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- PDB-8hyc: Crystal structure of B1 NDM-1 MBL in complex with 2-amino-5-(2-(t... -

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Basic information

Entry
Database: PDB / ID: 8hyc
TitleCrystal structure of B1 NDM-1 MBL in complex with 2-amino-5-(2-(thiophen-2-yl)ethyl)thiazole-4-carboxylic acid
ComponentsMetallo-beta-lactamase type 2
KeywordsHYDROLASE / Beta-lactamase class B NDM-1
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-60J / Metallo-beta-lactamase type 2
Similarity search - Component
Biological speciesKlebsiella pneumoniae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.151 Å
AuthorsYan, Y.-H. / Zhu, K.-R. / Li, G.-B.
Funding support China, 3items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)81874291 China
National Natural Science Foundation of China (NSFC)82122065 China
National Natural Science Foundation of China (NSFC)82073698 China
CitationJournal: To Be Published
Title: 2-Aminothiazole-4-carboxylic acids as cross-class metallo-beta-lactamase inhibitors by mimicking beta-lactam hydrolysate binding
Authors: Yan, Y.-H. / Zhu, K.-R. / Yang, L.-L. / Li, G.-B.
History
DepositionJan 6, 2023Deposition site: PDBJ / Processing site: PDBC
Revision 1.0Jun 19, 2024Provider: repository / Type: Initial release

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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)51,9208
Polymers51,1502
Non-polymers7706
Water4,810267
1
A: Metallo-beta-lactamase type 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,9604
Polymers25,5751
Non-polymers3853
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Metallo-beta-lactamase type 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,9604
Polymers25,5751
Non-polymers3853
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)39.053, 78.384, 131.614
Angle α, β, γ (deg.)90.00, 90.00, 90.00
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: 25574.768 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: Depositor stated that they had conducted structure refinement for several times and the Rwork value was still about 0.2493, which may due to the trivial density in asymmetric units.
Source: (gene. exp.) Klebsiella pneumoniae (bacteria) / Gene: blaNDM-1 / Production host: Escherichia coli BL21(DE3) (bacteria) / 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-60J / 2-azanyl-5-(2-thiophen-2-ylethyl)-1,3-thiazole-4-carboxylic acid


Mass: 254.329 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H10N2O2S2 / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 267 / Source method: isolated from a natural source / Formula: H2O
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: 1.97 Å3/Da / Density % sol: 37.54 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: 0.1M Bis-Tris, pH 6.0, 0.2 M Lithium sulfate, 25%-37% (v/v) Polyethylene glycol 3350

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Data collection

DiffractionMean temperature: 195 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS3 X CdTe 1M / Detector: PIXEL / Date: Oct 7, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.1508→19.53 Å / Num. obs: 114363 / % possible obs: 77.6 % / Redundancy: 10.6 % / CC1/2: 0.999 / Net I/σ(I): 9.3
Reflection shellResolution: 1.1508→1.18 Å / Num. unique obs: 1646 / CC1/2: 0.032

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Processing

Software
NameVersionClassification
PHENIX(1.10.1_2155: ???)refinement
HKL-3000data reduction
PHASERphasing
HKL-3000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.151→19.526 Å / SU ML: 0.3 / Cross valid method: THROUGHOUT / σ(F): 1.44 / Phase error: 53.22 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2765 2000 1.8 %
Rwork0.2493 --
obs0.2498 111065 77.24 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.151→19.526 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3594 0 36 267 3897
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0163748
X-RAY DIFFRACTIONf_angle_d1.1475080
X-RAY DIFFRACTIONf_dihedral_angle_d17.5621308
X-RAY DIFFRACTIONf_chiral_restr0.083560
X-RAY DIFFRACTIONf_plane_restr0.008676
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.151-1.17960.6964180.6102981X-RAY DIFFRACTION10
1.1796-1.21150.6209420.62692273X-RAY DIFFRACTION23
1.2115-1.24710.6258730.61094031X-RAY DIFFRACTION40
1.2471-1.28740.62281060.60335736X-RAY DIFFRACTION57
1.2874-1.33340.60061400.58677663X-RAY DIFFRACTION77
1.3334-1.38670.55531710.5499328X-RAY DIFFRACTION93
1.3867-1.44980.51881830.48269975X-RAY DIFFRACTION100
1.4498-1.52620.39151830.41349960X-RAY DIFFRACTION100
1.5262-1.62180.39081850.331810077X-RAY DIFFRACTION100
1.6218-1.7470.33631820.28939954X-RAY DIFFRACTION99
1.747-1.92260.29461830.26269974X-RAY DIFFRACTION99
1.9226-2.20050.25211810.23919866X-RAY DIFFRACTION97
2.2005-2.77110.25391790.22659711X-RAY DIFFRACTION95
2.7711-19.5260.21251740.18349536X-RAY DIFFRACTION90

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