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- PDB-4tzf: Structure of metallo-beta lactamase -

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Basic information

Entry
Database: PDB / ID: 4tzf
TitleStructure of metallo-beta lactamase
ComponentsNDM-8 metallo-beta-lactamase
KeywordsHYDROLASE / metallo-beta-lactamase / antibiotic resistance
Function / homology
Function and homology information


beta-lactamase activity / metal ion binding
Similarity search - Function
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
Metallo-beta-lactamase NDM-8
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.22 Å
AuthorsFerguson, J.A. / Makena, A. / Brem, J. / McDonough, M.A. / Schofield, C.J.
CitationJournal: To Be Published
Title: structure of metallo-beta lactamase
Authors: Ferguson, J.A. / Makena, A. / Brem, J. / McDonough, M.A. / Schofield, C.J.
History
DepositionJul 10, 2014Deposition site: RCSB / Processing site: PDBE
Revision 1.0Jul 29, 2015Provider: 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 / pdbx_struct_conn_angle / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: NDM-8 metallo-beta-lactamase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,3983
Polymers24,2671
Non-polymers1312
Water5,170287
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area220 Å2
ΔGint-79 kcal/mol
Surface area9480 Å2
MethodPISA
Unit cell
Length a, b, c (Å)40.936, 58.480, 84.838
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein NDM-8 metallo-beta-lactamase / NDM-8


Mass: 24267.299 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: blaNDM-8 / Plasmid: OPINF / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): PlysS / References: UniProt: M1VE66
#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 / Water


Mass: 18.015 Da / Num. of mol.: 287 / 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: 2.09 Å3/Da / Density % sol: 41.09 % / Description: cubic
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 5.5 / Details: 0.1 M Bis Tris pH 5.5, 25% PEG 3350

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I02 / 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: 1.22→42.47 Å / Num. all: 61432 / Num. obs: 61432 / % possible obs: 99.7 % / Redundancy: 6.2 % / Rmerge(I) obs: 0.065 / Net I/av σ(I): 13.4 / Net I/σ(I): 13.4
Reflection shellResolution: 1.22→1.25 Å / Redundancy: 6.1 % / Rmerge(I) obs: 0.66 / Mean I/σ(I) obs: 2.4 / % possible all: 99.6

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Processing

Software
NameVersionClassification
PHENIX(phenix.refine: 1.8.2_1309)refinement
XDSdata reduction
PHASER2.5.3phasing
Coot0.6.2model building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3SPU

3spu


Resolution: 1.22→42.419 Å / SU ML: 0.12 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 21.65 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.1778 3780 3.25 %Random selection
Rwork0.1517 ---
obs0.1526 61432 98.95 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.22→42.419 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1688 0 2 287 1977
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0111795
X-RAY DIFFRACTIONf_angle_d1.42461
X-RAY DIFFRACTIONf_dihedral_angle_d11.86622
X-RAY DIFFRACTIONf_chiral_restr0.083269
X-RAY DIFFRACTIONf_plane_restr0.008327
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.2188-1.23420.32321380.31164148X-RAY DIFFRACTION98
1.2342-1.25050.39141430.28254161X-RAY DIFFRACTION99
1.2505-1.26760.31421380.28014164X-RAY DIFFRACTION99
1.2676-1.28570.25171390.274172X-RAY DIFFRACTION99
1.2857-1.30490.32781440.24624237X-RAY DIFFRACTION99
1.3049-1.32530.31031410.24144184X-RAY DIFFRACTION99
1.3253-1.3470.23431390.2164170X-RAY DIFFRACTION99
1.347-1.37020.22191380.20964189X-RAY DIFFRACTION100
1.3702-1.39520.26521380.19434156X-RAY DIFFRACTION99
1.3952-1.4220.211420.18624205X-RAY DIFFRACTION99
1.422-1.4510.19241440.17264151X-RAY DIFFRACTION100
1.451-1.48260.21671390.17524165X-RAY DIFFRACTION99
1.4826-1.51710.23551470.16474251X-RAY DIFFRACTION100
1.5171-1.5550.18071400.15414144X-RAY DIFFRACTION100
1.555-1.59710.21581440.1464190X-RAY DIFFRACTION100
1.5971-1.6440.21331360.13824195X-RAY DIFFRACTION100
1.644-1.69710.17431430.13134214X-RAY DIFFRACTION99
1.6971-1.75780.1661350.12584176X-RAY DIFFRACTION99
1.7578-1.82820.15331360.12394180X-RAY DIFFRACTION99
1.8282-1.91140.17171390.12824124X-RAY DIFFRACTION98
1.9114-2.01210.16511400.12374165X-RAY DIFFRACTION99
2.0121-2.13820.11621430.12014146X-RAY DIFFRACTION98
2.1382-2.30330.17141340.12274138X-RAY DIFFRACTION98
2.3033-2.5350.12861420.12564117X-RAY DIFFRACTION98
2.535-2.90180.14861460.1344056X-RAY DIFFRACTION97
2.9018-3.65560.13561350.13584126X-RAY DIFFRACTION98
3.6556-42.44470.17241370.15284140X-RAY DIFFRACTION98

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