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- PDB-6t5k: ECV-1 from Echinicola vietnamensis. Environmental metallo-beta-la... -

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Basic information

Entry
Database: PDB / ID: 6t5k
TitleECV-1 from Echinicola vietnamensis. Environmental metallo-beta-lactamases exhibit high enzymatic activity under zinc deprivation
ComponentsZn-dependent hydrolase, glyoxylase
KeywordsANTIMICROBIAL PROTEIN / beta-lactamase / carbapenemase / environmental
Function / homology
Function and homology information


antibiotic catabolic process / beta-lactamase activity / beta-lactamase / periplasmic space / response to antibiotic / zinc ion binding
Similarity search - Function
Beta-lactamases class B signature 2. / Beta-lactamase, class-B, conserved site / : / 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
Metallo-beta-lactamase type 2
Similarity search - Component
Biological speciesEchinicola vietnamensis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.33 Å
AuthorsFrohlich, C.
Funding support Sweden, 2items
OrganizationGrant numberCountry
Swedish Research Council2013-08633 Sweden
Swedish Research Council2018-02835 Sweden
CitationJournal: J.Antimicrob.Chemother. / Year: 2020
Title: Structural and biochemical characterization of the environmental MBLs MYO-1, ECV-1 and SHD-1.
Authors: Frohlich, C. / Sorum, V. / Huber, S. / Samuelsen, O. / Berglund, F. / Kristiansson, E. / Kotsakis, S.D. / Marathe, N.P. / Larsson, D.G.J. / Leiros, H.S.
History
DepositionOct 16, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 27, 2020Provider: repository / Type: Initial release
Revision 1.1Jun 10, 2020Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.identifier_ORCID / _citation_author.name
Revision 1.2Sep 2, 2020Group: Database references / Derived calculations / Category: citation / pdbx_struct_conn_angle / struct_conn
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr2_auth_seq_id
Revision 1.3Jan 24, 2024Group: Advisory / Data collection ...Advisory / Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_unobs_or_zero_occ_atoms
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
C: Zn-dependent hydrolase, glyoxylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,8358
Polymers26,3941
Non-polymers4417
Water4,576254
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1080 Å2
ΔGint-66 kcal/mol
Surface area9600 Å2
MethodPISA
Unit cell
Length a, b, c (Å)51.926, 65.676, 128.501
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number20
Space group name H-MC2221
Space group name HallC2c2
Symmetry operation#1: x,y,z
#2: x,-y,-z
#3: -x,y,-z+1/2
#4: -x,-y,z+1/2
#5: x+1/2,y+1/2,z
#6: x+1/2,-y+1/2,-z
#7: -x+1/2,y+1/2,-z+1/2
#8: -x+1/2,-y+1/2,z+1/2
Components on special symmetry positions
IDModelComponents
11C-1352-

HOH

21C-1489-

HOH

31C-1499-

HOH

41C-1541-

HOH

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Components

#1: Protein Zn-dependent hydrolase, glyoxylase


Mass: 26393.510 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Echinicola vietnamensis (bacteria) / Gene: Echvi_2632 / Production host: Escherichia coli (E. coli) / References: UniProt: L0FY79
#2: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C2H6O2
#3: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 254 / 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: 2.08 Å3/Da / Density % sol: 40.74 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop
Details: 25-26% PEG3350, ), 0.1 M BIS-TRIS buffer pH 6 and 0.2 M sodium acetate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: MASSIF-3 / Wavelength: 0.9677 Å
DetectorType: DECTRIS EIGER X 4M / Detector: PIXEL / Date: Oct 22, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9677 Å / Relative weight: 1
ReflectionResolution: 1.33→25 Å / Num. obs: 49538 / % possible obs: 97.1 % / Redundancy: 5.3 % / Biso Wilson estimate: 17.49 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.094 / Rpim(I) all: 0.064 / Net I/σ(I): 7.8
Reflection shellResolution: 1.33→1.36 Å / Rmerge(I) obs: 1.3 / Mean I/σ(I) obs: 1 / Num. unique obs: 2951 / CC1/2: 0.413 / Rpim(I) all: 0.671

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Processing

Software
NameVersionClassification
PHENIX1.14_3260refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1znb

1znb


Resolution: 1.33→25 Å / SU ML: 0.1738 / Cross valid method: FREE R-VALUE / Phase error: 20.026
RfactorNum. reflection% reflection
Rfree0.1835 2098 4.24 %
Rwork0.1471 --
obs0.1486 49509 97.05 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 25.28 Å2
Refinement stepCycle: LAST / Resolution: 1.33→25 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1742 0 22 254 2018
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00991901
X-RAY DIFFRACTIONf_angle_d1.11162590
X-RAY DIFFRACTIONf_chiral_restr0.0887288
X-RAY DIFFRACTIONf_plane_restr0.0075341
X-RAY DIFFRACTIONf_dihedral_angle_d18.8063675
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.33-1.360.36791100.33872482X-RAY DIFFRACTION76.8
1.36-1.391252834X-RAY DIFFRACTION87.34
1.39-1.430.36451330.31013023X-RAY DIFFRACTION94.83
1.43-1.470.30551400.25623148X-RAY DIFFRACTION97.65
1.47-1.520.27671430.20723231X-RAY DIFFRACTION99.94
1.52-1.570.21831420.17933216X-RAY DIFFRACTION100
1.57-1.640.20611430.16143223X-RAY DIFFRACTION99.91
1.64-1.710.21491430.14783231X-RAY DIFFRACTION100
1.71-1.80.17871440.13413262X-RAY DIFFRACTION99.97
1.8-1.920.16151440.11913237X-RAY DIFFRACTION100
1.92-2.060.15691440.11743254X-RAY DIFFRACTION99.88
2.06-2.270.16531440.123258X-RAY DIFFRACTION99.85
2.27-2.60.14911450.12813271X-RAY DIFFRACTION99.42
2.6-3.270.17291460.13693314X-RAY DIFFRACTION99.97
3.27-24.080.17051520.14423427X-RAY DIFFRACTION99.86

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