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- PDB-9gx8: Crystal structure of CIM-2, a membrane-bound B1 metallo-beta-lact... -

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Basic information

Entry
Database: PDB / ID: 9gx8
TitleCrystal structure of CIM-2, a membrane-bound B1 metallo-beta-lactamase from Chryseobacterium indologenes
ComponentsMetallo-beta-lactamase type 2
KeywordsANTIMICROBIAL PROTEIN / NDM-1 / homologue / environmental / MBL / AMR
Function / homology
Function and homology information


: / Metallo-beta-lactamase superfamily / Metallo-beta-lactamase superfamily / Metallo-beta-lactamase / Ribonuclease Z/Hydroxyacylglutathione hydrolase-like / Prokaryotic membrane lipoprotein lipid attachment site profile.
Similarity search - Domain/homology
ISOPROPYL ALCOHOL / R-1,2-PROPANEDIOL / Subclass B1 metallo-beta-lactamase
Similarity search - Component
Biological speciesChryseobacterium indologenes (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.56 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

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)52,53313
Polymers51,7682
Non-polymers76511
Water8,017445
1
A: Metallo-beta-lactamase type 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,2296
Polymers25,8841
Non-polymers3455
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Metallo-beta-lactamase type 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,3057
Polymers25,8841
Non-polymers4216
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)164.287, 43.131, 75.691
Angle α, β, γ (deg.)90.000, 115.959, 90.000
Int Tables number5
Space group name H-MC121
Space group name HallC2y
Symmetry operation#1: x,y,z
#2: -x,y,-z
#3: x+1/2,y+1/2,z
#4: -x+1/2,y+1/2,-z

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Components

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Protein , 1 types, 2 molecules AB

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


Mass: 25884.088 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Chryseobacterium indologenes (bacteria)
Gene: AOB46_06505 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A0N0IX17, beta-lactamase

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Non-polymers , 6 types, 456 molecules

#2: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Zn
#3: Chemical ChemComp-MPD / (4S)-2-METHYL-2,4-PENTANEDIOL


Mass: 118.174 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H14O2 / Comment: precipitant*YM
#4: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#5: Chemical ChemComp-IPA / ISOPROPYL ALCOHOL / 2-PROPANOL


Mass: 60.095 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O / Comment: alkaloid*YM
#6: Chemical ChemComp-PGR / R-1,2-PROPANEDIOL


Mass: 76.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O2
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 445 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestN
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: 2.33 Å3/Da / Density % sol: 47.18 %
Crystal growTemperature: 292.15 K / Method: vapor diffusion, sitting drop
Details: 0.1M Tris/Bicine pH8.5, 0.12 M (1,6-Hexanediol, 1-Butanol, 1,2-Propanediol, 2-Propanol, 1,4-Butanediol, 1,3-Propanediol), 37.5% (MPD, PEG1000, Peg3350)

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 1.27021 Å
DetectorType: DECTRIS EIGER2 XE 16M / Detector: PIXEL / Date: Feb 3, 2024
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.27021 Å / Relative weight: 1
ReflectionResolution: 1.56→73.86 Å / Num. obs: 67879 / % possible obs: 99.2 % / Redundancy: 6.7 % / Biso Wilson estimate: 23.51 Å2 / CC1/2: 0.998 / Rpim(I) all: 0.044 / Net I/σ(I): 12
Reflection shellResolution: 1.56→1.59 Å / Mean I/σ(I) obs: 0.5 / Num. unique obs: 3287 / CC1/2: 0.283 / Rpim(I) all: 1.053 / % possible all: 96.5

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Processing

Software
NameVersionClassification
PHENIX1.18.2_3874refinement
DIALSdata reduction
DIALSdata scaling
CRANK2phasing
RefinementMethod to determine structure: SAD / Resolution: 1.56→41.76 Å / SU ML: 0.2448 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 23.4419
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.1946 1941 2.87 %
Rwork0.168 65639 -
obs0.1687 67580 98.72 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 30.14 Å2
Refinement stepCycle: LAST / Resolution: 1.56→41.76 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3526 0 35 445 4006
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00573764
X-RAY DIFFRACTIONf_angle_d0.78325112
X-RAY DIFFRACTIONf_chiral_restr0.0562558
X-RAY DIFFRACTIONf_plane_restr0.0044665
X-RAY DIFFRACTIONf_dihedral_angle_d23.97261357
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.56-1.60.40961200.37424420X-RAY DIFFRACTION93.2
1.6-1.640.35391110.32194693X-RAY DIFFRACTION99.15
1.64-1.690.30351160.28014689X-RAY DIFFRACTION99.46
1.69-1.740.28621270.25514692X-RAY DIFFRACTION98.99
1.74-1.810.26461430.2414682X-RAY DIFFRACTION98.83
1.81-1.880.27881320.22014626X-RAY DIFFRACTION98.35
1.88-1.960.20591530.18064672X-RAY DIFFRACTION99.1
1.96-2.070.18891690.16834664X-RAY DIFFRACTION99.42
2.07-2.20.21421600.16654686X-RAY DIFFRACTION99.63
2.2-2.370.19671380.16184711X-RAY DIFFRACTION99.14
2.37-2.610.19161280.16264685X-RAY DIFFRACTION98.24
2.61-2.980.18181580.15644748X-RAY DIFFRACTION100
2.98-3.760.15651430.13884801X-RAY DIFFRACTION99.84
3.76-41.760.16971430.14254870X-RAY DIFFRACTION98.8

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