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- PDB-7aez: Crystal structure of the metallo-beta-lactamase NDM-7 with 407 -

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Basic information

Entry
Database: PDB / ID: 7aez
TitleCrystal structure of the metallo-beta-lactamase NDM-7 with 407
ComponentsMetallo-beta-lactamase NDM-7
KeywordsHYDROLASE / HYDROLASE 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 superfamily / Metallo-beta-lactamase; Chain A / Metallo-beta-lactamase / Ribonuclease Z/Hydroxyacylglutathione hydrolase-like / 4-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
2-ETHOXYETHANOL / Chem-R8W / Metallo-beta-lactamase type 2
Similarity search - Component
Biological speciesKlebsiella pneumoniae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.018 Å
AuthorsBrem, J. / Schofield, C.J.
Funding support United Kingdom, 2items
OrganizationGrant numberCountry
Innovative Medicines InitiativeENABLE United Kingdom
Biotechnology and Biological Sciences Research Council (BBSRC)(BB/S50676X/1 United Kingdom
CitationJournal: To Be Published
Title: Not available yet
Authors: Brem, J. / Schofield, C.J.
History
DepositionSep 18, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 6, 2021Provider: repository / Type: Initial release
Revision 1.1Jan 31, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / diffrn_source / pdbx_initial_refinement_model
Item: _diffrn_source.pdbx_synchrotron_site

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Metallo-beta-lactamase NDM-7
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,2519
Polymers24,4001
Non-polymers8518
Water5,981332
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration, monomer
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area950 Å2
ΔGint-88 kcal/mol
Surface area9760 Å2
MethodPISA
Unit cell
Length a, b, c (Å)41.746, 58.736, 83.897
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

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Protein , 1 types, 1 molecules A

#1: Protein Metallo-beta-lactamase NDM-7 / NDM-7 / New Delhi metallo beta lactamase 7


Mass: 24400.400 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: CYS208 is sp2 hybridised at CA / Source: (gene. exp.) Klebsiella pneumoniae (bacteria) / Gene: blaNDM-7 / Production host: Escherichia coli (E. coli) / Strain (production host): pLyS / References: UniProt: X5CZV5

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Non-polymers , 7 types, 340 molecules

#2: Chemical ChemComp-R8W / 7-propan-2-yl-3-[4-(1,2,4-triazol-1-ylmethyl)phenyl]-1~{H}-indole-2-carboxylic acid


Mass: 360.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C21H20N4O2 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#5: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#6: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#7: Chemical ChemComp-ETX / 2-ETHOXYETHANOL


Mass: 90.121 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O2
#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 332 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 2.11 Å3/Da / Density % sol: 41.82 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 5.5 / Details: 0.1M Bis Tris pH 5.5 25% PEG3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.9763 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: May 7, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9763 Å / Relative weight: 1
ReflectionResolution: 1.01843→27.97 Å / Num. obs: 97817 / % possible obs: 92.2 % / Redundancy: 11.4 % / Biso Wilson estimate: 8.56 Å2 / CC1/2: 1 / Rmerge(I) obs: 0.057 / Rpim(I) all: 0.017 / Rrim(I) all: 0.06 / Net I/σ(I): 24.8
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. measured allNum. unique obsCC1/2Rpim(I) allRrim(I) allNet I/σ(I) obs% possible all
1.01843-1.045.70.6452046836030.8210.2810.7072.646.7
4.55-27.9711.60.0371551213400.9990.0110.03862.699.5

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Phasing

PhasingMethod: molecular replacement
Phasing MR
Highest resolutionLowest resolution
Rotation6.09 Å27.97 Å
Translation6.09 Å27.97 Å

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Processing

Software
NameVersionClassification
PHENIX1.12_2829refinement
Aimless0.5.31data scaling
PHASER2.6.0phasing
PDB_EXTRACT3.25data extraction
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4TZF

4tzf


Resolution: 1.018→27.719 Å / SU ML: 0.06 / Cross valid method: THROUGHOUT / σ(F): 1.36 / Phase error: 9.59 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1129 1999 2.05 %
Rwork0.1044 95723 -
obs0.1046 97722 92.16 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 50.2 Å2 / Biso mean: 13.1449 Å2 / Biso min: 6.05 Å2
Refinement stepCycle: final / Resolution: 1.018→27.719 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1710 0 103 358 2171
Biso mean--26.75 26.95 -
Num. residues----231
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0062008
X-RAY DIFFRACTIONf_angle_d1.0182764
X-RAY DIFFRACTIONf_chiral_restr0.082294
X-RAY DIFFRACTIONf_plane_restr0.008379
X-RAY DIFFRACTIONf_dihedral_angle_d12.961723
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
1.0184-1.04390.1883710.2122338146
1.0439-1.07210.203950.1716465564
1.0721-1.10370.14351260.1329596281
1.1037-1.13930.13221500.1132722098
1.1393-1.180.1041530.09547337100
1.18-1.22730.09731550.09287357100
1.2273-1.28310.10411530.08857386100
1.2831-1.35080.09981550.0897366100
1.3508-1.43540.10091540.08757410100
1.4354-1.54620.10131560.08427407100
1.5462-1.70180.10031540.08957418100
1.7018-1.9480.10181560.09317496100
1.948-2.4540.10331590.09917529100
2.454-27.70.12761620.12137799100

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