I) obs: 2.24

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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→43.13 Å / Cross valid method: THROUGHOUT
RfactorNum. reflection% reflection
Rfree0.2197 4100 -
Rwork0.1848 --
obs-83386 95.55 %
Refinement stepCycle: final / Resolution: 1.95→43.13 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7932 0 160 780 8872
Biso mean--65.86 43.08 -
Num. residues----968
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0088257
X-RAY DIFFRACTIONf_angle_d0.83511172
X-RAY DIFFRACTIONf_chiral_restr0.0531175
X-RAY DIFFRACTIONf_plane_restr0.0051451
X-RAY DIFFRACTIONf_dihedral_angle_d18.3834863
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A6123X-RAY DIFFRACTION4.693TORSIONAL
12B6123X-RAY DIFFRACTION4.693TORSIONAL
13C6123X-RAY DIFFRACTION4.693TORSIONAL
14D6123X-RAY DIFFRACTION4.693TORSIONAL
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 29

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.95-1.9730.33961290.3062388251785
1.973-1.9970.28241460.26232790293699
1.997-2.02230.26161600.25052786294698
2.0223-2.04890.27021440.25272758290298
2.0489-2.0770.39561390.35132575271491
2.077-2.10660.27781450.23232766291198
2.1066-2.13810.22971490.20742767291699
2.1381-2.17150.22051360.19642825296199
2.1715-2.20710.2161620.18972771293399
2.2071-2.24520.2095870.18951719180690
2.2452-2.2860.23311250.19252286241182
2.286-2.32990.21331320.18032798293099
2.3299-2.37750.17881390.18032791293099
2.3775-2.42920.19541350.17042819295499
2.4292-2.48570.19251560.17332821297799
2.4857-2.54790.24451370.17172815295299
2.5479-2.61670.24131470.17332832297999
2.6167-2.69370.21741400.18932783292397
2.6937-2.78070.23781470.1692807295499
2.7807-2.880.21821340.17932848298299
2.88-2.99530.22381450.18132814295999
2.9953-3.13160.22351520.17432793294598
3.1316-3.29670.16871400.17372830297098
3.2967-3.50320.23471400.17752800294097
3.5032-3.77350.21231450.16872809295497
3.7735-4.15310.18971400.16282792293296
4.1531-4.75350.18891440.15262818296297
4.7535-5.98680.2081510.17172880303197
5.9868-45.99390.21671510.20542947309896
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)
10.4046-0.1545-0.12130.88450.05830.9287-0.00940.0146-0.0088-0.09740.02950.0173-0.00490.0745-00.2145-0.0035-0.00580.2360.00450.20289.073258.77682.4545
20.3606-0.01770.00490.8740.33040.71840.0165-0.0659-0.00870.13140.0164-0.02440.0459-0.00430.00010.1777-0.0106-0.0020.19620.00820.200488.9698219.5929-2.4712
30.5799-0.0398-0.00050.9505-0.3940.92540.00420.04370.0748-0.01430.10520.0452-0.0819-0.205100.2326-0.00670.01940.27580.02580.229684.982221.595731.9716
40.5248-0.05660.05110.6762-0.42331.1149-0.01580.06420.04750.00760.0575-0.0181-0.131-0.063300.24120.00120.01140.19550.01240.2007129.3556226.887331.8353
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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