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- PDB-5y6e: VIM-2 metallo-beta-lactamase in complex with (R)-2-(4-hydroxyphen... -

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Basic information

Entry
Database: PDB / ID: 5y6e
TitleVIM-2 metallo-beta-lactamase in complex with (R)-2-(4-hydroxyphenyl)-2-((S)-3-mercapto-2-methylpropanamido)acetic acid (compound 12)
ComponentsBeta-lactamase class B VIM-2
KeywordsHYDROLASE / Metallo-beta-lactamase VIM-2
Function / homology
Function and homology information


antibiotic catabolic process / beta-lactamase / periplasmic space / hydrolase activity / response to antibiotic / metal ion binding
Similarity search - Function
: / : / Metallo-beta-lactamase superfamily / Ribonuclease Z/Hydroxyacylglutathione hydrolase-like / Metallo-beta-lactamase superfamily / Metallo-beta-lactamase; Chain A / Metallo-beta-lactamase / Ribonuclease Z/Hydroxyacylglutathione hydrolase-like / 4-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Chem-8PO / FORMIC ACID / beta-lactamase
Similarity search - Component
Biological speciesPseudomonas aeruginosa (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.8 Å
AuthorsLi, G.-B.
Funding support China, 1items
OrganizationGrant numberCountry
NSFC81502989 China
CitationJournal: Eur J Med Chem / Year: 2018
Title: ((S)-3-Mercapto-2-methylpropanamido)acetic acid derivatives as metallo-beta-lactamase inhibitors: Synthesis, kinetic and crystallographic studies.
Authors: Liu, S. / Jing, L. / Yu, Z.-J. / Wu, C. / Zheng, Y. / Zhang, E. / Chen, Q. / Yu, Y. / Guo, L. / Wu, Y. / Li, G.-B.
History
DepositionAug 11, 2017Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jan 24, 2018Provider: repository / Type: Initial release
Revision 1.1Feb 7, 2018Group: Database references / Category: citation
Item: _citation.journal_abbrev / _citation.journal_id_ISSN ..._citation.journal_abbrev / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2Nov 22, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn
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_asym_id / _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.ptnr2_auth_asym_id / _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_asym_id / _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.value / _struct_conn.pdbx_dist_value / _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.ptnr1_symmetry / _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_label_seq_id / _struct_conn.ptnr2_symmetry

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)50,47414
Polymers49,3592
Non-polymers1,11512
Water8,539474
1
A: Beta-lactamase class B VIM-2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,2377
Polymers24,6791
Non-polymers5586
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area350 Å2
ΔGint-27 kcal/mol
Surface area9310 Å2
MethodPISA
2
B: Beta-lactamase class B VIM-2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,2377
Polymers24,6791
Non-polymers5586
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area350 Å2
ΔGint-27 kcal/mol
Surface area9300 Å2
MethodPISA
Unit cell
Length a, b, c (Å)101.355, 74.452, 64.456
Angle α, β, γ (deg.)90.000, 129.460, 90.000
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-234-

GLN

21B-234-

GLN

31A-411-

HOH

41A-544-

HOH

51B-416-

HOH

61B-542-

HOH

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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 / Fragment: UNP residues 32-262
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
Plasmid: opinf vector based / Details (production host): plasmid derived / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / Variant (production host): PLYSS / References: UniProt: Q9K2N0
#2: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Zn
#3: Chemical ChemComp-8PO / (2R)-2-(4-hydroxyphenyl)-2-[[(2S)-2-methyl-3-sulfanyl-propanoyl]amino]ethanoic acid / (R)-2-(4-hydroxyphenyl)-2-((S)-3-mercapto-2-methylpropanamido)acetic acid


Mass: 269.317 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C12H15NO4S
#4: Chemical
ChemComp-FMT / FORMIC ACID


Mass: 46.025 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: CH2O2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 474 / 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: 1.9 Å3/Da / Density % sol: 35.33 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop
Details: 0.1M Magnesium Formate, 23%-30% (v/v) Polyethylene glycol 3350

