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- PDB-7pep: Crystal Structure of a Class D Carbapenemase Complexed with Hydro... -

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Basic information

Entry
Database: PDB / ID: 7pep
TitleCrystal Structure of a Class D Carbapenemase Complexed with Hydrolyzed Imipenem
ComponentsBeta-lactamase
KeywordsHYDROLASE / OXA / Imipenem
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 / Chem-HIW / Beta-lactamase
Similarity search - Component
Biological speciesKlebsiella pneumoniae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.7 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 11, 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)122,91416
Polymers121,0174
Non-polymers1,89712
Water15,817878
1
AAA: Beta-lactamase
DDD: Beta-lactamase
hetero molecules


  • defined by author
  • Evidence: gel filtration
  • 61.3 kDa, 2 polymers
Theoretical massNumber of molelcules
Total (without water)61,3036
Polymers60,5082
Non-polymers7954
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
BBB: Beta-lactamase
CCC: Beta-lactamase
hetero molecules


  • defined by author
  • 61.6 kDa, 2 polymers
Theoretical massNumber of molelcules
Total (without water)61,61110
Polymers60,5082
Non-polymers1,1038
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)83.946, 107.930, 124.420
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
111GLYGLYPROPROAAAA22 - 26517 - 260
211GLYGLYPROPROBBBB22 - 26517 - 260
322LYSLYSILEILEAAAA23 - 26418 - 259
422LYSLYSILEILECCCC23 - 26418 - 259
533GLYGLYILEILEAAAA22 - 26417 - 259
633GLYGLYILEILEDDDD22 - 26417 - 259
744LYSLYSILEILEBBBB23 - 26418 - 259
844LYSLYSILEILECCCC23 - 26418 - 259
955GLYGLYILEILEBBBB22 - 26417 - 259
1055GLYGLYILEILEDDDD22 - 26417 - 259
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: 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-HIW / (2R,4S)-2-[(1S,2R)-1-carboxy-2-hydroxypropyl]-4-[(2-{[(Z)-iminomethyl]amino}ethyl)sulfanyl]-3,4-dihydro-2H-pyrrole-5-ca rboxylic acid / Hydrolyzed Imipenem


Mass: 317.361 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C12H19N3O5S / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical
ChemComp-BR / BROMIDE ION


Mass: 79.904 Da / Num. of mol.: 6 / 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.: 878 / 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: 2.33 Å3/Da / Density % sol: 47.18 %
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: 0.918381 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: 0.918381 Å / Relative weight: 1
ReflectionResolution: 1.7→69.685 Å / Num. obs: 124585 / % possible obs: 100 % / Redundancy: 13.3 % / CC1/2: 0.999 / Net I/σ(I): 9.8
Reflection shellResolution: 1.7→1.73 Å / Mean I/σ(I) obs: 1 / Num. unique obs: 6116 / CC1/2: 0.706

