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- PDB-7pei: Crystal Structure of a Class D carbapenemase_E185A/R186A/R206A -

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Basic information

Entry
Database: PDB / ID: 7pei
TitleCrystal Structure of a Class D carbapenemase_E185A/R186A/R206A
ComponentsBeta-lactamase
KeywordsHYDROLASE / OXA / interface mutant
Function / homology
Function and homology information


penicillin binding / antibiotic catabolic process / cell wall organization / beta-lactamase activity / beta-lactamase / response to antibiotic
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
Biological speciesKlebsiella pneumoniae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 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 10, 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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)60,89611
Polymers60,0482
Non-polymers8499
Water4,630257
1
AAA: Beta-lactamase
hetero molecules


  • defined by author
  • Evidence: gel filtration
  • 30.5 kDa, 1 polymers
Theoretical massNumber of molelcules
Total (without water)30,4966
Polymers30,0241
Non-polymers4725
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
BBB: Beta-lactamase
hetero molecules


  • defined by author
  • 30.4 kDa, 1 polymers
Theoretical massNumber of molelcules
Total (without water)30,4005
Polymers30,0241
Non-polymers3764
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)146.186, 146.186, 54.887
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number171
Space group name H-MP62
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11AAA
21BBB

NCS domain segments:

Component-ID: 1 / Ens-ID: 1 / Beg auth comp-ID: GLU / Beg label comp-ID: GLU / End auth comp-ID: PRO / End label comp-ID: PRO / Auth seq-ID: 24 - 265 / Label seq-ID: 19 - 260

Dom-IDAuth asym-IDLabel asym-ID
1AAAA
2BBBB

NCS ensembles : (Details: Local NCS retraints between domains: 1 2)

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Components

#1: Protein Beta-lactamase


Mass: 30023.863 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Klebsiella pneumoniae (bacteria) / Gene: blaOXA / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0A482LRD5, beta-lactamase
#2: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C3H8O3
#3: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 257 / 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: 2.82 Å3/Da / Density % sol: 56.37 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 6.8 / Details: 0.2M LiSO4, 21% PEG3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U1 / Wavelength: 0.97915 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jun 26, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97915 Å / Relative weight: 1
ReflectionResolution: 1.9→19.69 Å / Num. obs: 52999 / % possible obs: 99.9 % / Redundancy: 20.6 % / CC1/2: 0.999 / Net I/σ(I): 16.1
Reflection shellResolution: 1.9→1.94 Å / Mean I/σ(I) obs: 1 / Num. unique obs: 3549 / CC1/2: 0.726

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Processing

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

4s2p


Resolution: 1.9→19.69 Å / Cor.coef. Fo:Fc: 0.975 / Cor.coef. Fo:Fc free: 0.965 / SU B: 5.396 / SU ML: 0.132 / Cross valid method: FREE R-VALUE / ESU R: 0.123 / ESU R Free: 0.119
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.2112 2657 5.015 %
Rwork0.1773 50321 -
all0.179 --
obs-52978 99.855 %
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: 38.061 Å2
Baniso -1Baniso -2Baniso -3
1--2.323 Å2-1.161 Å2-0 Å2
2---2.323 Å20 Å2
3---7.535 Å2
Refinement stepCycle: LAST / Resolution: 1.9→19.69 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3934 0 49 257 4240
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0134114
X-RAY DIFFRACTIONr_bond_other_d0.0010.0183819
X-RAY DIFFRACTIONr_angle_refined_deg1.5831.6295579
X-RAY DIFFRACTIONr_angle_other_deg1.2991.5848773
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.9545496
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.8823.319229
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.32715702
X-RAY DIFFRACTIONr_dihedral_angle_4_deg22.0211520
X-RAY DIFFRACTIONr_chiral_restr0.0740.2519
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.024699
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021009
X-RAY DIFFRACTIONr_nbd_refined0.2040.2662
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1670.23045
X-RAY DIFFRACTIONr_nbtor_refined0.1590.21904
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0770.21677
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.180.2176
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_other0.0140.21
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.0690.24
X-RAY DIFFRACTIONr_nbd_other0.1530.216
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.1110.26
X-RAY DIFFRACTIONr_mcbond_it2.9123.761948
X-RAY DIFFRACTIONr_mcbond_other2.8973.7591947
X-RAY DIFFRACTIONr_mcangle_it3.9865.6182435
X-RAY DIFFRACTIONr_mcangle_other3.9865.6192436
X-RAY DIFFRACTIONr_scbond_it4.0124.2112166
X-RAY DIFFRACTIONr_scbond_other3.9654.2042147
X-RAY DIFFRACTIONr_scangle_it6.0966.1513137
X-RAY DIFFRACTIONr_scangle_other6.0686.1423108
X-RAY DIFFRACTIONr_lrange_it7.07643.0024506
X-RAY DIFFRACTIONr_lrange_other7.01942.6934454
X-RAY DIFFRACTIONr_ncsr_local_group_10.0690.057782
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDRefine-IDTypeRms dev position (Å)Weight position
11AAAX-RAY DIFFRACTIONLocal ncs0.068770.05009
12BBBX-RAY DIFFRACTIONLocal ncs0.068770.05009
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.9-1.9490.4921980.4363706X-RAY DIFFRACTION99.7955
1.949-2.0030.3662040.3763577X-RAY DIFFRACTION100
2.003-2.0610.2841790.3373511X-RAY DIFFRACTION100
2.061-2.1240.3371620.2963431X-RAY DIFFRACTION100
2.124-2.1940.2691680.2593304X-RAY DIFFRACTION100
2.194-2.2710.2761760.2213191X-RAY DIFFRACTION100
2.271-2.3560.2361590.223082X-RAY DIFFRACTION100
2.356-2.4530.2391850.1862942X-RAY DIFFRACTION100
2.453-2.5620.2391830.1752859X-RAY DIFFRACTION100
2.562-2.6870.231270.182728X-RAY DIFFRACTION100
2.687-2.8320.2151600.1672576X-RAY DIFFRACTION100
2.832-3.0040.2211040.1632506X-RAY DIFFRACTION100
3.004-3.2110.1921350.1722297X-RAY DIFFRACTION100
3.211-3.4680.173900.162191X-RAY DIFFRACTION100
3.468-3.7990.2121070.1561986X-RAY DIFFRACTION100
3.799-4.2460.169800.131847X-RAY DIFFRACTION100
4.246-4.9020.16820.1171589X-RAY DIFFRACTION100
4.902-6.0020.181660.1351373X-RAY DIFFRACTION100
6.002-8.4790.157610.1411058X-RAY DIFFRACTION100

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