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- PDB-4ua4: Structure of the VIM-2 Metallo-beta-Lactamase in Complex with a B... -

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Basic information

Entry
Database: PDB / ID: 4ua4
TitleStructure of the VIM-2 Metallo-beta-Lactamase in Complex with a Bisthiazolidine Inhibitor
ComponentsBeta-lactamase class B VIM-2
KeywordsHYDROLASE / Hydrolase Metallo-beta-Lactamase Complex
Function / homology
Function and homology information


beta-lactamase / hydrolase activity / 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-3C7 / beta-lactamase
Similarity search - Component
Biological speciesPseudomonas aeruginosa (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.25 Å
AuthorsSpencer, J.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of HealthR01AI100560 United States
CitationJournal: To Be Published
Title: Structure of the VIM-2 Metallo-beta-Lactamase in Complex with a Bisthiazolidine Inhibitor
Authors: Spencer, J.
History
DepositionAug 8, 2014Deposition site: RCSB / Processing site: PDBE
Revision 1.0Sep 17, 2014Provider: repository / Type: Initial release
Revision 1.1Dec 20, 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 / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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.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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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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)52,72913
Polymers51,3872
Non-polymers1,34211
Water6,395355
1
A: Beta-lactamase class B VIM-2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,3916
Polymers25,6931
Non-polymers6985
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Beta-lactamase class B VIM-2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,3387
Polymers25,6931
Non-polymers6446
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)52.888, 61.404, 68.918
Angle α, β, γ (deg.)90.00, 100.87, 90.00
Int Tables number4
Space group name H-MP1211

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Components

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


Mass: 25693.488 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas aeruginosa (bacteria) / Plasmid: pOPINF / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): pLysS / 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-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C3H8O3
#4: Chemical ChemComp-3C7 / (3R,5R,7aS)-5-(sulfanylmethyl)tetrahydro[1,3]thiazolo[4,3-b][1,3]thiazole-3-carboxylic acid


Mass: 237.363 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C7H11NO2S3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 355 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.14 Å3/Da / Density % sol: 42.6 %
Crystal growTemperature: 293 K / Method: vapor diffusion / pH: 9 / Details: 0.1 M Bicine pH 9.0; 65 % 2-methyl-2,4-pentandiol

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04-1 / Wavelength: 0.92 Å
DetectorType: DECTRIS PILATUS 2M / Detector: PIXEL / Date: May 27, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.92 Å / Relative weight: 1
ReflectionResolution: 1.25→29.64 Å / Num. obs: 115461 / % possible obs: 96.7 % / Redundancy: 2.6 % / Rmerge(I) obs: 0.04 / Net I/σ(I): 11.1
Reflection shellResolution: 1.25→1.32 Å / Redundancy: 2.4 % / Rmerge(I) obs: 0.395 / Mean I/σ(I) obs: 2.3 / % possible all: 91.8

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Processing

Software
NameVersionClassification
REFMAC5.6.0117refinement
XDSdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1KO3

1ko3


Resolution: 1.25→67.68 Å / Cor.coef. Fo:Fc: 0.976 / Cor.coef. Fo:Fc free: 0.972 / SU B: 1.209 / SU ML: 0.024 / Cross valid method: THROUGHOUT / ESU R: 0.044 / ESU R Free: 0.041 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
RfactorNum. reflection% reflectionSelection details
Rfree0.16427 5780 5 %RANDOM
Rwork0.14447 ---
obs0.14545 109653 96.49 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 16.888 Å2
Baniso -1Baniso -2Baniso -3
1-0.14 Å2-0 Å20.05 Å2
2---0.02 Å2-0 Å2
3----0.09 Å2
Refinement stepCycle: 1 / Resolution: 1.25→67.68 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3490 0 67 355 3912
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0060.023785
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.4591.9825203
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.7585497
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.13523.75160
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.67115549
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.1011524
X-RAY DIFFRACTIONr_chiral_restr0.1070.2613
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0212906
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr2.61133785
X-RAY DIFFRACTIONr_sphericity_free20.6565122
X-RAY DIFFRACTIONr_sphericity_bonded9.81453917
LS refinement shellResolution: 1.25→1.282 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.271 373 -
Rwork0.241 6920 -
obs--84.29 %

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