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- PDB-9c5p: Inhibitor bound VIM1 -

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Basic information

Entry
Database: PDB / ID: 9c5p
TitleInhibitor bound VIM1
ComponentsMetallo-beta-lactamase type 2
KeywordsHYDROLASE
Function / homology
Function and homology information


antibiotic catabolic process / beta-lactamase / hydrolase activity
Similarity search - Function
: / : / Metallo-beta-lactamase superfamily / Metallo-beta-lactamase superfamily / Metallo-beta-lactamase / Ribonuclease Z/Hydroxyacylglutathione hydrolase-like
Similarity search - Domain/homology
: / Metallo-beta-lactamase type 2
Similarity search - Component
Biological speciesPseudomonas aeruginosa (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 1.15 Å
AuthorsFischmann, T.O. / Scapin, G.
Funding support1items
OrganizationGrant numberCountry
Not funded
Citation
Journal: Bioorg.Med.Chem.Lett. / Year: 2024
Title: Discovery of sulfone containing metallo-beta-lactamase inhibitors with reduced bacterial cell efflux and histamine release issues.
Authors: Bennett, F. / Huang, Y. / Dong, S. / Jiang, J. / Hunter, D. / Zhao, Z. / Gu, X. / Scott, J.D. / Tang, H. / Yang, D. / Xiao, L. / Scapin, G. / Fischmann, T. / Mirza, A. / Dayananth, P. / ...Authors: Bennett, F. / Huang, Y. / Dong, S. / Jiang, J. / Hunter, D. / Zhao, Z. / Gu, X. / Scott, J.D. / Tang, H. / Yang, D. / Xiao, L. / Scapin, G. / Fischmann, T. / Mirza, A. / Dayananth, P. / Painter, R.E. / Villafania, A. / Garlisi, C.G. / Zhang, R. / Mayhood, T.W. / Si, Q. / Li, N. / Amin, R.P. / Chen, F. / Bhatt, B. / Regan, C.P. / Regan, H. / Lin, X. / Wu, J. / Leithead, A. / Young, K. / Pasternak, A.
#1: Journal: BMCL / Year: 2024
Title: Discovery of sulfone containing metallo-beta-lactamase inhibitors with reduced bacterial cell efflux and histamine release issues
Authors: Bennett, F. / Huang, Y. / Dong, S. / Jiang, J. / Hunter, D.N. / Zhao, Z. / Gu, X. / Scott, J.D. / Tang, H. / Xiao, L. / Scapin, G. / Fischmann, T. / Mirza, A. / Dayananth, P. / Painter, R.E. ...Authors: Bennett, F. / Huang, Y. / Dong, S. / Jiang, J. / Hunter, D.N. / Zhao, Z. / Gu, X. / Scott, J.D. / Tang, H. / Xiao, L. / Scapin, G. / Fischmann, T. / Mirza, A. / Dayananth, P. / Painter, R.E. / Villafania, A. / Garlisi, C.G. / Zhang, R. / Mayhood, T.W. / Si, Q. / Li, N. / Amin, R.P. / Chen, F. / Bhatt, B. / Regan, C.P. / Regan, H. / Lin, X. / Wu, J. / Leithead, A. / Black, T. / Young, K. / Pasternak, A.
History
DepositionJun 6, 2024Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 16, 2024Provider: repository / Type: Initial release
Revision 1.1Oct 30, 2024Group: Database references / Category: citation / citation_author

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Metallo-beta-lactamase type 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,7535
Polymers26,0661
Non-polymers6874
Water5,729318
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)39.610, 67.880, 40.170
Angle α, β, γ (deg.)90.00, 91.44, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Metallo-beta-lactamase type 2 / B2 metallo-beta-lactamase / Metallo-beta-lactamase type II


Mass: 26065.904 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas aeruginosa (bacteria) / Gene: vim5 / Production host: Escherichia coli (E. coli) / References: UniProt: Q70GD3, beta-lactamase
#2: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#3: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#4: Chemical ChemComp-A1AUQ / (2M)-4-(piperidine-4-sulfonyl)-4'-(piperidin-4-yl)-2-(1H-tetrazol-5-yl)[1,1'-biphenyl]-3-sulfonamide


Mass: 531.651 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C23H29N7O4S2 / Feature type: SUBJECT OF INVESTIGATION
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 318 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationN

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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: 2.07 Å3/Da / Density % sol: 40.61 %
Crystal growTemperature: 300 K / Method: vapor diffusion, sitting drop
Details: 25% Peg 3350, 200 mM MgCl2, 100 mM Tris-Cl pH=8.5, 1 mM TCEP

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 17-ID / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Aug 22, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.15→67.884 Å / Num. obs: 72070 / % possible obs: 95.8 % / Redundancy: 3.3 % / Rmerge(I) obs: 0.037 / Rpim(I) all: 0.024 / Rrim(I) all: 0.044 / Net I/σ(I): 17.9
Reflection shellResolution: 1.15→1.154 Å / Redundancy: 3.2 % / Rmerge(I) obs: 0.529 / Mean I/σ(I) obs: 2.1 / Num. unique obs: 2271 / Rpim(I) all: 0.343 / Rrim(I) all: 0.633 / % possible all: 94.4

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Processing

Software
NameVersionClassification
BUSTER2.11.5refinement
XDSdata reduction
Aimlessdata scaling
BUSTERphasing
RefinementMethod to determine structure: FOURIER SYNTHESIS / Resolution: 1.15→16.84 Å / Cor.coef. Fo:Fc: 0.9693 / Cor.coef. Fo:Fc free: 0.96 / SU R Cruickshank DPI: 0.033 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.034 / SU Rfree Blow DPI: 0.036 / SU Rfree Cruickshank DPI: 0.035
RfactorNum. reflection% reflectionSelection details
Rfree0.1754 3619 5.02 %RANDOM
Rwork0.1548 ---
obs0.1559 72027 95.7 %-
Displacement parametersBiso mean: 17.79 Å2
Baniso -1Baniso -2Baniso -3
1--1.959 Å20 Å20.5373 Å2
2--0.0856 Å20 Å2
3---1.8734 Å2
Refine analyzeLuzzati coordinate error obs: 0.124 Å
Refinement stepCycle: 1 / Resolution: 1.15→16.84 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1751 0 39 318 2108
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.011839HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.112534HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d614SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes44HARMONIC2
X-RAY DIFFRACTIONt_gen_planes301HARMONIC5
X-RAY DIFFRACTIONt_it1839HARMONIC20
X-RAY DIFFRACTIONt_nbd4SEMIHARMONIC5
X-RAY DIFFRACTIONt_omega_torsion4.84
X-RAY DIFFRACTIONt_other_torsion15.04
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion239SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact2397SEMIHARMONIC4
LS refinement shellResolution: 1.15→1.18 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.2107 261 5.11 %
Rwork0.1947 4846 -
all0.1955 5107 -
obs--95.7 %
Refinement TLS params.Method: refined / Origin x: -16.8936 Å / Origin y: -2.5216 Å / Origin z: -5.3031 Å
111213212223313233
T-0.0427 Å2-0.0064 Å20.0036 Å2--0.0311 Å2-0.0016 Å2---0.0204 Å2
L0.6698 °2-0.191 °2-0.0935 °2-0.7857 °20.1518 °2--0.8576 °2
S-0.0142 Å °0.0013 Å °0.0298 Å °-0.0451 Å °0.0228 Å °-0.0615 Å °-0.0219 Å °0.0328 Å °-0.0086 Å °
Refinement TLS groupSelection details: { A|* }

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