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- PDB-8jao: Crystal structure of B1 IMP-1 MBL in complex with 2-amino-5-phene... -

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Basic information

Entry
Database: PDB / ID: 8jao
TitleCrystal structure of B1 IMP-1 MBL in complex with 2-amino-5-phenethylthiazole-4-carboxylic acid
ComponentsBeta-lactamase
KeywordsHYDROLASE / Beta-lactamase class B IMP-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
Beta-lactamases class B signature 2. / Beta-lactamases class B signature 1. / Beta-lactamase, class-B, conserved site / : / Metallo-beta-lactamase superfamily / Metallo-beta-lactamase superfamily / Metallo-beta-lactamase / Ribonuclease Z/Hydroxyacylglutathione hydrolase-like
Similarity search - Domain/homology
Chem-5ZX / Beta-lactamase
Similarity search - Component
Biological speciesPseudomonas aeruginosa (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.194 Å
AuthorsYan, Y.-H. / 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: J.Med.Chem. / Year: 2023
Title: Discovery of 2-Aminothiazole-4-carboxylic Acids as Broad-Spectrum Metallo-beta-lactamase Inhibitors by Mimicking Carbapenem Hydrolysate Binding.
Authors: Yan, Y.H. / Zhang, T.T. / Li, R. / Wang, S.Y. / Wei, L.L. / Wang, X.Y. / Zhu, K.R. / Li, S.R. / Liang, G.Q. / Yang, Z.B. / Yang, L.L. / Qin, S. / Li, G.B.
History
DepositionMay 6, 2023Deposition site: PDBJ / Processing site: PDBC
Revision 1.0Nov 1, 2023Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)49,1708
Polymers48,4112
Non-polymers7586
Water3,081171
1
A: Beta-lactamase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,5854
Polymers24,2061
Non-polymers3793
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Beta-lactamase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,5854
Polymers24,2061
Non-polymers3793
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)48.758, 52.231, 200.973
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 Beta-lactamase


Mass: 24205.635 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas aeruginosa (bacteria) / Gene: blaIMP-1, bla IMP, bla-imp, blaESP, imp / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q79MP6, 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-5ZX / 2-azanyl-5-(2-phenylethyl)-1,3-thiazole-4-carboxylic acid


Mass: 248.301 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C12H12N2O2S / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 171 / 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: 2.64 Å3/Da / Density % sol: 53.46 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: 0.1M sodium acetate pH 4.5, 20-28% PEG8000, 0.2M lithium sulfate

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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: Apr 12, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.2→50 Å / Num. obs: 27187 / % possible obs: 100 % / Redundancy: 12.8 % / CC1/2: 0.958 / Net I/σ(I): 7.8
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2CC starRpim(I) allRrim(I) allΧ2% possible all
2.2-2.2413.10.6713170.9580.9890.190.6970.876100
2.24-2.2813.20.59513380.9660.9910.1690.6190.871100
2.28-2.3212.90.5413490.9710.9930.1560.5630.887100
2.32-2.3712.80.45913180.9780.9940.1330.4780.9100
2.37-2.4212.40.37513200.9760.9940.1110.3910.929100
2.42-2.48120.32213460.9850.9960.0960.3360.925100
2.48-2.5412.50.29513300.9840.9960.0860.3070.927100
2.54-2.6113.50.26213480.990.9970.0740.2720.939100
2.61-2.6913.40.23513330.990.9970.0660.2440.951100
2.69-2.7713.30.19613630.9920.9980.0550.2040.958100
2.77-2.8713.20.16913500.9940.9980.0480.1761.002100
2.87-2.9913.20.1413300.9960.9990.040.1451.021100
2.99-3.1212.50.11313560.9960.9990.0330.1181.102100
3.12-3.2912.10.09813660.9970.9990.0290.1021.15399.9
3.29-3.4913.50.08313640.9970.9990.0230.0861.086100
3.49-3.7613.40.07313720.9980.9990.0210.0761.045100
3.76-4.1413.10.06613580.9980.9990.0190.0690.93199.9
4.14-4.7411.90.0613990.99810.0180.0630.88699.9
4.74-5.9712.80.05414120.99810.0160.0570.768100
5.97-5011.50.0615180.99810.0180.0630.82799.7

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Processing

Software
NameVersionClassification
PHENIX1.10.1-2155refinement
HKL-2000data reduction
PHASERphasing
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 7YH9

7yh9


Resolution: 2.194→26.668 Å / SU ML: 0.23 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 23.43 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2288 1985 7.4 %
Rwork0.1787 --
obs0.1825 26833 98.63 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.194→26.668 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3424 0 38 171 3633
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0183567
X-RAY DIFFRACTIONf_angle_d1.1534814
X-RAY DIFFRACTIONf_dihedral_angle_d17.0822074
X-RAY DIFFRACTIONf_chiral_restr0.059530
X-RAY DIFFRACTIONf_plane_restr0.007602
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.194-2.24860.28671070.2291517X-RAY DIFFRACTION84
2.2486-2.30930.29371420.21771737X-RAY DIFFRACTION99
2.3093-2.37720.25681360.20071757X-RAY DIFFRACTION99
2.3772-2.45390.22431480.19141772X-RAY DIFFRACTION100
2.4539-2.54160.25521410.19351749X-RAY DIFFRACTION100
2.5416-2.64320.2311370.19561783X-RAY DIFFRACTION100
2.6432-2.76340.33181430.19551783X-RAY DIFFRACTION100
2.7634-2.90890.27951470.21221772X-RAY DIFFRACTION100
2.9089-3.09090.23021420.18291795X-RAY DIFFRACTION100
3.0909-3.32920.25671410.18631782X-RAY DIFFRACTION100
3.3292-3.66340.22461450.1721784X-RAY DIFFRACTION100
3.6634-4.19180.20531510.16691816X-RAY DIFFRACTION99
4.1918-5.27450.20071480.13711856X-RAY DIFFRACTION100
5.2745-26.6680.17781570.17441945X-RAY DIFFRACTION100

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