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- PDB-5o7n: Beta-lactamase VIM-2 in complex with (2R)-1-(2-Benzyl-3-mercaptop... -

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Basic information

Entry
Database: PDB / ID: 5o7n
TitleBeta-lactamase VIM-2 in complex with (2R)-1-(2-Benzyl-3-mercaptopropanoyl)piperidine-2-carboxylic acid
ComponentsBeta-lactamase VIM-2
KeywordsHYDROLASE / Inhibitor / Complex / MBL / Beta-lactamase VIM-2 / (2R)-1-(2-Benzyl-3-mercaptopropanoyl)piperidine-2-carboxylic acid
Function / homology
Function and homology information


antibiotic catabolic process / beta-lactamase / hydrolase activity / metal ion binding
Similarity search - Function
: / : / Metallo-beta-lactamase superfamily / Metallo-beta-lactamase superfamily / Metallo-beta-lactamase / Ribonuclease Z/Hydroxyacylglutathione hydrolase-like
Similarity search - Domain/homology
Chem-9NK / FORMIC ACID / Metallo-beta-lactamase type 2
Similarity search - Component
Biological speciesKlebsiella pneumoniae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / molecular replacement / Resolution: 1.5 Å
AuthorsBuettner, D. / Kramer, J.S. / Pogoryelov, D. / Proschak, E.
CitationJournal: Acs Infect Dis. / Year: 2018
Title: Challenges in the Development of a Thiol-Based Broad-Spectrum Inhibitor for Metallo-beta-Lactamases.
Authors: Buttner, D. / Kramer, J.S. / Klingler, F.M. / Wittmann, S.K. / Hartmann, M.R. / Kurz, C.G. / Kohnhauser, D. / Weizel, L. / Bruggerhoff, A. / Frank, D. / Steinhilber, D. / Wichelhaus, T.A. / ...Authors: Buttner, D. / Kramer, J.S. / Klingler, F.M. / Wittmann, S.K. / Hartmann, M.R. / Kurz, C.G. / Kohnhauser, D. / Weizel, L. / Bruggerhoff, A. / Frank, D. / Steinhilber, D. / Wichelhaus, T.A. / Pogoryelov, D. / Proschak, E.
History
DepositionJun 9, 2017Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 20, 2018Provider: repository / Type: Initial release
Revision 1.1Jul 3, 2019Group: Data collection / Database references / Category: citation / citation_author / pdbx_database_proc
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2May 8, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_conn_angle / struct_conn / struct_conn_type
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr1_symmetry / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr2_symmetry / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.ptnr3_symmetry / _pdbx_struct_conn_angle.value / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.pdbx_ptnr1_label_alt_id / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_symmetry / _struct_conn_type.id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Beta-lactamase VIM-2
B: Beta-lactamase VIM-2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)56,33322
Polymers54,7032
Non-polymers1,63020
Water6,089338
1
A: Beta-lactamase VIM-2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,16711
Polymers27,3511
Non-polymers81510
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Beta-lactamase VIM-2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,16711
Polymers27,3511
Non-polymers81510
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)101.989, 79.308, 67.645
Angle α, β, γ (deg.)90.000, 130.450, 90.000
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-435-

HOH

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein Beta-lactamase VIM-2


Mass: 27351.303 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Klebsiella pneumoniae (bacteria) / Gene: blaVIM-2 / Plasmid: pdest14 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0A173FE28

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Non-polymers , 5 types, 358 molecules

#2: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: Zn
#3: Chemical ChemComp-9NK / (2~{R})-1-[(2~{S})-2-(phenylmethyl)-3-sulfanyl-propanoyl]piperidine-2-carboxylic acid


Mass: 307.408 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C16H21NO3S
#4: Chemical
ChemComp-FMT / FORMIC ACID


Mass: 46.025 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: CH2O2
#5: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Formula: C2H6O2
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 338 / Source method: isolated from a natural source / Formula: H2O

