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- PDB-7o9n: OXA-48 with carbamylated Lys73 in complex with bicarbonate ions a... -

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Basic information

Entry
Database: PDB / ID: 7o9n
TitleOXA-48 with carbamylated Lys73 in complex with bicarbonate ions at neutral pH
ComponentsBeta-lactamase
KeywordsHYDROLASE / OXA / Bicarbonate
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/transpeptidase-like
Similarity search - Domain/homology
BICARBONATE ION / Beta-lactamase OXA-48
Similarity search - Component
Biological speciesKlebsiella pneumoniae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.97 Å
AuthorsZhou, Q. / He, Y. / Jin, Y.
Funding support China, 1items
OrganizationGrant numberCountry
National Science Foundation (NSF, China)31400663 China
CitationJournal: Acs Cent.Sci. / Year: 2023
Title: An Ion-Pair Induced Intermediate Complex Captured in Class D Carbapenemase Reveals Chloride Ion as a Janus Effector Modulating Activity
Authors: Zhou, Q. / Catalan, P. / Bell, H. / Baumann, P. / Cooke, R. / Evans, R. / Yang, J. / Zhang, Z. / Zappala, D. / Zhang, Y. / Blackburn, G.M. / He, Y. / Jin, Y.
History
DepositionApr 16, 2021Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 4, 2022Provider: repository / Type: Initial release
Revision 1.1Jan 31, 2024Group: Data collection / Derived calculations / Refinement description
Category: atom_type / chem_comp_atom ...atom_type / chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model / struct_ncs_dom_lim
Item: _atom_type.pdbx_N_electrons / _atom_type.pdbx_scat_Z ..._atom_type.pdbx_N_electrons / _atom_type.pdbx_scat_Z / _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
Revision 1.2Mar 6, 2024Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.title / _citation.year
Revision 1.3Aug 6, 2025Group: Structure summary
Category: pdbx_entry_details / pdbx_modification_feature / struct
Item: _pdbx_entry_details.has_protein_modification / _struct.title

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
AAA: Beta-lactamase
BBB: Beta-lactamase
CCC: Beta-lactamase
DDD: Beta-lactamase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)121,3229
Polymers121,0174
Non-polymers3055
Water11,025612
1
AAA: Beta-lactamase
DDD: Beta-lactamase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)60,6915
Polymers60,5082
Non-polymers1833
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
BBB: Beta-lactamase
CCC: Beta-lactamase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)60,6304
Polymers60,5082
Non-polymers1222
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)81.807, 106.404, 124.706
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
11AAA
21BBB
32AAA
42CCC
53AAA
63DDD
74BBB
84CCC
95BBB
105DDD
116CCC
126DDD

NCS domain segments:

End auth comp-ID: ILE / End label comp-ID: ILE

Dom-IDComponent-IDEns-IDBeg auth comp-IDBeg label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
111GLYGLYAAAA22 - 26417 - 259
221GLYGLYBBBB22 - 26417 - 259
312GLYGLYAAAA22 - 26417 - 259
422GLYGLYCCCC22 - 26417 - 259
513LYSLYSAAAA23 - 26418 - 259
623LYSLYSDDDD23 - 26418 - 259
714GLNGLNBBBB21 - 26416 - 259
824GLNGLNCCCC21 - 26416 - 259
915LYSLYSBBBB23 - 26418 - 259
1025LYSLYSDDDD23 - 26418 - 259
1116LYSLYSCCCC23 - 26418 - 259
1226LYSLYSDDDD23 - 26418 - 259

NCS ensembles :
IDDetails
1Local NCS retraints between domains: 1 2
2Local NCS retraints between domains: 3 4
3Local NCS retraints between domains: 5 6
4Local NCS retraints between domains: 7 8
5Local NCS retraints between domains: 9 10
6Local NCS retraints between domains: 11 12

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Components

#1: Protein
Beta-lactamase


Mass: 30254.133 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Klebsiella pneumoniae (bacteria)
Gene: bla OXA-48, bla_2, blaOXA-48, G5637_27540, KPE71T_00045, SAMEA3649466_05396
Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q6XEC0, beta-lactamase
#2: Chemical
ChemComp-BCT / BICARBONATE ION


Mass: 61.017 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: CHO3 / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 612 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationY

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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: 2.24 Å3/Da / Density % sol: 45.15 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 0.1M HEPES pH 7.5, 11.6% PEG8000, 8% 1-BuOH, mixed with the 10 mg/mL protein stock at 1:1 ratio.

