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- PDB-9gx9: Crystal structure of CJO-1, a membrane-bound B1 metallo-beta-lact... -

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Basic information

Entry
Database: PDB / ID: 9gx9
TitleCrystal structure of CJO-1, a membrane-bound B1 metallo-beta-lactamase from Chryseobacterium joostei
ComponentsMetallo-beta-lactamase type 2
KeywordsANTIMICROBIAL PROTEIN / NDM-1 / homologue / environmental / MBL / AMR
Function / homology
Function and homology information


antibiotic catabolic process / beta-lactamase / beta-lactamase activity / periplasmic space / response to antibiotic / zinc ion binding
Similarity search - Function
Beta-lactamases class B signature 2. / 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
Biological speciesChryseobacterium joostei (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.34 Å
AuthorsHinchliffe, P. / Spencer, J.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)R01AI100560 United States
CitationJournal: Antimicrob.Agents Chemother. / Year: 2025
Title: Active site loops of membrane-anchored metallo-beta-lactamases from environmental bacteria determine cephalosporinase activity.
Authors: Carnevale, M.C. / Palacios, A.R. / Hinchliffe, P. / Delmonti, J. / Drusin, S.I. / Moreno, D.M. / Bonomo, R.A. / Spencer, J. / Vila, A.J.
History
DepositionSep 28, 2024Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 9, 2025Provider: repository / Type: Initial release

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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)26,6504
Polymers26,4271
Non-polymers2233
Water4,540252
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area480 Å2
ΔGint-77 kcal/mol
Surface area10130 Å2
Unit cell
Length a, b, c (Å)47.517, 68.156, 135.004
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number20
Space group name H-MC2221
Space group name HallC2c2
Symmetry operation#1: x,y,z
#2: x,-y,-z
#3: -x,y,-z+1/2
#4: -x,-y,z+1/2
#5: x+1/2,y+1/2,z
#6: x+1/2,-y+1/2,-z
#7: -x+1/2,y+1/2,-z+1/2
#8: -x+1/2,-y+1/2,z+1/2

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Components

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


Mass: 26426.609 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Chryseobacterium joostei (bacteria) / Gene: SAMN05421768_105265 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0A1N7IHJ9, beta-lactamase
#2: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#3: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 252 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN
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: 2.07 Å3/Da / Density % sol: 40.52 %
Crystal growTemperature: 292.15 K / Method: vapor diffusion, sitting drop
Details: 0.2 M MgCl2, 0.1 M Bis-Tris pH 5.5, 25% (w/v) PEG 3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 1.27012 Å
DetectorType: DECTRIS EIGER2 XE 16M / Detector: PIXEL / Date: Dec 1, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.27012 Å / Relative weight: 1
ReflectionResolution: 1.34→67.502 Å / Num. obs: 39335 / % possible obs: 92.8 % / Redundancy: 12.5 % / Biso Wilson estimate: 15.96 Å2 / CC1/2: 1 / Rpim(I) all: 0.019 / Net I/σ(I): 18.3
Reflection shellResolution: 1.34→1.456 Å / Redundancy: 6.8 % / Mean I/σ(I) obs: 1.5 / Num. unique obs: 1967 / CC1/2: 0.719 / Rpim(I) all: 0.356 / % possible all: 51.9

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Processing

Software
NameVersionClassification
PHENIX1.18.2_3874refinement
autoPROCdata reduction
STARANISOdata scaling
CRANK2phasing
RefinementMethod to determine structure: SAD / Resolution: 1.34→67.5 Å / SU ML: 0.1166 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 21.4013
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.1719 1952 4.96 %
Rwork0.1421 37378 -
obs0.1436 39330 79.8 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 21.83 Å2
Refinement stepCycle: LAST / Resolution: 1.34→67.5 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1815 0 8 252 2075
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00851881
X-RAY DIFFRACTIONf_angle_d1.07362547
X-RAY DIFFRACTIONf_chiral_restr0.0866278
X-RAY DIFFRACTIONf_plane_restr0.0063330
X-RAY DIFFRACTIONf_dihedral_angle_d15.7395685
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.34-1.380.3131150.2799185X-RAY DIFFRACTION5.82
1.38-1.410.2422370.2209542X-RAY DIFFRACTION16.68
1.41-1.460.2481470.20461110X-RAY DIFFRACTION33.41
1.46-1.50.2271860.18632115X-RAY DIFFRACTION63.08
1.5-1.560.22651620.16253128X-RAY DIFFRACTION94.24
1.56-1.620.20581790.1583313X-RAY DIFFRACTION100
1.62-1.690.19531600.14963322X-RAY DIFFRACTION100
1.69-1.780.19821720.14593338X-RAY DIFFRACTION100
1.78-1.890.18361790.13543349X-RAY DIFFRACTION100
1.89-2.040.17171560.12623340X-RAY DIFFRACTION99.97
2.04-2.240.18881830.13383351X-RAY DIFFRACTION100
2.24-2.570.17012070.13463341X-RAY DIFFRACTION100
2.57-3.240.1591890.1393402X-RAY DIFFRACTION100
3.24-67.50.15091800.14493542X-RAY DIFFRACTION99.92

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