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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: 1.7→69.685 Å / Cor.coef. Fo:Fc: 0.966 / Cor.coef. Fo:Fc free: 0.95 / WRfactor Rfree: 0.199 / WRfactor Rwork: 0.168 / SU B: 3.924 / SU ML: 0.112 / Average fsc free: 0.7896 / Average fsc work: 0.801 / Cross valid method: FREE R-VALUE / ESU R: 0.115 / ESU R Free: 0.111
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.2306 6286 5.049 %
Rwork0.1986 118202 -
all0.2 --
obs-124488 99.937 %
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: 23.851 Å2
Baniso -1Baniso -2Baniso -3
1-3.209 Å20 Å20 Å2
2---0.405 Å20 Å2
3----2.804 Å2
Refinement stepCycle: LAST / Resolution: 1.7→69.685 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7989 0 100 878 8967
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0138450
X-RAY DIFFRACTIONr_bond_other_d0.0010.0187903
X-RAY DIFFRACTIONr_angle_refined_deg1.5181.65711441
X-RAY DIFFRACTIONr_angle_other_deg1.3691.60718156
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.01851004
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.6422.686484
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.152151465
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.9091552
X-RAY DIFFRACTIONr_chiral_restr0.0740.21073
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.029667
X-RAY DIFFRACTIONr_gen_planes_other0.0010.022122
X-RAY DIFFRACTIONr_nbd_refined0.2210.21709
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1720.27370
X-RAY DIFFRACTIONr_nbtor_refined0.1670.24018
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0770.23755
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1640.2711
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.1810.211
X-RAY DIFFRACTIONr_nbd_other0.2030.263
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.1690.235
X-RAY DIFFRACTIONr_mcbond_it1.7522.2783935
X-RAY DIFFRACTIONr_mcbond_other1.752.2773934
X-RAY DIFFRACTIONr_mcangle_it2.5473.4064921
X-RAY DIFFRACTIONr_mcangle_other2.5473.4064922
X-RAY DIFFRACTIONr_scbond_it2.4772.5984515
X-RAY DIFFRACTIONr_scbond_other2.4772.5994516
X-RAY DIFFRACTIONr_scangle_it3.8313.7856505
X-RAY DIFFRACTIONr_scangle_other3.8313.7856506
X-RAY DIFFRACTIONr_lrange_it5.25127.21110003
X-RAY DIFFRACTIONr_lrange_other5.11526.7419765
X-RAY DIFFRACTIONr_ncsr_local_group_10.0590.058634
X-RAY DIFFRACTIONr_ncsr_local_group_20.0630.058516
X-RAY DIFFRACTIONr_ncsr_local_group_30.0680.058528
X-RAY DIFFRACTIONr_ncsr_local_group_40.0650.058486
X-RAY DIFFRACTIONr_ncsr_local_group_50.0680.058494
X-RAY DIFFRACTIONr_ncsr_local_group_60.060.058571
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDRefine-IDTypeRms dev position (Å)Weight position
11AAAX-RAY DIFFRACTIONLocal ncs0.059420.0501
12BBBX-RAY DIFFRACTIONLocal ncs0.059420.0501
23AAAX-RAY DIFFRACTIONLocal ncs0.062720.05009
24CCCX-RAY DIFFRACTIONLocal ncs0.062720.05009
35AAAX-RAY DIFFRACTIONLocal ncs0.067610.05009
36DDDX-RAY DIFFRACTIONLocal ncs0.067610.05009
47BBBX-RAY DIFFRACTIONLocal ncs0.064930.05009
48CCCX-RAY DIFFRACTIONLocal ncs0.064930.05009
59BBBX-RAY DIFFRACTIONLocal ncs0.067950.05009
510DDDX-RAY DIFFRACTIONLocal ncs0.067950.05009
611CCCX-RAY DIFFRACTIONLocal ncs0.060440.05009
612DDDX-RAY DIFFRACTIONLocal ncs0.060440.05009
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.7-1.7440.3994770.4028639X-RAY DIFFRACTION99.7483
1.744-1.7920.3614530.3678376X-RAY DIFFRACTION99.7853
1.792-1.8440.324370.348205X-RAY DIFFRACTION99.8729
1.844-1.9010.3234320.3027994X-RAY DIFFRACTION99.8933
1.901-1.9630.2923980.2787731X-RAY DIFFRACTION99.9262
1.963-2.0320.2514060.2277494X-RAY DIFFRACTION99.9747
2.032-2.1080.2643800.2197224X-RAY DIFFRACTION99.9869
2.108-2.1950.2213830.1866972X-RAY DIFFRACTION100
2.195-2.2920.2353860.1856659X-RAY DIFFRACTION100
2.292-2.4040.2093390.1716439X-RAY DIFFRACTION99.9852
2.404-2.5340.1943420.1586086X-RAY DIFFRACTION100
2.534-2.6880.2213000.1575770X-RAY DIFFRACTION100
2.688-2.8730.2012930.1585436X-RAY DIFFRACTION100
2.873-3.1030.2042440.1725131X-RAY DIFFRACTION100
3.103-3.3990.2142360.1764702X-RAY DIFFRACTION100
3.399-3.80.2162170.1734283X-RAY DIFFRACTION100
3.8-4.3870.1672040.1523776X-RAY DIFFRACTION100
4.387-5.3710.1741580.1413251X-RAY DIFFRACTION100
5.371-7.5890.1761310.1522552X-RAY DIFFRACTION100

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