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- PDB-9ic4: Crystal structure of beta-lactamase-like domain of ComEC from Moo... -

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Basic information

Entry
Database: PDB / ID: 9ic4
TitleCrystal structure of beta-lactamase-like domain of ComEC from Moorella glycerini
ComponentsCompetence protein
KeywordsMETAL BINDING PROTEIN / Deoxyribonuclease / Metallo-beta-lactamase / DNA translocation / Natural transformation
Function / homology
Function and homology information


establishment of competence for transformation / plasma membrane
Similarity search - Function
ComEC/Rec2-related protein / Competence protein ComEC/Rec2 / Domain of unknown function DUF4131 / Competence protein / Domain of unknown function (DUF4131) / ComA-like, MBL domain / : / Metallo-beta-lactamase superfamily / Metallo-beta-lactamase superfamily / Metallo-beta-lactamase / Ribonuclease Z/Hydroxyacylglutathione hydrolase-like
Similarity search - Domain/homology
PHOSPHATE ION / Competence protein
Similarity search - Component
Biological speciesNeomoorella glycerini (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.86 Å
AuthorsStedman, M.J.M. / Wang, D. / Hospenthal, M.K.
Funding support Switzerland, 1items
OrganizationGrant numberCountry
Swiss National Science FoundationPR00P3_179728 Switzerland
CitationJournal: Nucleic Acids Res. / Year: 2025
Title: Molecular interplay between ComEC domains allows for selective degradation of the non-translocating strand during natural transformation.
Authors: Stedman, M.J.M. / Deselaers, S. / Braus, S.A.G. / Wang, D. / Balaguer, M.G. / Gossert, A.D. / Hospenthal, M.K.
History
DepositionFeb 14, 2025Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 1, 2025Provider: repository / Type: Initial release
Revision 1.1Oct 8, 2025Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.identifier_ORCID

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Competence protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,2042
Polymers29,1091
Non-polymers951
Water2,486138
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)80.957, 96.849, 71.719
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 Competence protein


Mass: 29108.957 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Neomoorella glycerini (bacteria) / Gene: MGLY_18620 / Plasmid: pOPINS / Production host: Escherichia coli BL21 (bacteria) / References: UniProt: A0A6I5ZRL0
#2: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: PO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 138 / Source method: isolated from a natural source / Formula: H2O
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: 2.41 Å3/Da / Density % sol: 49.06 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 30% (w/v) precipitant mix 1 (PEG 500 MME, PEG 20000), 0.1 M buffer system 1 (1M MES and 1M imidazole mixed in 56:44 ratio to achieve pH 6.5), 0.09 M NPS mix (0.3 M sodium phosphate dibasic ...Details: 30% (w/v) precipitant mix 1 (PEG 500 MME, PEG 20000), 0.1 M buffer system 1 (1M MES and 1M imidazole mixed in 56:44 ratio to achieve pH 6.5), 0.09 M NPS mix (0.3 M sodium phosphate dibasic dihydrate, 0.3 M ammonium sulfate, 0.3 M sodium nitrate)

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 0.999989 Å
DetectorType: DECTRIS EIGER2 S 16M / Detector: PIXEL / Date: Dec 12, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.999989 Å / Relative weight: 1
ReflectionResolution: 1.86→62.11 Å / Num. obs: 23812 / % possible obs: 99.52 % / Redundancy: 6.6 % / Biso Wilson estimate: 22.46 Å2 / Rmerge(I) obs: 0.069 / Net I/σ(I): 13.7
Reflection shellResolution: 1.86→1.9 Å / Rmerge(I) obs: 0.352 / Mean I/σ(I) obs: 4.6 / Num. unique obs: 2457 / % possible all: 99.16

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Processing

Software
NameVersionClassification
PHENIX1.21.2_5419refinement
MOSFLMdata reduction
Aimlessdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.86→62.11 Å / SU ML: 0.1789 / Cross valid method: FREE R-VALUE / σ(F): 1.91 / Phase error: 17.5443
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2029 1193 5.01 %
Rwork0.1695 22619 -
obs0.1712 23812 99.52 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 29.39 Å2
Refinement stepCycle: LAST / Resolution: 1.86→62.11 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2053 0 5 138 2196
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00522115
X-RAY DIFFRACTIONf_angle_d0.88052880
X-RAY DIFFRACTIONf_chiral_restr0.0553318
X-RAY DIFFRACTIONf_plane_restr0.0096385
X-RAY DIFFRACTIONf_dihedral_angle_d15.0593780
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.86-1.940.24151320.2112457X-RAY DIFFRACTION99.16
1.94-2.030.19471310.17252484X-RAY DIFFRACTION99.81
2.03-2.130.22351320.16642498X-RAY DIFFRACTION99.89
2.13-2.270.2191310.1642481X-RAY DIFFRACTION99.2
2.27-2.440.17871320.15742485X-RAY DIFFRACTION99.85
2.44-2.690.22081320.16062514X-RAY DIFFRACTION99.92
2.69-3.080.24881320.1832532X-RAY DIFFRACTION99.89
3.08-3.870.20951320.17282534X-RAY DIFFRACTION99.11
3.87-62.110.16541390.16312634X-RAY DIFFRACTION98.93

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