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- PDB-5acu: VIM-2-NAT, Discovery of novel inhibitor scaffolds against the met... -

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Basic information

Entry
Database: PDB / ID: 5acu
TitleVIM-2-NAT, Discovery of novel inhibitor scaffolds against the metallo- beta-lactamase VIM-2 by SPR based fragment screening
ComponentsBETA-LACTAMASE
KeywordsHYDROLASE
Function / homology
Function and homology information


antibiotic catabolic process / beta-lactamase / hydrolase activity / metal ion binding
Similarity search - Function
: / : / Metallo-beta-lactamase superfamily / Ribonuclease Z/Hydroxyacylglutathione hydrolase-like / Metallo-beta-lactamase; Chain A / Metallo-beta-lactamase superfamily / Metallo-beta-lactamase / Ribonuclease Z/Hydroxyacylglutathione hydrolase-like / 4-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
HYDROXIDE ION / Metallo-beta-lactamase type 2
Similarity search - Component
Biological speciesPSEUDOMONAS AERUGINOSA (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.1 Å
AuthorsChristopeit, T. / Carlsen, T.J.O. / Helland, R. / Leiros, H.K.S.
CitationJournal: J.Med.Chem. / Year: 2015
Title: Discovery of Novel Inhibitor Scaffolds Against the Metallo-Beta-Lactamase Vim-2 by Spr Based Fragment Screening
Authors: Christopeit, T. / Carlsen, T.J.O. / Helland, R. / Leiros, H.K.S.
History
DepositionAug 18, 2015Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 4, 2015Provider: repository / Type: Initial release
Revision 1.1Nov 25, 2015Group: Database references
Revision 1.2Jan 10, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _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.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.pdbx_dist_value / _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_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 / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: BETA-LACTAMASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,6377
Polymers28,3531
Non-polymers2846
Water1,69394
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)64.422, 75.795, 79.292
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number23
Space group name H-MI222
Components on special symmetry positions
IDModelComponents
11A-2086-

HOH

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Components

#1: Protein BETA-LACTAMASE


Mass: 28352.836 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) PSEUDOMONAS AERUGINOSA (bacteria) / Strain: 301-5473 / Plasmid: PDEST14 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q9K2N0, beta-lactamase
#2: Chemical ChemComp-OH / HYDROXIDE ION


Mass: 17.007 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: HO
#3: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Zn
#4: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 94 / 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

CrystalDescription: NONE
Crystal growpH: 7.2
Details: 22-27% (PEG) 3350, 0.2 M MAGNESIUM FORMATE,5 MM BETA-MERCAPTOETHANOL, pH 7.2

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Wavelength: 1.5418
DetectorType: RIGAKU R-AXIS IV++ / Detector: IMAGE PLATE
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.1→25 Å / Num. obs: 11392 / % possible obs: 97.7 % / Observed criterion σ(I): 0 / Redundancy: 3.7 % / Biso Wilson estimate: 25.44 Å2 / Rmerge(I) obs: 0.06 / Net I/σ(I): 14.2
Reflection shellResolution: 2.1→2.31 Å / Redundancy: 3.9 % / Rmerge(I) obs: 0.23 / Mean I/σ(I) obs: 5.3 / % possible all: 97

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Processing

Software
NameVersionClassification
PHENIX(PHENIX.REFINE)refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1KO3

1ko3


Resolution: 2.1→24.957 Å / SU ML: 0.29 / σ(F): 1.35 / Phase error: 30.38 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2869 539 4.7 %
Rwork0.2559 --
obs0.2574 11392 97.71 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.1→24.957 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1704 0 6 94 1804
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0031790
X-RAY DIFFRACTIONf_angle_d0.6722451
X-RAY DIFFRACTIONf_dihedral_angle_d12.167625
X-RAY DIFFRACTIONf_chiral_restr0.028280
X-RAY DIFFRACTIONf_plane_restr0.003323
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.1-2.31120.3211210.2722654X-RAY DIFFRACTION97
2.3112-2.64530.33241420.27782667X-RAY DIFFRACTION98
2.6453-3.33160.28851460.27292705X-RAY DIFFRACTION98
3.3316-24.95860.26111300.23612827X-RAY DIFFRACTION98

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