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- PDB-7cjl: Metallo-Beta-Lactamase VIM-2 in complex with (S)-N-(3-(2H-tetrazo... -

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Basic information

Entry
Database: PDB / ID: 7cjl
TitleMetallo-Beta-Lactamase VIM-2 in complex with (S)-N-(3-(2H-tetrazol-5-yl)phenyl)-3-mercapto-2-methylpropanamide
ComponentsBeta-lactamase class B VIM-2
KeywordsHYDROLASE / Metallo-beta-lactamase VIM-2 / VIM-2
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
FORMIC ACID / Chem-G0O / Metallo-beta-lactamase type 2
Similarity search - Component
Biological speciesPseudomonas aeruginosa (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.789 Å
AuthorsYan, Y.-H. / Chen, J. / Zhan, Z. / Yu, Z.-J. / Li, G. / Li, G.-B. / Guo, L. / Wu, Y.
Funding support China, 2items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)81874291 China
National Natural Science Foundation of China (NSFC)81502989 China
CitationJournal: Rsc Adv / Year: 2020
Title: Discovery of mercaptopropanamide-substituted aryl tetrazoles as new broad-spectrum metallo-beta-lactamase inhibitors.
Authors: Yan, Y.H. / Chen, J. / Zhan, Z. / Yu, Z.J. / Li, G. / Guo, L. / Li, G.B. / Wu, Y. / Zheng, Y.
History
DepositionJul 11, 2020Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jul 14, 2021Provider: repository / Type: Initial release
Revision 1.1Aug 3, 2022Group: Database references / Category: citation / citation_author / database_2
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 / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.2Nov 29, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)50,1939
Polymers49,3592
Non-polymers8347
Water4,504250
1
B: Beta-lactamase class B VIM-2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,1205
Polymers24,6791
Non-polymers4404
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area160 Å2
ΔGint-0 kcal/mol
Surface area9300 Å2
MethodPISA
2
A: Beta-lactamase class B VIM-2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,0744
Polymers24,6791
Non-polymers3943
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area9480 Å2
MethodPISA
Unit cell
Length a, b, c (Å)45.356, 90.132, 125.849
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Beta-lactamase class B VIM-2 / BlaVIM-2 / Metallo beta lactamase VIM-2 / Metallo beta-lactamase / Metallo-beta lactamase protein / ...BlaVIM-2 / Metallo beta lactamase VIM-2 / Metallo beta-lactamase / Metallo-beta lactamase protein / Metallo-beta-lactamase VIM-2 / VIM-2 class B beta-lactamase / VIM-2 class B metallo b-lactamase / VIM-2 metallo beta-lactamase / VIM-2 type metallo-beta-lactamase


Mass: 24679.439 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas aeruginosa (bacteria)
Gene: blaVIM-2, bla vim-2, bla-VIM-2, blasVIM-2, blaVIM2, blm, VIM-2, vim-2, PAERUG_P32_London_17_VIM_2_10_11_06255
Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q9K2N0
#2: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Zn
#3: Chemical ChemComp-FMT / FORMIC ACID


Mass: 46.025 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: CH2O2
#4: Chemical ChemComp-G0O / (S)-N-(3-(2H-tetrazol-5-yl)phenyl)-3-mercapto-2-methylpropanamide


Mass: 263.319 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C11H13N5OS / Feature type: SUBJECT OF INVESTIGATION
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 250 / 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: 2.61 Å3/Da / Density % sol: 52.8 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / Details: 28%-32% PEG3350, 0.1M Mg(COOH)2

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Data collection

DiffractionMean temperature: 195 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.97918 Å
DetectorType: DECTRIS PILATUS3 X CdTe 1M / Detector: PIXEL / Date: Jul 3, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97918 Å / Relative weight: 1
ReflectionResolution: 1.78→50 Å / Num. obs: 50198 / % possible obs: 99.9 % / Redundancy: 10.6 % / Biso Wilson estimate: 20.14 Å2 / Rmerge(I) obs: 0.158 / Rpim(I) all: 0.048 / Rrim(I) all: 0.165 / Χ2: 0.904 / Net I/σ(I): 6.1 / Num. measured all: 533790
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
1.78-1.845.51.77948990.3320.7921.960.63599.2
1.84-1.928.21.63549440.5290.5941.7430.695100
1.92-29.91.26249470.7820.4161.3310.75899.9
2-2.1110.40.8749630.8770.280.9160.875100
2.11-2.2411.90.65949980.9320.1970.6891.08100
2.24-2.4211.90.45149830.9540.1350.4711.08100
2.42-2.6611.70.29450070.970.0880.3081.044100
2.66-3.0412.50.20450460.9810.0590.2130.965100
3.04-3.8312.20.13450700.9930.0390.1390.736100
3.83-5011.80.09553410.9920.0290.10.90999.9

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Phasing

PhasingMethod: molecular replacement
Phasing MR
Highest resolutionLowest resolution
Rotation5.31 Å45.07 Å
Translation5.31 Å45.07 Å

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Processing

Software
NameVersionClassification
HKL-3000data reduction
HKL-3000data scaling
PHASER2.6.0phasing
PHENIX1.10.1_2155refinement
PDB_EXTRACT3.24data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6JN6

6jn6


Resolution: 1.789→45.066 Å / SU ML: 0.22 / Cross valid method: THROUGHOUT / σ(F): 1.36 / Phase error: 28.66 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2464 1999 4.71 %
Rwork0.2053 40399 -
obs0.2073 42398 85.48 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 89.89 Å2 / Biso mean: 29.3913 Å2 / Biso min: 7.27 Å2
Refinement stepCycle: final / Resolution: 1.789→45.066 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3456 0 43 250 3749
Biso mean--40.3 32.19 -
Num. residues----462
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0193596
X-RAY DIFFRACTIONf_angle_d1.134897
X-RAY DIFFRACTIONf_chiral_restr0.062562
X-RAY DIFFRACTIONf_plane_restr0.008642
X-RAY DIFFRACTIONf_dihedral_angle_d13.0182078
LS refinement shell

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

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
1.7893-1.83410.3066100.40581876
1.8341-1.88370.3883530.3506109733
1.8837-1.93910.33651160.2925233770
1.9391-2.00170.3051520.2678306792
2.0017-2.07320.27651610.2535323797
2.0732-2.15620.28641650.2434334199
2.1562-2.25440.29621630.23263309100
2.2544-2.37320.30091660.2223354100
2.3732-2.52190.25831670.21323365100
2.5219-2.71660.24521650.20673341100
2.7166-2.98990.25371670.20273378100
2.9899-3.42250.23351660.18713373100
3.4225-4.31140.19881720.16163453100
4.3114-45.0660.21161760.1838356099

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