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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: 1.84 Å3/Da / Density % sol: 32.99 %
Crystal growTemperature: 290.15 K / Method: vapor diffusion, hanging drop / pH: 7.2
Details: The VIM-2 in crystallization buffer (50 mM Tris/HCl pH 7.2, 100 uM ZnCl2 and 150 mM NaCl) was concentrated to 11,4 mg/mL, before 5 % Glycerol was added and the protein was flash frozen in ...Details: The VIM-2 in crystallization buffer (50 mM Tris/HCl pH 7.2, 100 uM ZnCl2 and 150 mM NaCl) was concentrated to 11,4 mg/mL, before 5 % Glycerol was added and the protein was flash frozen in liquid nitrogen. For crystallisation the thrawed protein solutions was mixed with precipitation solution (34% PEG3350, 0,25 M Mg formate, 5 mM BME + 2.5% of a 1M DMSO inhibitor stock in the drop) in differant ratios. As reservoir precipitation solution without inhibitor was used.

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: MASSIF-3 / Wavelength: 0.9677 Å
DetectorType: DECTRIS EIGER X 4M / Detector: PIXEL / Date: Sep 22, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9677 Å / Relative weight: 1
ReflectionResolution: 1.5→55.5074 Å / Num. obs: 128072 / % possible obs: 99.13 % / Redundancy: 3.6 % / Biso Wilson estimate: 13.97 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.07561 / Rpim(I) all: 0.04672 / Net I/σ(I): 10.74
Reflection shellResolution: 1.5→1.554 Å / Redundancy: 3.6 % / Rmerge(I) obs: 0.5409 / Mean I/σ(I) obs: 2.17 / Num. unique obs: 12879 / CC1/2: 0.763 / Rpim(I) all: 0.338 / % possible all: 99.62

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
PHENIXrefinement
PDB_EXTRACT3.2data extraction
XDSdata reduction
AutoSolphasing
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: SAD / Resolution: 1.5→55.5074 Å / SU ML: 0.18 / Cross valid method: FREE R-VALUE / Phase error: 21.42
RfactorNum. reflection% reflectionSelection details
Rfree0.2112 3573 2.79 %Random selection
Rwork0.1869 ---
obs0.1874 128064 99.13 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 68.01 Å2 / Biso mean: 18.2 Å2 / Biso min: 0 Å2
Refinement stepCycle: final / Resolution: 1.5→55.5074 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3489 0 82 338 3909
Biso mean--22.37 29.79 -
Num. residues----463
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0073730
X-RAY DIFFRACTIONf_angle_d0.9365094
X-RAY DIFFRACTIONf_chiral_restr0.065574
X-RAY DIFFRACTIONf_plane_restr0.006674
X-RAY DIFFRACTIONf_dihedral_angle_d19.9941304
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
1.5-1.51970.29151460.28364821100
1.5197-1.54060.27421330.27494798100
1.5406-1.56260.28371450.26014796100
1.5626-1.58590.25021260.25384789100
1.5859-1.61070.27721520.24634816100
1.6107-1.63710.27111280.24324819100
1.6371-1.66530.27141340.24364807100
1.6653-1.69560.29271380.23044826100
1.6956-1.72820.2281420.23034850100
1.7282-1.76350.24831460.22374842100
1.7635-1.80190.27711260.21454800100
1.8019-1.84380.22171430.19884797100
1.8438-1.88990.22091470.18074810100
1.8899-1.9410.20251410.18034803100
1.941-1.99810.18071200.17054820100
1.9981-2.06260.18351480.1711476299
2.0626-2.13630.20161310.1716480599
2.1363-2.22190.22131280.1788478099
2.2219-2.3230.2351350.1862477198
2.323-2.44540.2314122449294
2.4454-2.59870.1753125461894
2.5987-2.79930.18741424795100
2.7993-3.0810.241464832100
3.081-3.52670.18111520.16594801100
3.5267-4.4430.18731400.15134819100
4.443-51.480.17871370.1752482299

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