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.9785 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jul 15, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9785 Å / Relative weight: 1
ReflectionResolution: 1.57→50 Å / Num. obs: 64049 / % possible obs: 99.9 % / Redundancy: 6.4 % / Biso Wilson estimate: 13.25 Å2 / Rmerge(I) obs: 0.102 / Rpim(I) all: 0.043 / Rrim(I) all: 0.111 / Χ2: 0.946 / Net I/σ(I): 10.2
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
1.57-1.660.26725060.9490.1170.2930.92999.9
1.6-1.636.40.25325440.9530.1080.2750.93399.9
1.63-1.666.40.22725650.9650.0970.2470.938100
1.66-1.696.30.21325840.9720.0910.2320.918100
1.69-1.736.30.19825120.9660.0860.2160.934100
1.73-1.776.10.18525390.9770.080.2020.92399.9
1.77-1.815.90.16825700.9730.0740.1840.89599.9
1.81-1.866.40.16125480.9780.0680.1750.88699.9
1.86-1.926.60.15125230.9760.0630.1640.85999.9
1.92-1.986.60.14125770.980.0590.1530.85100
1.98-2.056.40.13125630.9820.0560.1430.796100
2.05-2.136.10.12525190.9820.0540.1360.77699.9
2.13-2.236.20.11726040.9810.0510.1271.167100
2.23-2.356.70.11625660.9890.0480.1261.182100
2.35-2.496.60.11225530.9860.0460.1211.137100
2.49-2.686.50.10525620.9870.0440.1141.06199.8
2.68-2.956.30.09825650.9840.0420.1070.96999.9
2.95-3.386.80.09425890.9880.0390.1020.94100
3.38-4.266.40.08925740.9880.0380.0960.87399.9
4.26-506.60.08826330.9870.0370.0950.9299.9

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Phasing

PhasingMethod: molecular replacement
Phasing MR
Highest resolutionLowest resolution
Rotation1.57 Å49.77 Å
Translation1.57 Å49.77 Å

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Processing

Software
NameVersionClassification
HKL-3000data scaling
PHASER2.6.0phasing
PHENIX1.10.1_2155refinement
PDB_EXTRACT3.22data extraction
HKL-3000data reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5LCA

5lca


Resolution: 1.8→49.739 Å / SU ML: 0.15 / Cross valid method: FREE R-VALUE / σ(F): 1.38 / Phase error: 16.25
Details: THE STRUCTURE FACTOR FILE CONTAINS FRIEDEL PAIRS IN I_PLUS/MINUS COLUMNS
RfactorNum. reflection% reflection
Rfree0.1727 2521 3.94 %
Rwork0.1365 --
obs0.1379 64049 94.98 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 54.07 Å2 / Biso mean: 14.4939 Å2 / Biso min: 2.97 Å2
Refinement stepCycle: final / Resolution: 1.8→49.739 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3459 0 54 477 3990
Biso mean--12.8 23.99 -
Num. residues----462
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0223607
X-RAY DIFFRACTIONf_angle_d1.0454896
X-RAY DIFFRACTIONf_chiral_restr0.057564
X-RAY DIFFRACTIONf_plane_restr0.006639
X-RAY DIFFRACTIONf_dihedral_angle_d14.0442068
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 18

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.8-1.83460.20431350.14442960309583
1.8346-1.87210.19951130.14733206331989
1.8721-1.91280.25671290.1583348347791
1.9128-1.95730.21611370.14653337347492
1.9573-2.00620.20641180.14813200331891
2.0062-2.06050.18291330.13843211334489
2.0605-2.12110.17551360.14183248338490
2.1211-2.18960.19051420.13323479362196
2.1896-2.26780.20921400.13053548368899
2.2678-2.35860.17661570.12873579373699
2.3586-2.4660.15381410.12643548368999
2.466-2.5960.20621390.13463587372699
2.596-2.75860.1631560.12923531368799
2.7586-2.97160.19471360.13983567370399
2.9716-3.27060.18571500.13323616376699
3.2706-3.74370.15051490.13013513366298
3.7437-4.71610.12921530.12063501365498
4.7161-49.75750.14851570.15833549370699

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