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

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Basic information

Entry
Database: PDB / ID: 8hyb
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 / ACETATE ION / Beta-lactamase
Similarity search - Component
Biological speciesPseudomonas aeruginosa (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.193 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 1.0Jan 24, 2024Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)98,67121
Polymers96,8234
Non-polymers1,84917
Water2,648147
1
A: Beta-lactamase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,7627
Polymers24,2061
Non-polymers5566
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area70 Å2
ΔGint-3 kcal/mol
Surface area10170 Å2
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
Buried area200 Å2
ΔGint-79 kcal/mol
Surface area10150 Å2
MethodPISA
3
C: Beta-lactamase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,6445
Polymers24,2061
Non-polymers4384
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area200 Å2
ΔGint-79 kcal/mol
Surface area10140 Å2
MethodPISA
4
D: Beta-lactamase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,6815
Polymers24,2061
Non-polymers4754
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area110 Å2
ΔGint-6 kcal/mol
Surface area10080 Å2
MethodPISA
Unit cell
Length a, b, c (Å)48.899, 201.103, 52.319
Angle α, β, γ (deg.)90.00, 89.97, 90.00
Int Tables number4
Space group name H-MP1211

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Components

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Protein , 1 types, 4 molecules ABCD

#1: Protein
Beta-lactamase


Mass: 24205.635 Da / Num. of mol.: 4
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

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Non-polymers , 5 types, 164 molecules

#2: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 8 / 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.: 4 / Source method: obtained synthetically / Formula: C12H12N2O2S / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical
ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Formula: C2H3O2
#5: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 147 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 2.66 Å3/Da / Density % sol: 53.71 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: 0.1M Sodium acetate, pH 4.5, 0.2 M Lithium sulfate, 20%-28% (v/v) Polyethylene glycol 8000

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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 17, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.38→19.41 Å / Num. obs: 134737 / % possible obs: 99.93 % / Redundancy: 6.11 % / CC1/2: 0.999 / Rmerge(I) obs: 0.105 / Net I/σ(I): 7.1
Reflection shellResolution: 2.06→2.36 Å / Redundancy: 2.48 % / Rmerge(I) obs: 0.699 / Num. unique obs: 20554 / % possible all: 99.93

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Processing

Software
NameVersionClassification
PHENIX1.10.1_2155refinement
HKL-3000data reduction
PHASERphasing
HKL-3000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.193→19.342 Å / SU ML: 0.24 / Cross valid method: THROUGHOUT / σ(F): 1.85 / Phase error: 27.79 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2272 1002 1.97 %
Rwork0.1772 --
obs0.1782 50923 98.97 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.193→19.342 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6848 0 97 147 7092
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0177157
X-RAY DIFFRACTIONf_angle_d1.1729659
X-RAY DIFFRACTIONf_dihedral_angle_d15.0014153
X-RAY DIFFRACTIONf_chiral_restr0.0611062
X-RAY DIFFRACTIONf_plane_restr0.0081210
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.193-2.30790.28861520.23827193X-RAY DIFFRACTION100
2.3079-2.45230.26971450.21877133X-RAY DIFFRACTION100
2.4523-2.64120.28461500.21777156X-RAY DIFFRACTION100
2.6412-2.90620.3221390.22937170X-RAY DIFFRACTION99
2.9062-3.32480.27571320.19957122X-RAY DIFFRACTION99
3.3248-4.1820.1981470.16477125X-RAY DIFFRACTION99
4.182-19.3420.1751370.13827022X-RAY DIFFRACTION97

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