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- PDB-7psf: Crystal Structure of a Class D Carbapenemase Complexed with Imipenem -

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Basic information

Entry
Database: PDB / ID: 7psf
TitleCrystal Structure of a Class D Carbapenemase Complexed with Imipenem
ComponentsBeta-lactamase
KeywordsHYDROLASE / OXA / Imipenem
Function / homology
Function and homology information


penicillin binding / antibiotic catabolic process / cell wall organization / beta-lactamase / beta-lactamase activity / 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
1-BUTANOL / BROMIDE ION / Imipenem / Beta-lactamase OXA-48
Similarity search - Component
Biological speciesKlebsiella pneumoniae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 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
DepositionSep 23, 2021Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 5, 2022Provider: repository / Type: Initial release
Revision 1.1Jan 31, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model / 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
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

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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)122,08712
Polymers121,0174
Non-polymers1,0718
Water4,161231
1
AAA: Beta-lactamase
DDD: Beta-lactamase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)60,9695
Polymers60,5082
Non-polymers4613
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
BBB: Beta-lactamase
CCC: Beta-lactamase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)61,1187
Polymers60,5082
Non-polymers6095
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)83.420, 107.600, 124.590
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:
Dom-IDComponent-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
111GLUGLUILEILEAAAA24 - 26419 - 259
221GLUGLUILEILEBBBB24 - 26419 - 259
332LYSLYSILEILEAAAA23 - 26418 - 259
442LYSLYSILEILECCCC23 - 26418 - 259
553GLYGLYPROPROAAAA22 - 26517 - 260
663GLYGLYPROPRODDDD22 - 26517 - 260
774GLUGLUILEILEBBBB24 - 26419 - 259
884GLUGLUILEILECCCC24 - 26419 - 259
995GLUGLUILEILEBBBB24 - 26419 - 259
10105GLUGLUILEILEDDDD24 - 26419 - 259
11116LYSLYSILEILECCCC23 - 26418 - 259
12126LYSLYSILEILEDDDD23 - 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-ID1 / Imipenem


Mass: 301.362 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C12H19N3O4S / Comment: antibiotic*YM
#3: Chemical
ChemComp-BR / BROMIDE ION


Mass: 79.904 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Br
#4: Chemical ChemComp-1BO / 1-BUTANOL / BUTAN-1-OL


Mass: 74.122 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C4H10O
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 231 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 2.31 Å3/Da / Density % sol: 46.76 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: HEPES pH 7.5 no Cl-, 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: I04 / Wavelength: 0.91838 Å
DetectorType: DECTRIS EIGER2 X 16M / Detector: PIXEL / Date: Dec 14, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.91838 Å / Relative weight: 1
ReflectionResolution: 2.1→49.39 Å / Num. obs: 66086 / % possible obs: 99.9 % / Redundancy: 13.6 % / CC1/2: 0.998 / Net I/σ(I): 8.2
Reflection shellResolution: 2.1→2.15 Å / Mean I/σ(I) obs: 1 / Num. unique obs: 4413 / CC1/2: 0.695

