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- PDB-4eyf: Crystal structure of NDM-1 bound to hydrolyzed benzylpenicillin -

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Basic information

Entry
Database: PDB / ID: 4eyf
TitleCrystal structure of NDM-1 bound to hydrolyzed benzylpenicillin
ComponentsBeta-lactamase NDM-1
KeywordsHydrolase/antibiotic / Metallo Beta Lactamase / antibiotic / Hydrolase-antibiotic complex
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 superfamily / Metallo-beta-lactamase; Chain A / Metallo-beta-lactamase / Ribonuclease Z/Hydroxyacylglutathione hydrolase-like / 4-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Chem-PNK / Metallo-beta-lactamase type 2
Similarity search - Component
Biological speciesKlebsiella pneumoniae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsStrynadka, N.C.J. / King, D.T.
CitationJournal: J.Am.Chem.Soc. / Year: 2012
Title: New Delhi Metallo-Beta-Lactamase: Structural Insights into Beta-Lactam Recognition and Inhibition
Authors: King, D.T. / Worrall, L.J. / Gruninger, R. / Strynadka, N.C.
History
DepositionMay 1, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 8, 2012Provider: repository / Type: Initial release
Revision 1.1Nov 15, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 1.2Feb 28, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_conn_angle / struct_conn / struct_site
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_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_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_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_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_asym_id / _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_asym_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_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Beta-lactamase NDM-1
B: Beta-lactamase NDM-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)58,15210
Polymers57,0552
Non-polymers1,0978
Water5,585310
1
A: Beta-lactamase NDM-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,0765
Polymers28,5271
Non-polymers5494
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Beta-lactamase NDM-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,0765
Polymers28,5271
Non-polymers5494
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
A: Beta-lactamase NDM-1
hetero molecules

B: Beta-lactamase NDM-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)58,15210
Polymers57,0552
Non-polymers1,0978
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_545-x,y-1/2,-z+1/21
Buried area1970 Å2
ΔGint-85 kcal/mol
Surface area18090 Å2
MethodPISA
Unit cell
Length a, b, c (Å)39.030, 79.490, 134.210
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
DetailsIt is uncertain whether the biologically active form is monomeric or dimeric

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Components

#1: Protein Beta-lactamase NDM-1 / NDM-1 / Metallo-beta-lactamase NDM-1


Mass: 28527.428 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Klebsiella pneumoniae (bacteria) / Gene: blaNDM-1 / Production host: Escherichia coli (E. coli) / References: UniProt: C7C422, beta-lactamase
#2: Chemical ChemComp-PNK / (2R,4S)-2-{(R)-carboxy[(phenylacetyl)amino]methyl}-5,5-dimethyl-1,3-thiazolidine-4-carboxylic acid / Penicillin, hydroxylated form


Mass: 352.405 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C16H20N2O5S
#3: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Zn
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 310 / Source method: isolated from a natural source / Formula: H2O
Nonpolymer detailsHYDROLYSIS OF PENICILLIN BY BETA-LACTAMASE NDM-1 OCCURRED DURING CRYSTALLIZATION

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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: 1.82 Å3/Da / Density % sol: 32.58 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 5.5
Details: 0.2M MgCl2, 25% PEG3350, 0.1M bis-tris, pH 5.5, VAPOR DIFFUSION, SITTING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: CLSI / Beamline: 08B1-1 / Wavelength: 1
DetectorType: RAYONIX MX300HE / Detector: CCD / Date: Nov 22, 2011
RadiationMonochromator: toroidal focusing mirror / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.8→29.7 Å / Num. all: 39550 / Num. obs: 39036 / % possible obs: 98.7 % / Observed criterion σ(I): -3
Reflection shellResolution: 1.8→1.9 Å / % possible all: 97.6

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Processing

Software
NameVersionClassification
MxDCdata collection
PHASERphasing
REFMAC5.5.0102refinement
MOSFLMdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.8→29.7 Å / Cor.coef. Fo:Fc: 0.951 / Cor.coef. Fo:Fc free: 0.927 / SU B: 2.296 / SU ML: 0.072 / Cross valid method: THROUGHOUT / ESU R: 0.13 / ESU R Free: 0.119 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.19735 1952 5 %RANDOM
Rwork0.1627 ---
obs0.16445 37046 98.33 %-
all-37675 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 11.505 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0.09 Å20 Å2
3----0.09 Å2
Refinement stepCycle: LAST / Resolution: 1.8→29.7 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3594 0 54 310 3958
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0213733
X-RAY DIFFRACTIONr_angle_refined_deg1.2911.9455087
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.2815482
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.77424.534161
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.13115554
X-RAY DIFFRACTIONr_dihedral_angle_4_deg24.0751518
X-RAY DIFFRACTIONr_chiral_restr0.1060.2567
X-RAY DIFFRACTIONr_gen_planes_refined0.0150.0212892
X-RAY DIFFRACTIONr_mcbond_it1.431.52389
X-RAY DIFFRACTIONr_mcangle_it2.09823806
X-RAY DIFFRACTIONr_scbond_it3.48831344
X-RAY DIFFRACTIONr_scangle_it5.1884.51280
LS refinement shellResolution: 1.8→1.847 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.273 141 -
Rwork0.227 2668 -
obs--96.7 %

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