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- PDB-3pg4: The crystal structure of New Delhi Metallo-beta lactamase (NDM-1) -

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Basic information

Entry
Database: PDB / ID: 3pg4
TitleThe crystal structure of New Delhi Metallo-beta lactamase (NDM-1)
ComponentsMetallo-beta-lactamase
KeywordsHYDROLASE
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
: / 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 speciesKlebsiella pneumoniae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsKim, H.T. / Cho, Y.S. / Chang, H.J.
CitationJournal: To be Published
Title: The crystal structure of New Delhi Metallo-beta lactamase (NDM-1)
Authors: Kim, H.T. / Cho, Y.S. / Chang, H.J.
History
DepositionOct 29, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 16, 2011Provider: repository / Type: Initial release
Revision 1.1Sep 6, 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 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Metallo-beta-lactamase


Theoretical massNumber of molelcules
Total (without water)24,4331
Polymers24,4331
Non-polymers00
Water2,378132
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)77.539, 77.539, 177.740
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number97
Space group name H-MI422

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Components

#1: Protein Metallo-beta-lactamase


Mass: 24432.514 Da / Num. of mol.: 1 / Fragment: UNP residues 49-270
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Klebsiella pneumoniae (bacteria) / Strain: 05-506 / Gene: bla NDM-1, blaNDM-1 / Plasmid: modifed pET21b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: C7C422, beta-lactamase
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 132 / Source method: isolated from a natural source / Formula: H2O

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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: 2.73 Å3/Da / Density % sol: 55 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop
Details: 4.0M Sodium formate, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: PAL/PLS / Beamline: 6B / Wavelength: 1.1 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Oct 21, 2010
RadiationMonochromator: double mirrors / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.1 Å / Relative weight: 1
ReflectionResolution: 2→50 Å / Num. all: 30478 / Num. obs: 17504 / % possible obs: 92.6 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Redundancy: 7.9 % / Biso Wilson estimate: 15.7 Å2 / Rmerge(I) obs: 0.057 / Rsym value: 0.056 / Net I/σ(I): 31.8
Reflection shellResolution: 2→2.07 Å / Redundancy: 3.4 % / Rmerge(I) obs: 0.195 / Mean I/σ(I) obs: 3.62 / Num. unique all: 1454 / Rsym value: 0.224 / % possible all: 78.9

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Processing

Software
NameVersionClassification
HKL-2000data collection
PHASESphasing
CNS1.1refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: VIM-4 METALLO-BETA-LACTAMASE PDB ENTRY 2WHG

2whg


Resolution: 2→34.52 Å / Rfactor Rfree error: 0.008 / Data cutoff high absF: 189489.77 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Maximum likelihood
RfactorNum. reflection% reflectionSelection details
Rfree0.237 844 4.8 %RANDOM
Rwork0.202 ---
obs0.202 17439 92.7 %-
all-18806 --
Solvent computationSolvent model: FLAT MODEL / Bsol: 50.938 Å2 / ksol: 0.375478 e/Å3
Displacement parametersBiso mean: 33 Å2
Baniso -1Baniso -2Baniso -3
1-1.87 Å20 Å20 Å2
2--1.87 Å20 Å2
3----3.73 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.29 Å0.23 Å
Luzzati d res low-5 Å
Luzzati sigma a0.29 Å0.23 Å
Refinement stepCycle: LAST / Resolution: 2→34.52 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1720 0 0 132 1852
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.005
X-RAY DIFFRACTIONc_angle_deg1.3
X-RAY DIFFRACTIONc_dihedral_angle_d24.8
X-RAY DIFFRACTIONc_improper_angle_d0.74
X-RAY DIFFRACTIONc_mcbond_it1.391.5
X-RAY DIFFRACTIONc_mcangle_it2.262
X-RAY DIFFRACTIONc_scbond_it2.12
X-RAY DIFFRACTIONc_scangle_it3.042.5
Refine LS restraints NCSNCS model details: NONE
LS refinement shell
Resolution (Å)% reflection Rfree (%)Num. reflection RworkRefine-IDNum. reflection obsTotal num. of bins used% reflection obs (%)
2-2.074.82390X-RAY DIFFRACTION1454678.9
2.07-2.15X-RAY DIFFRACTION1603685.8
2.15-2.25X-RAY DIFFRACTION1632688.8
2.25-2.37X-RAY DIFFRACTION1685690.3
2.37-2.52X-RAY DIFFRACTION1722692.6
2.52-2.71X-RAY DIFFRACTION1793695.8
2.71-2.99X-RAY DIFFRACTION1839696.8
2.99-3.42X-RAY DIFFRACTION1852698.3
3.42-4.31X-RAY DIFFRACTION1907698.8
4.31-50X-RAY DIFFRACTION2017698.7
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2dna-rna_rep.paramdna-rna.top
X-RAY DIFFRACTION3water_rep.paramwater.top
X-RAY DIFFRACTION4ion.paramion.top

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