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- PDB-4tyf: Structure of a Metallo-beta-lactamase -

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Basic information

Entry
Database: PDB / ID: 4tyf
TitleStructure of a Metallo-beta-lactamase
ComponentsNDM-4
KeywordsHYDROLASE / Metallo-Beta-Lactamase / antibiotic resistance
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
Metallo-beta-lactamase type 2 / Metallo-beta-lactamase type 2
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.1 Å
AuthorsFerguson, J.A. / Makena, A. / Brem, J. / McDonough, M.A. / Schofield, C.J.
Funding support United Kingdom, 1items
OrganizationGrant numberCountry
Medical Research Council (United Kingdom)G1100135 United Kingdom
CitationJournal: To Be Published
Title: Structure of a Metallo-beta-lactamase
Authors: Ferguson, J.A. / Makena, A. / Brem, J. / McDonough, M.A. / Schofield, C.J.
History
DepositionJul 8, 2014Deposition site: RCSB / Processing site: PDBE
Revision 1.0Jul 15, 2015Provider: repository / Type: Initial release
Revision 2.0Sep 13, 2017Group: Advisory / Atomic model ...Advisory / Atomic model / Author supporting evidence / Data collection / Derived calculations
Category: atom_site / atom_site_anisotrop ...atom_site / atom_site_anisotrop / diffrn_detector / pdbx_audit_support / pdbx_struct_conn_angle / pdbx_validate_close_contact / struct_conn / struct_site_gen
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site_anisotrop.U[1][1] / _atom_site_anisotrop.U[1][2] / _atom_site_anisotrop.U[1][3] / _atom_site_anisotrop.U[2][2] / _atom_site_anisotrop.U[2][3] / _atom_site_anisotrop.U[3][3] / _diffrn_detector.pdbx_collection_date / _pdbx_audit_support.funding_organization / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_validate_close_contact.auth_seq_id_1 / _pdbx_validate_close_contact.auth_seq_id_2 / _struct_conn.ptnr2_auth_seq_id / _struct_site_gen.auth_seq_id
Revision 2.1Jan 31, 2018Group: Database references / Category: pdbx_related_exp_data_set
Revision 2.2Dec 20, 2023Group: 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
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: NDM-4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,4563
Polymers24,3251
Non-polymers1312
Water4,432246
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area210 Å2
ΔGint-79 kcal/mol
Surface area9810 Å2
MethodPISA
Unit cell
Length a, b, c (Å)41.700, 59.080, 42.000
Angle α, β, γ (deg.)90.00, 97.61, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein NDM-4


Mass: 24325.334 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: blaNDM-4 / Plasmid: OPINF / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: X2JGA4, UniProt: H6WZS9*PLUS
#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 246 / 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: 2.11 Å3/Da / Density % sol: 41.59 % / Description: Rhombohedral
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 7 / Details: 10% PEG 1000 w/v, 10% PEG 8000 w/v / Temp details: Room Temperature

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I02 / Wavelength: 0.9785 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Jul 12, 2013
RadiationMonochromator: double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9785 Å / Relative weight: 1
ReflectionResolution: 1.1→41.33 Å / Num. all: 80791 / Num. obs: 80791 / % possible obs: 98.8 % / Redundancy: 4.3 % / Biso Wilson estimate: 13.85 Å2 / Rsym value: 0.046 / Net I/σ(I): 13.8
Reflection shellResolution: 1.1→1.13 Å / Redundancy: 3.9 % / Rmerge(I) obs: 0.676 / Mean I/σ(I) obs: 1.8 / % possible all: 96.4

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Processing

Software
NameVersionClassification
XDSdata reduction
PHASER2.5.3phasing
PHENIX1.8.2refinement
Coot0.6.2model building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 3SPU
Resolution: 1.1→41.33 Å / Cross valid method: FREE R-VALUE / Phase error: 17.83
RfactorNum. reflection% reflectionSelection details
Rfree0.1735 4056 5 %Random selection
Rwork0.1503 ---
obs0.1515 80763 98.71 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 11.92 Å2
Refinement stepCycle: LAST / Resolution: 1.1→41.33 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1706 0 2 246 1954
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONBond_length0.017
X-RAY DIFFRACTIONBond_angle1.674

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