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.976254 Å
DetectorType: DECTRIS EIGER2 XE 16M / Detector: PIXEL / Date: Dec 14, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.976254 Å / Relative weight: 1
ReflectionResolution: 1.97→81.81 Å / Num. obs: 77632 / % possible obs: 100 % / Redundancy: 13.2 % / CC1/2: 0.995 / Net I/σ(I): 6
Reflection shellResolution: 1.97→2.01 Å / Mean I/σ(I) obs: 1 / Num. unique obs: 4552 / CC1/2: 0.582

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Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
xia2data reduction
Aimlessdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4S2P

4s2p


Resolution: 1.97→68.496 Å / Cor.coef. Fo:Fc: 0.952 / Cor.coef. Fo:Fc free: 0.887 / SU B: 16.454 / SU ML: 0.191 / Cross valid method: FREE R-VALUE / ESU R Free: 0.197
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.2861 3748 4.834 %
Rwork0.1954 73791 -
all0.2 --
obs-77539 99.981 %
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT
Displacement parametersBiso mean: 25.536 Å2
Baniso -1Baniso -2Baniso -3
1--1.123 Å2-0 Å2-0 Å2
2---0.957 Å20 Å2
3---2.08 Å2
Refinement stepCycle: LAST / Resolution: 1.97→68.496 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8029 0 20 614 8663
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0138270
X-RAY DIFFRACTIONr_bond_other_d0.0040.0187711
X-RAY DIFFRACTIONr_angle_refined_deg1.4661.63311185
X-RAY DIFFRACTIONr_angle_other_deg1.3271.58617690
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.4945982
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.02422.908478
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.572151442
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.0491548
X-RAY DIFFRACTIONr_chiral_restr0.070.21036
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.029502
X-RAY DIFFRACTIONr_gen_planes_other0.0020.022070
X-RAY DIFFRACTIONr_nbd_refined0.2170.21685
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1820.27334
X-RAY DIFFRACTIONr_nbtor_refined0.1660.23975
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0750.23641
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1840.2487
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_other0.0550.26
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.3140.238
X-RAY DIFFRACTIONr_nbd_other0.2490.296
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.1480.220
X-RAY DIFFRACTIONr_mcbond_it4.2152.5133928
X-RAY DIFFRACTIONr_mcbond_other4.2092.5133927
X-RAY DIFFRACTIONr_mcangle_it5.2953.7824907
X-RAY DIFFRACTIONr_mcangle_other5.2943.7834908
X-RAY DIFFRACTIONr_scbond_it4.8032.7864342
X-RAY DIFFRACTIONr_scbond_other4.7982.7854339
X-RAY DIFFRACTIONr_scangle_it5.8064.0796277
X-RAY DIFFRACTIONr_scangle_other5.7934.0786274
X-RAY DIFFRACTIONr_lrange_it6.6729.3179677
X-RAY DIFFRACTIONr_lrange_other6.58229.1719566
X-RAY DIFFRACTIONr_rigid_bond_restr9.944315981
X-RAY DIFFRACTIONr_ncsr_local_group_10.0450.058546
X-RAY DIFFRACTIONr_ncsr_local_group_20.0720.058403
X-RAY DIFFRACTIONr_ncsr_local_group_30.0660.058436
X-RAY DIFFRACTIONr_ncsr_local_group_40.0720.058464
X-RAY DIFFRACTIONr_ncsr_local_group_50.0640.058497
X-RAY DIFFRACTIONr_ncsr_local_group_60.0570.058503
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDRefine-IDTypeRms dev position (Å)Weight position
11AAAX-RAY DIFFRACTIONLocal ncs0.044880.0501
12BBBX-RAY DIFFRACTIONLocal ncs0.044880.0501
23AAAX-RAY DIFFRACTIONLocal ncs0.071710.05009
24CCCX-RAY DIFFRACTIONLocal ncs0.071710.05009
35AAAX-RAY DIFFRACTIONLocal ncs0.065770.05009
36DDDX-RAY DIFFRACTIONLocal ncs0.065770.05009
47BBBX-RAY DIFFRACTIONLocal ncs0.071960.05009
48CCCX-RAY DIFFRACTIONLocal ncs0.071960.05009
59BBBX-RAY DIFFRACTIONLocal ncs0.063840.05009
510DDDX-RAY DIFFRACTIONLocal ncs0.063840.05009
611CCCX-RAY DIFFRACTIONLocal ncs0.057010.05009
612DDDX-RAY DIFFRACTIONLocal ncs0.057010.05009
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.97-2.0210.3562670.3155383X-RAY DIFFRACTION100
2.021-2.0770.3942310.3055296X-RAY DIFFRACTION100
2.077-2.1370.3512600.2655111X-RAY DIFFRACTION99.9814
2.137-2.2020.3182660.2264985X-RAY DIFFRACTION99.9619
2.202-2.2750.3212710.234795X-RAY DIFFRACTION99.9605
2.275-2.3540.3052420.2054643X-RAY DIFFRACTION100
2.354-2.4430.2782260.1894534X-RAY DIFFRACTION100
2.443-2.5430.272140.1924351X-RAY DIFFRACTION100
2.543-2.6560.2782130.1774178X-RAY DIFFRACTION99.9772
2.656-2.7860.272050.1763974X-RAY DIFFRACTION100
2.786-2.9360.291930.1863812X-RAY DIFFRACTION100
2.936-3.1140.2721890.163615X-RAY DIFFRACTION99.9737
3.114-3.3290.2851730.1773406X-RAY DIFFRACTION100
3.329-3.5960.2631760.1823147X-RAY DIFFRACTION100
3.596-3.9390.2781510.1572955X-RAY DIFFRACTION100
3.939-4.4030.2171030.1442681X-RAY DIFFRACTION100
4.403-5.0830.2331400.1512359X-RAY DIFFRACTION100
5.083-6.2230.2181050.1372029X-RAY DIFFRACTION100
6.223-8.7890.297770.1741601X-RAY DIFFRACTION100

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