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- PDB-7pgo: Crystal Structure of a Class D Carbapenemase_R250A -

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Basic information

Entry
Database: PDB / ID: 7pgo
TitleCrystal Structure of a Class D Carbapenemase_R250A
ComponentsBeta-lactamase
KeywordsHYDROLASE / OXA
Function / homology
Function and homology information


penicillin binding / antibiotic catabolic process / cell wall organization / 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/transpeptidase-like
Similarity search - Domain/homology
1-BUTANOL / BROMIDE ION / Beta-lactamase
Similarity search - Component
Biological speciesKlebsiella pneumoniae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.85 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
DepositionAug 15, 2021Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 24, 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)121,36813
Polymers120,6724
Non-polymers6969
Water16,232901
1
AAA: Beta-lactamase
DDD: Beta-lactamase
hetero molecules


  • defined by author
  • Evidence: gel filtration
  • 60.7 kDa, 2 polymers
Theoretical massNumber of molelcules
Total (without water)60,7187
Polymers60,3362
Non-polymers3825
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
BBB: Beta-lactamase
CCC: Beta-lactamase
hetero molecules


  • defined by author
  • 60.6 kDa, 2 polymers
Theoretical massNumber of molelcules
Total (without water)60,6506
Polymers60,3362
Non-polymers3144
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)84.546, 108.200, 124.610
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:

Refine code: 1

Dom-IDComponent-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
111GLYGLYPROPROAAAA22 - 26517 - 260
211GLYGLYPROPROBBBB22 - 26517 - 260
322LYSLYSILEILEAAAA23 - 26418 - 259
422LYSLYSILEILECCCC23 - 26418 - 259
533GLYGLYPROPROAAAA22 - 26517 - 260
633GLYGLYPROPRODDDD22 - 26517 - 260
744LYSLYSILEILEBBBB23 - 26418 - 259
844LYSLYSILEILECCCC23 - 26418 - 259
955GLYGLYPROPROBBBB22 - 26517 - 260
1055GLYGLYPROPRODDDD22 - 26517 - 260
1166LYSLYSILEILECCCC23 - 26418 - 259
1266LYSLYSILEILEDDDD23 - 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: 30168.016 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, bla_4, blaOXA-48, G5637_27540, KPE71T_00045, SAMEA3649466_05396, SAMEA3649630_05289, SAMEA3649650_05830
Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q6XEC0, beta-lactamase
#2: Chemical
ChemComp-1BO / 1-BUTANOL / BUTAN-1-OL


Mass: 74.122 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C4H10O
#3: Chemical
ChemComp-BR / BROMIDE ION


Mass: 79.904 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: Br
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 901 / 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: 2.36 Å3/Da / Density % sol: 47.92 %
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: 0.918395 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: May 21, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.918395 Å / Relative weight: 1
ReflectionResolution: 1.85→58.75 Å / Num. obs: 98044 / % possible obs: 100 % / Redundancy: 23.2 % / CC1/2: 0.996 / Net I/σ(I): 6.6
Reflection shellResolution: 1.85→1.88 Å / Mean I/σ(I) obs: 1.1 / Num. unique obs: 4809 / CC1/2: 0.737

