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- PDB-4tz9: Structure of Metallo-beta-lactamase -

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Basic information

Entry
Database: PDB / ID: 4tz9
TitleStructure of Metallo-beta-lactamase
ComponentsClass B metallo-beta-lactamase
KeywordsHYDROLASE / Metallo-beta-lactamase / antibiotic resistance
Function / homology
Function and homology information


Metallo-beta-lactamase superfamily / Metallo-beta-lactamase superfamily / Metallo-beta-lactamase / Ribonuclease Z/Hydroxyacylglutathione hydrolase-like / Metallo-beta-lactamase; Chain A / Ribonuclease Z/Hydroxyacylglutathione hydrolase-like / 4-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
: / : / NICKEL (II) ION / Metallo-beta-lactamase NDM-3
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1269 Å
AuthorsFerguson, J.A. / Brem, J. / Makena, A. / McDonough, A.M. / 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 Metallo-beta-lactamase
Authors: Ferguson, J.A. / Makena, A. / Brem, J. / McDonough, A.M. / Schofield, C.J.
History
DepositionJul 9, 2014Deposition site: RCSB / Processing site: PDBE
Revision 1.0Jul 29, 2015Provider: repository / Type: Initial release
Revision 2.0Sep 13, 2017Group: Atomic model / Author supporting evidence / Derived calculations
Category: atom_site / pdbx_audit_support ...atom_site / pdbx_audit_support / pdbx_struct_conn_angle / 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 / _pdbx_audit_support.funding_organization / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _struct_conn.ptnr2_auth_seq_id / _struct_site_gen.auth_seq_id
Revision 3.0Dec 20, 2023Group: Atomic model / Data collection ...Atomic model / Data collection / Database references / Derived calculations / Refinement description
Category: atom_site / chem_comp_atom ...atom_site / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn
Item: _atom_site.occupancy / _database_2.pdbx_DOI ..._atom_site.occupancy / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_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_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr2_symmetry / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_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_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_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_symmetry

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Class B metallo-beta-lactamase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,8148
Polymers24,3421
Non-polymers4727
Water2,162120
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area720 Å2
ΔGint-75 kcal/mol
Surface area9780 Å2
MethodPISA
Unit cell
Length a, b, c (Å)120.908, 120.908, 90.190
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number97
Space group name H-MI422
Components on special symmetry positions
IDModelComponents
11A-305-

NI

21A-437-

HOH

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Components

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Protein , 1 types, 1 molecules A

#1: Protein Class B metallo-beta-lactamase / Metallo-beta-lactamase NDM-3 / NDM-3 metallo-beta-lactamase


Mass: 24342.387 Da / Num. of mol.: 1 / Fragment: UNP residues 42-270
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: NDM-3, blaNDM-3 / Plasmid: OpinF / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): PlysS / References: UniProt: I3VKD5

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Non-polymers , 5 types, 127 molecules

#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#3: Chemical ChemComp-CO / COBALT (II) ION


Mass: 58.933 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Co
#4: Chemical
ChemComp-NI / NICKEL (II) ION / Nickel


Mass: 58.693 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Ni
#5: Chemical ChemComp-CD / CADMIUM ION


Mass: 112.411 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cd
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 120 / 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: 3.39 Å3/Da / Density % sol: 63.7 % / Description: Cubic
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 0.008M CdCl2, NiCl2, MgCl2, CoCl2 0.1 HEPES pH 7.5 14% PEG 3350

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.9793 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Feb 10, 2014
RadiationMonochromator: Double Crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9793 Å / Relative weight: 1
ReflectionResolution: 2.1→46.37 Å / Num. all: 18919 / Num. obs: 18919 / % possible obs: 91.6 % / Redundancy: 6.5 % / Biso Wilson estimate: 36.74 Å2 / Rmerge(I) obs: 0.217 / Net I/σ(I): 6.12
Reflection shellResolution: 2.1→2.18 Å / Redundancy: 5.8 % / Rmerge(I) obs: 0.683 / Mean I/σ(I) obs: 1.5 / % possible all: 88.3

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Processing

Software
NameVersionClassification
HKL-2000v701c3data reduction
HKL-2000v701c3data scaling
Coot0.6.2model building
PHASER2.5.3phasing
PHENIX2.5.3refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3ZR9

3zr9


Resolution: 2.1269→2.1895 Å / Cross valid method: FREE R-VALUE
RfactorNum. reflection% reflectionSelection details
Rfree0.2485 1888 10 %Random selection
Rwork0.2286 ---
obs0.2307 18885 91.47 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.1269→2.1895 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1695 0 7 120 1822
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONbond length0.007
X-RAY DIFFRACTIONbond angle0.74

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