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- PDB-6jkb: Crystal structure of metallo-beta-lactamse, NDM-1, in complex wit... -

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Basic information

Entry
Database: PDB / ID: 6jkb
TitleCrystal structure of metallo-beta-lactamse, NDM-1, in complex with hydrolyzed ampicillin
ComponentsMetallo-beta-lactamase type 2
KeywordsHYDROLASE / ANTIBIOTIC
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 / Metallo-beta-lactamase superfamily / Metallo-beta-lactamase / Ribonuclease Z/Hydroxyacylglutathione hydrolase-like
Similarity search - Domain/homology
Chem-ZZ7 / Metallo-beta-lactamase type 2
Similarity search - Component
Biological speciesKlebsiella pneumoniae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.444 Å
AuthorsKamo, T. / Kuroda, K. / Kondo, S. / Hayashi, U. / Fudo, S. / Nukaga, M. / Hoshino, T.
CitationJournal: Chem Pharm Bull (Tokyo) / Year: 2021
Title: Identification of the Inhibitory Compounds for Metallo-beta-lactamases and Structural Analysis of the Binding Modes.
Authors: Kamo, T. / Kuroda, K. / Kondo, S. / Hayashi, U. / Fudo, S. / Yoneda, T. / Takaya, A. / Nukaga, M. / Hoshino, T.
History
DepositionFeb 28, 2019Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Mar 25, 2020Provider: repository / Type: Initial release
Revision 1.1Dec 15, 2021Group: Database references / Derived calculations
Category: citation / citation_author ...citation / citation_author / database_2 / struct_conn
Item: _citation.journal_abbrev / _citation.journal_id_CSD ..._citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _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
Revision 1.2Nov 22, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Metallo-beta-lactamase type 2
B: Metallo-beta-lactamase type 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)52,5688
Polymers51,5722
Non-polymers9966
Water79344
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1780 Å2
ΔGint-19 kcal/mol
Surface area19250 Å2
Unit cell
Length a, b, c (Å)39.111, 79.248, 132.617
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Metallo-beta-lactamase type 2 / B2 metallo-beta-lactamase / Beta-lactamase type II / Metallo-beta-lactamase NDM-1 / Metallo-beta- ...B2 metallo-beta-lactamase / Beta-lactamase type II / Metallo-beta-lactamase NDM-1 / Metallo-beta-lactamase type II / New Delhi metallo-beta-lactamase-1 / NDM-1


Mass: 25785.988 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Klebsiella pneumoniae (bacteria) / Gene: blaNDM-1 / Plasmid: pET48b / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta(DE3)pLys / References: UniProt: C7C422, beta-lactamase
#2: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Zn
#3: Chemical ChemComp-ZZ7 / (2R,4S)-2-[(R)-{[(2R)-2-amino-2-phenylacetyl]amino}(carboxy)methyl]-5,5-dimethyl-1,3-thiazolidine-4-carboxylic acid / AMPICILLIN (open form)


Mass: 367.420 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C16H21N3O5S
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 44 / 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: 1.99 Å3/Da / Density % sol: 38.27 % / Mosaicity: 1.194 °
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 7.2
Details: 0.1M Bis-Tris, 25%(v/v) PEG3350, 0.25M Ammonium Sulfate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: AR-NW12A / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: May 16, 2014 / Details: mirrors
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.45→50 Å / Num. obs: 15802 / % possible obs: 99.9 % / Redundancy: 7 % / Biso Wilson estimate: 48.31 Å2 / Rmerge(I) obs: 0.141 / Rpim(I) all: 0.058 / Rrim(I) all: 0.153 / Χ2: 1.068 / Net I/σ(I): 6.8 / Num. measured all: 110767
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
2.45-2.527.10.91712650.7360.370.991.03499.9
2.52-2.67.10.74512890.8030.30.8041.063100
2.6-2.77.10.61212860.8730.2460.661.083100
2.7-2.87.10.49112970.9110.1980.531.098100
2.8-2.937.20.39212950.9320.1560.4221.09100
2.93-3.097.20.31512970.9520.1260.341.079100
3.09-3.287.10.21613230.9740.0870.2341.084100
3.28-3.537.10.16713070.9830.0670.181.055100
3.53-3.897.10.13413100.9840.0540.1441.08100
3.89-4.456.90.10313320.9890.0430.1121.04299.8
4.45-5.616.90.08913480.9910.0370.0971.09399.8
5.61-506.40.07914530.9930.0330.0861.00599.8

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Processing

Software
NameVersionClassification
PHENIX1.11.1_2575refinement
SCALEPACKdata scaling
PDB_EXTRACT3.24data extraction
HKL-2000data reduction
REFMACphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3Q6X

3q6x
PDB Unreleased entry


Resolution: 2.444→39.624 Å / SU ML: 0.26 / Cross valid method: THROUGHOUT / σ(F): 1.36 / Phase error: 24.78 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2479 774 4.91 %
Rwork0.2025 14977 -
obs0.2048 15751 98.86 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 130.48 Å2 / Biso mean: 54.7791 Å2 / Biso min: 28.48 Å2
Refinement stepCycle: final / Resolution: 2.444→39.624 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3626 0 54 44 3724
Biso mean--72.1 48.26 -
Num. residues----488
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0053762
X-RAY DIFFRACTIONf_angle_d0.995128
X-RAY DIFFRACTIONf_chiral_restr0.099570
X-RAY DIFFRACTIONf_plane_restr0.004682
X-RAY DIFFRACTIONf_dihedral_angle_d3.6592204
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 6

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.444-2.59710.29271090.22862315242493
2.5971-2.79760.33771260.235324792605100
2.7976-3.0790.28891300.221224752605100
3.079-3.52430.26661430.201224982641100
3.5243-4.43930.22161320.18725382670100
4.4393-39.62920.21931340.198526722806100

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