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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: 1.85→58.75 Å / Cor.coef. Fo:Fc: 0.96 / Cor.coef. Fo:Fc free: 0.946 / SU B: 4.159 / SU ML: 0.114 / Cross valid method: FREE R-VALUE / ESU R: 0.153 / ESU R Free: 0.137
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.234 5022 5.127 %
Rwork0.2052 92933 -
all0.207 --
obs-97955 99.914 %
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: 20.915 Å2
Baniso -1Baniso -2Baniso -3
1-2.548 Å20 Å20 Å2
2---0.76 Å20 Å2
3----1.788 Å2
Refinement stepCycle: LAST / Resolution: 1.85→58.75 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7956 0 25 901 8882
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0138252
X-RAY DIFFRACTIONr_bond_other_d0.0010.0187743
X-RAY DIFFRACTIONr_angle_refined_deg1.4351.63311173
X-RAY DIFFRACTIONr_angle_other_deg1.3661.58617788
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.0275998
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.62223.07469
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.713151444
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.9091545
X-RAY DIFFRACTIONr_chiral_restr0.0730.21042
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.029472
X-RAY DIFFRACTIONr_gen_planes_other0.0010.022046
X-RAY DIFFRACTIONr_nbd_refined0.2180.21658
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1710.27274
X-RAY DIFFRACTIONr_nbtor_refined0.1680.23985
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0760.23815
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1660.2680
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.2670.215
X-RAY DIFFRACTIONr_nbd_other0.220.270
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.1510.244
X-RAY DIFFRACTIONr_mcbond_it1.8242.0353926
X-RAY DIFFRACTIONr_mcbond_other1.8242.0343925
X-RAY DIFFRACTIONr_mcangle_it2.9433.0424907
X-RAY DIFFRACTIONr_mcangle_other2.9433.0434908
X-RAY DIFFRACTIONr_scbond_it2.1492.2514326
X-RAY DIFFRACTIONr_scbond_other2.1492.2524327
X-RAY DIFFRACTIONr_scangle_it3.4533.2766253
X-RAY DIFFRACTIONr_scangle_other3.4523.2766254
X-RAY DIFFRACTIONr_lrange_it5.39523.7549850
X-RAY DIFFRACTIONr_lrange_other5.31323.3989621
X-RAY DIFFRACTIONr_ncsr_local_group_10.0510.058612
X-RAY DIFFRACTIONr_ncsr_local_group_20.070.058397
X-RAY DIFFRACTIONr_ncsr_local_group_30.0710.058424
X-RAY DIFFRACTIONr_ncsr_local_group_40.070.058421
X-RAY DIFFRACTIONr_ncsr_local_group_50.0740.058436
X-RAY DIFFRACTIONr_ncsr_local_group_60.0570.058445
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDRefine-IDTypeRms dev position (Å)Weight position
11AAAX-RAY DIFFRACTIONLocal ncs0.050820.0501
12BBBX-RAY DIFFRACTIONLocal ncs0.050820.0501
23AAAX-RAY DIFFRACTIONLocal ncs0.070040.05009
24CCCX-RAY DIFFRACTIONLocal ncs0.070040.05009
35AAAX-RAY DIFFRACTIONLocal ncs0.070820.05009
36DDDX-RAY DIFFRACTIONLocal ncs0.070820.05009
47BBBX-RAY DIFFRACTIONLocal ncs0.06980.05009
48CCCX-RAY DIFFRACTIONLocal ncs0.06980.05009
59BBBX-RAY DIFFRACTIONLocal ncs0.073690.05009
510DDDX-RAY DIFFRACTIONLocal ncs0.073690.05009
611CCCX-RAY DIFFRACTIONLocal ncs0.056520.05009
612DDDX-RAY DIFFRACTIONLocal ncs0.056520.05009
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.85-1.8980.3463710.3546769X-RAY DIFFRACTION99.665
1.898-1.950.3553730.3686626X-RAY DIFFRACTION99.7719
1.95-2.0070.3153540.3026429X-RAY DIFFRACTION99.8822
2.007-2.0680.2733070.2646280X-RAY DIFFRACTION99.8333
2.068-2.1360.2573160.2376084X-RAY DIFFRACTION99.8596
2.136-2.2110.252980.2265931X-RAY DIFFRACTION99.9358
2.211-2.2950.2873270.2535662X-RAY DIFFRACTION99.9666
2.295-2.3880.2253010.2065459X-RAY DIFFRACTION99.9826
2.388-2.4940.223020.1865255X-RAY DIFFRACTION100
2.494-2.6160.2152520.1775052X-RAY DIFFRACTION100
2.616-2.7570.2312760.1694782X-RAY DIFFRACTION100
2.757-2.9250.2042570.1714554X-RAY DIFFRACTION100
2.925-3.1260.2152290.1714287X-RAY DIFFRACTION100
3.126-3.3770.2152030.1784023X-RAY DIFFRACTION100
3.377-3.6990.2251750.1793707X-RAY DIFFRACTION100
3.699-4.1350.1912020.1573333X-RAY DIFFRACTION100
4.135-4.7740.1691530.1382991X-RAY DIFFRACTION100
4.774-5.8440.1821510.1492526X-RAY DIFFRACTION99.9627
5.844-8.2560.2031010.1572018X-RAY DIFFRACTION100

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