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Processing

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

4s2p


Resolution: 2.1→49.39 Å / Cor.coef. Fo:Fc: 0.949 / Cor.coef. Fo:Fc free: 0.934 / SU B: 10.753 / SU ML: 0.242 / Cross valid method: FREE R-VALUE / ESU R: 0.272 / ESU R Free: 0.216
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.2778 3258 4.935 %
Rwork0.2408 62754 -
all0.243 --
obs-66012 99.853 %
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: 36.852 Å2
Baniso -1Baniso -2Baniso -3
1-4.549 Å20 Å20 Å2
2---0.138 Å20 Å2
3----4.41 Å2
Refinement stepCycle: LAST / Resolution: 2.1→49.39 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7967 0 54 231 8252
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0138229
X-RAY DIFFRACTIONr_bond_other_d0.0010.0187687
X-RAY DIFFRACTIONr_angle_refined_deg1.5231.63611132
X-RAY DIFFRACTIONr_angle_other_deg1.2791.58617640
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.6245973
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.8922.729480
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.607151427
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.6661548
X-RAY DIFFRACTIONr_chiral_restr0.070.21037
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.029413
X-RAY DIFFRACTIONr_gen_planes_other0.0010.022047
X-RAY DIFFRACTIONr_nbd_refined0.2170.21751
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1750.27378
X-RAY DIFFRACTIONr_nbtor_refined0.1660.23983
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0770.23985
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1630.2298
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.2690.214
X-RAY DIFFRACTIONr_nbd_other0.2530.270
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.2190.216
X-RAY DIFFRACTIONr_mcbond_it3.0173.7513892
X-RAY DIFFRACTIONr_mcbond_other3.0163.7513891
X-RAY DIFFRACTIONr_mcangle_it4.3065.6224859
X-RAY DIFFRACTIONr_mcangle_other4.3065.6224860
X-RAY DIFFRACTIONr_scbond_it3.3754.0474337
X-RAY DIFFRACTIONr_scbond_other3.3754.0474337
X-RAY DIFFRACTIONr_scangle_it5.0075.9516271
X-RAY DIFFRACTIONr_scangle_other5.0075.9516271
X-RAY DIFFRACTIONr_lrange_it6.4442.8139504
X-RAY DIFFRACTIONr_lrange_other6.43342.8129471
X-RAY DIFFRACTIONr_ncsr_local_group_10.0410.058510
X-RAY DIFFRACTIONr_ncsr_local_group_20.0540.058486
X-RAY DIFFRACTIONr_ncsr_local_group_30.0530.058469
X-RAY DIFFRACTIONr_ncsr_local_group_40.0530.058463
X-RAY DIFFRACTIONr_ncsr_local_group_50.0520.058410
X-RAY DIFFRACTIONr_ncsr_local_group_60.0510.058463
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDRefine-IDTypeRms dev position (Å)Weight position
11AAAX-RAY DIFFRACTIONLocal ncs0.04050.0501
12BBBX-RAY DIFFRACTIONLocal ncs0.04050.0501
23AAAX-RAY DIFFRACTIONLocal ncs0.053570.05009
24CCCX-RAY DIFFRACTIONLocal ncs0.053570.05009
35AAAX-RAY DIFFRACTIONLocal ncs0.052610.05009
36DDDX-RAY DIFFRACTIONLocal ncs0.052610.05009
47BBBX-RAY DIFFRACTIONLocal ncs0.052940.05009
48CCCX-RAY DIFFRACTIONLocal ncs0.052940.05009
59BBBX-RAY DIFFRACTIONLocal ncs0.051870.05009
510DDDX-RAY DIFFRACTIONLocal ncs0.051870.05009
611CCCX-RAY DIFFRACTIONLocal ncs0.051220.05009
612DDDX-RAY DIFFRACTIONLocal ncs0.051220.05009
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.1-2.1550.4142540.4444569X-RAY DIFFRACTION99.9378
2.155-2.2140.3962420.4184434X-RAY DIFFRACTION99.7228
2.214-2.2780.3762360.3744358X-RAY DIFFRACTION99.8479
2.278-2.3480.3452040.3474241X-RAY DIFFRACTION99.9101
2.348-2.4250.3822210.3384073X-RAY DIFFRACTION99.8837
2.425-2.510.3382070.3113973X-RAY DIFFRACTION99.8328
2.51-2.6050.3272070.2823841X-RAY DIFFRACTION99.8766
2.605-2.7110.2962050.2583675X-RAY DIFFRACTION99.897
2.711-2.8310.3391770.2353582X-RAY DIFFRACTION99.9734
2.831-2.9690.2971590.2363409X-RAY DIFFRACTION99.8321
2.969-3.130.2461380.2083264X-RAY DIFFRACTION99.9706
3.13-3.320.2771460.223079X-RAY DIFFRACTION99.8143
3.32-3.5490.2591550.2072876X-RAY DIFFRACTION99.5402
3.549-3.8330.2421300.1822731X-RAY DIFFRACTION99.9301
3.833-4.1980.2111200.1712499X-RAY DIFFRACTION99.9237
4.198-4.6930.2181270.1632272X-RAY DIFFRACTION99.9167
4.693-5.4180.1961210.1671995X-RAY DIFFRACTION100
5.418-6.6320.218920.171723X-RAY DIFFRACTION100
6.632-9.3660.209710.1791375X-RAY DIFFRACTION100

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