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- PDB-7yha: Crystal structure of IMP-1 MBL in complex with (3-(4-(p-tolyl)-1H... -

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Basic information

Entry
Database: PDB / ID: 7yha
TitleCrystal structure of IMP-1 MBL in complex with (3-(4-(p-tolyl)-1H-1,2,3-triazol-1-yl)benzyl)phosphonic acid
ComponentsBeta-lactamase class B IMP-1
KeywordsHYDROLASE/INHIBITOR / Metallo-beta-lactamase IMP-1 / HYDROLASE / HYDROLASE-INHIBITOR complex
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 / Ribonuclease Z/Hydroxyacylglutathione hydrolase-like / Metallo-beta-lactamase superfamily / Metallo-beta-lactamase; Chain A / Metallo-beta-lactamase / Ribonuclease Z/Hydroxyacylglutathione hydrolase-like ...Beta-lactamases class B signature 2. / Beta-lactamases class B signature 1. / Beta-lactamase, class-B, conserved site / : / Metallo-beta-lactamase superfamily / Ribonuclease Z/Hydroxyacylglutathione hydrolase-like / Metallo-beta-lactamase superfamily / Metallo-beta-lactamase; Chain A / Metallo-beta-lactamase / Ribonuclease Z/Hydroxyacylglutathione hydrolase-like / 4-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Chem-ITK / Beta-lactamase
Similarity search - Component
Biological speciesPseudomonas aeruginosa (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.135 Å
AuthorsLi, G.-B. / Yan, Y.-H.
Funding support China, 3items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)82122065 China
National Natural Science Foundation of China (NSFC)82073698 China
National Natural Science Foundation of China (NSFC)81874291 China
CitationJournal: Eur.J.Med.Chem. / Year: 2023
Title: Metal binding pharmacophore click-derived discovery of new broad-spectrum metallo-beta-lactamase inhibitors.
Authors: Yan, Y.H. / Ding, H.S. / Zhu, K.R. / Mu, B.S. / Zheng, Y. / Huang, M.Y. / Zhou, C. / Li, W.F. / Wang, Z. / Wu, Y. / Li, G.B.
History
DepositionJul 13, 2022Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jun 7, 2023Provider: repository / Type: Initial release
Revision 1.1Nov 29, 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: Beta-lactamase class B IMP-1
B: Beta-lactamase class B IMP-1
C: Beta-lactamase class B IMP-1
D: Beta-lactamase class B IMP-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)99,98020
Polymers96,8234
Non-polymers3,15816
Water7,476415
1
A: Beta-lactamase class B IMP-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,9955
Polymers24,2061
Non-polymers7894
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Beta-lactamase class B IMP-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,9955
Polymers24,2061
Non-polymers7894
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Beta-lactamase class B IMP-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,9955
Polymers24,2061
Non-polymers7894
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: Beta-lactamase class B IMP-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,9955
Polymers24,2061
Non-polymers7894
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)51.915, 104.938, 103.686
Angle α, β, γ (deg.)90.000, 94.610, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
Beta-lactamase class B IMP-1


Mass: 24205.635 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Details: Pseudomonas aeruginosa / 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.: 8 / Source method: obtained synthetically / Formula: Zn
#3: Chemical
ChemComp-ITK / [3-[4-(4-methylphenyl)-1,2,3-triazol-1-yl]phenyl]methylphosphonic acid


Mass: 329.290 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C16H16N3O3P / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 415 / 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: 2.88 Å3/Da / Density % sol: 57.28 %
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 27, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.135→50 Å / Num. obs: 60655 / % possible obs: 100 % / Redundancy: 6.8 % / Biso Wilson estimate: 25.79 Å2 / Rmerge(I) obs: 0.205 / Rpim(I) all: 0.085 / Rrim(I) all: 0.218 / Χ2: 0.752 / Net I/σ(I): 2.4
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allΧ2% possible allRrim(I) all
2.15-2.196.80.95430340.8410.3950.571100
2.19-2.236.90.85329960.8580.350.6081000.923
2.23-2.276.90.7630510.8770.3120.6141000.822
2.27-2.326.80.72529690.8890.30.6381000.786
2.32-2.376.80.61130540.8960.2540.6581000.663
2.37-2.426.50.55630160.9250.2350.6711000.605
2.42-2.486.40.49730370.9340.2110.6981000.541
2.48-2.556.70.43930140.950.1840.6951000.477
2.55-2.627.10.40330300.9570.1630.6861000.435
2.62-2.717.10.35329850.9670.1430.6911000.381
2.71-2.8170.31630420.9670.1280.7141000.341
2.81-2.9270.28730380.9710.1160.741000.31
2.92-3.056.90.25630370.9740.1050.8061000.277
3.05-3.216.50.21730170.9680.0920.8631000.236
3.21-3.416.90.19230300.9790.0790.891000.208
3.41-3.687.20.17230410.9860.0690.8781000.186
3.68-4.057.10.16130500.9820.0660.9141000.174
4.05-4.636.60.15430370.9820.0640.9691000.167
4.63-5.836.90.14730800.9860.060.9151000.159
5.83-506.70.1430970.9880.0590.80799.70.152

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Phasing

PhasingMethod: molecular replacement
Phasing MR
Highest resolutionLowest resolution
Rotation6.12 Å36.84 Å
Translation6.12 Å36.84 Å

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Processing

Software
NameVersionClassification
PHENIX1.10.1refinement
SCALEPACKdata scaling
PHASER2.6.0phasing
PDB_EXTRACT3.27data extraction
HKL-2000data reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1DDK

1ddk


Resolution: 2.135→29.803 Å / SU ML: 0.29 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 44.04 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.3052 2046 3.51 %
Rwork0.2602 56167 -
obs0.2619 58213 94.67 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 74.32 Å2 / Biso mean: 29.0893 Å2 / Biso min: 9.48 Å2
Refinement stepCycle: final / Resolution: 2.135→29.803 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6848 0 192 415 7455
Biso mean--26.05 30.58 -
Num. residues----876
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0167264
X-RAY DIFFRACTIONf_angle_d0.9559820
X-RAY DIFFRACTIONf_chiral_restr0.0551060
X-RAY DIFFRACTIONf_plane_restr0.0061216
X-RAY DIFFRACTIONf_dihedral_angle_d16.8014164
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.135-2.18450.3917880.3412244962
2.1845-2.23910.37021170.3255342886
2.2391-2.29960.38361520.3192357592
2.2996-2.36720.371230.2952380396
2.3672-2.44360.35021490.283387498
2.4436-2.53090.35981440.2692385198
2.5309-2.63220.34511280.2661393999
2.6322-2.75190.32771450.2583393899
2.7519-2.89690.26251530.26483939100
2.8969-3.07820.32851320.2635392199
3.0782-3.31560.29811310.2604390099
3.3156-3.64870.29951430.238393299
3.6487-4.17550.31611440.2319393299
4.1755-5.25590.24021500.2295394099
5.2559-29.8030.26481470.259374693

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