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- PDB-3s0z: Crystal structure of New Delhi Metallo-beta-lactamase (NDM-1) -

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Basic information

Entry
Database: PDB / ID: 3s0z
TitleCrystal structure of New Delhi Metallo-beta-lactamase (NDM-1)
ComponentsMetallo-beta-lactamase
KeywordsHYDROLASE / New Delhi metallo-beta-lactamase 1 / NDM-1 / drug resistant / drug discovery
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; 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 speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 Å
AuthorsGuo, Y. / Wang, J. / Niu, G.J. / Shui, W.Q. / Sun, Y.N. / Lou, Z.Y. / Rao, Z.H.
CitationJournal: Protein Cell / Year: 2011
Title: A structural view of the antibiotic degradation enzyme NDM-1 from a superbug.
Authors: Guo, Y. / Wang, J. / Niu, G. / Shui, W. / Sun, Y. / Zhou, H. / Zhang, Y. / Yang, C. / Lou, Z. / Rao, Z.
History
DepositionMay 13, 2011Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Jun 1, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 1, 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 / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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: Metallo-beta-lactamase
B: Metallo-beta-lactamase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,4316
Polymers47,1692
Non-polymers2624
Water4,071226
1
A: Metallo-beta-lactamase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,7153
Polymers23,5851
Non-polymers1312
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Metallo-beta-lactamase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,7153
Polymers23,5851
Non-polymers1312
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)40.696, 40.696, 215.292
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number144
Space group name H-MP31

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Components

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


Mass: 23584.568 Da / Num. of mol.: 2 / Fragment: UNP RESIDUES 47-270
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: blaNDM-1 / Production host: Escherichia coli (E. coli) / References: UniProt: E5KIY2
#2: Chemical
ChemComp-ZN / ZINC ION


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


Mass: 18.015 Da / Num. of mol.: 226 / 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: 2.18 Å3/Da / Density % sol: 43.63 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 20mM CdCl2, 20mM CaCl2, 20mM CoCl2, 20% (v/w) PEG 3350, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 291K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: AR-NE3A / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 270 / Detector: CCD / Date: Mar 2, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.5→50 Å / Num. obs: 10177 / % possible obs: 71.3 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0

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Processing

Software
NameVersionClassification
ADSCQuantumdata collection
PHASERphasing
REFMAC5.5.0110refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2WRS

2wrs


Resolution: 2.5→30 Å / Cor.coef. Fo:Fc: 0.83 / Cor.coef. Fo:Fc free: 0.777 / SU B: 8.833 / SU ML: 0.21 / Cross valid method: THROUGHOUT / ESU R Free: 0.467 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.26742 502 5.1 %RANDOM
Rwork0.23425 ---
obs0.2359 9265 70.89 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 18.773 Å2
Baniso -1Baniso -2Baniso -3
1--0.91 Å2-0.45 Å20 Å2
2---0.91 Å20 Å2
3---1.36 Å2
Refinement stepCycle: LAST / Resolution: 2.5→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3240 0 4 226 3470
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.0213312
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.7851.9314506
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg9.1955436
X-RAY DIFFRACTIONr_dihedral_angle_2_deg39.72124.412136
X-RAY DIFFRACTIONr_dihedral_angle_3_deg24.40215486
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.2421514
X-RAY DIFFRACTIONr_chiral_restr0.1120.2510
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.0212534
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.5291.52178
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it0.89223454
X-RAY DIFFRACTIONr_scbond_it1.45531134
X-RAY DIFFRACTIONr_scangle_it2.1634.51052
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.5→2.565 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.192 46 -
Rwork0.217 828 -
obs--86.11 %

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