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- PDB-8hxi: Crystal structure of B3 L1 MBL in complex with 2-amino-5-(4-isopr... -

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Basic information

Entry
Database: PDB / ID: 8hxi
TitleCrystal structure of B3 L1 MBL in complex with 2-amino-5-(4-isopropylbenzyl)thiazole-4-carboxylic acid
Components(Metallo-beta-lactamase L1 type ...) x 2
KeywordsHYDROLASE / Beta-lactamase class B L1
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 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-5A5 / THIOCYANATE ION / Metallo-beta-lactamase L1 type 3
Similarity search - Component
Biological speciesStenotrophomonas maltophilia (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.81 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: 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
DepositionJan 4, 2023Deposition site: PDBJ / Processing site: PDBC
Revision 1.0Nov 1, 2023Provider: repository / Type: Initial release
Revision 1.1Oct 23, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Metallo-beta-lactamase L1 type 3
B: Metallo-beta-lactamase L1 type 3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)58,36615
Polymers57,1112
Non-polymers1,25513
Water7,242402
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A: Metallo-beta-lactamase L1 type 3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,0366
Polymers28,5121
Non-polymers5235
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Metallo-beta-lactamase L1 type 3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,3319
Polymers28,5991
Non-polymers7328
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)75.820, 75.820, 184.520
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212
Components on special symmetry positions
IDModelComponents
11A-418-

HOH

21B-404-

HOH

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Components

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Metallo-beta-lactamase L1 type ... , 2 types, 2 molecules AB

#1: Protein Metallo-beta-lactamase L1 type 3 / B3 metallo-beta-lactamase / Beta-lactamase type III / Metallo-beta-lactamase L1 type III / Penicillinase


Mass: 28512.180 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Stenotrophomonas maltophilia (bacteria)
Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P52700, beta-lactamase
#2: Protein Metallo-beta-lactamase L1 type 3 / B3 metallo-beta-lactamase / Beta-lactamase type III / Metallo-beta-lactamase L1 type III / Penicillinase


Mass: 28599.258 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Stenotrophomonas maltophilia (bacteria)
Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P52700, beta-lactamase

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Non-polymers , 5 types, 415 molecules

#3: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Zn
#4: Chemical ChemComp-5A5 / 2-azanyl-5-[(4-propan-2-ylphenyl)methyl]-1,3-thiazole-4-carboxylic acid


Mass: 276.354 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C14H16N2O2S / Feature type: SUBJECT OF INVESTIGATION
#5: Chemical
ChemComp-SCN / THIOCYANATE ION


Mass: 58.082 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: CNS
#6: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 402 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY
Has protein modificationY

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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: 2.32 Å3/Da / Density % sol: 47.02 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: 0.2M Sodium thiocyanate, 16%-22% (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 9, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.81→29.694 Å / Num. obs: 49738 / % possible obs: 99.3 % / Redundancy: 25 % / CC1/2: 1 / Net I/σ(I): 30.1
Reflection shellResolution: 1.81→1.86 Å / Redundancy: 26.5 % / Num. unique obs: 3632 / CC1/2: 0.887

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Processing

Software
NameVersionClassification
PHENIX1.10.1_2155refinement
xia2data reduction
PHASERphasing
xia2data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 7O0O

7o0o


Resolution: 1.81→29.694 Å / SU ML: 0.19 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 24.16 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2153 2000 4.03 %
Rwork0.1748 --
obs0.1765 49634 99.32 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.81→29.694 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4018 0 66 402 4486
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0174224
X-RAY DIFFRACTIONf_angle_d1.1945731
X-RAY DIFFRACTIONf_dihedral_angle_d12.9252492
X-RAY DIFFRACTIONf_chiral_restr0.059628
X-RAY DIFFRACTIONf_plane_restr0.008753
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.81-1.85530.2941410.24213360X-RAY DIFFRACTION100
1.8553-1.90540.3511400.27273339X-RAY DIFFRACTION100
1.9054-1.96150.37381330.32733145X-RAY DIFFRACTION94
1.9615-2.02480.27071420.21983380X-RAY DIFFRACTION100
2.0248-2.09710.28111400.23333336X-RAY DIFFRACTION98
2.0971-2.18110.26131410.19813367X-RAY DIFFRACTION100
2.1811-2.28030.24341410.21963356X-RAY DIFFRACTION99
2.2803-2.40050.21561420.18553385X-RAY DIFFRACTION100
2.4005-2.55080.25331430.1923410X-RAY DIFFRACTION100
2.5508-2.74760.2991440.19513431X-RAY DIFFRACTION100
2.7476-3.02390.23271450.18473446X-RAY DIFFRACTION100
3.0239-3.46090.20641450.17133455X-RAY DIFFRACTION100
3.4609-4.35820.17721470.13653510X-RAY DIFFRACTION100
4.3582-29.6940.15861560.14243714X-RAY DIFFRACTION100

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