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- PDB-9g3b: Crystal Structure of the artificial protein METP in complex with ... -

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Basic information

Entry
Database: PDB / ID: 9g3b
TitleCrystal Structure of the artificial protein METP in complex with cadmium ion at different temperature, 130 K
ComponentsMETP ARTIFICIAL PROTEIN
KeywordsDE NOVO PROTEIN / de novo design / room temperature / cadmium-sulphur cluster / denovo protein
Function / homology:
Function and homology information
Biological speciessynthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.9 Å
AuthorsDi Costanzo, L. / La Gatta, S. / Chino, M.
Funding support Italy, 1items
OrganizationGrant numberCountry
NextGenerationEU-MUR PNRR Extended Partnership initiative on Emerging Infectious Diseases (INF-ACT)CUP H53D23007950001 Italy
CitationJournal: J.Inorg.Biochem. / Year: 2025
Title: Structural insights into temperature-dependent dynamics of METPsc1, a miniaturized electron-transfer protein.
Authors: Di Costanzo, L.F. / Sgueglia, G. / Orlando, C. / Polentarutti, M. / Leone, L. / La Gatta, S. / De Fenza, M. / De Gioia, L. / Lombardi, A. / Arrigoni, F. / Chino, M.
History
DepositionJul 12, 2024Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 4, 2024Provider: repository / Type: Initial release
Revision 1.1Jan 22, 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.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
C: METP ARTIFICIAL PROTEIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)3,0682
Polymers2,9551
Non-polymers1121
Water32418
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: monomer
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)34.419, 56.352, 19.148
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
Components on special symmetry positions
IDModelComponents
11C-210-

HOH

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Components

#1: Protein/peptide METP ARTIFICIAL PROTEIN


Mass: 2955.254 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#2: Chemical ChemComp-CD / CADMIUM ION


Mass: 112.411 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cd / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 18 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
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: 2.8 Å3/Da / Density % sol: 56.6 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: drop containing 2.0 μL of 1:1 (v/v) mixture of protein solution (10 mg/mL, 7 mM DTT, 4 mM CdCl2) and 2.0 μL of precipitant buffer (0.1 M HEPES at pH 7.5, 1.4 M sodium citrate ...Details: drop containing 2.0 μL of 1:1 (v/v) mixture of protein solution (10 mg/mL, 7 mM DTT, 4 mM CdCl2) and 2.0 μL of precipitant buffer (0.1 M HEPES at pH 7.5, 1.4 M sodium citrate tribasic dihydrate) was equilibrated against 0.5 mL reservoir of precipitant buffer

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ELETTRA / Beamline: 5.2R / Wavelength: 0.534 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Jan 1, 2000
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.534 Å / Relative weight: 1
ReflectionResolution: 1.7→29.37 Å / Num. obs: 8740 / % possible obs: 95.1 % / Redundancy: 2.2 % / Biso Wilson estimate: 15.15 Å2 / CC1/2: 0.995 / Rmerge(I) obs: 0.079 / Net I/σ(I): 8.82
Reflection shellResolution: 1.7→1.8 Å / Num. unique obs: 450 / CC1/2: 0.903 / % possible all: 96.3

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Processing

Software
NameVersionClassification
PHENIX1.21_5207refinement
SCALAdata scaling
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: SAD / Resolution: 1.9→29.37 Å / SU ML: 0.2588 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 9.8902
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rwork0.1435 1513 -
obs0.1489 1585 98.08 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 20.31 Å2
Refinement stepCycle: LAST / Resolution: 1.9→29.37 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms204 0 1 18 223
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0127204
X-RAY DIFFRACTIONf_angle_d1.3349276
X-RAY DIFFRACTIONf_chiral_restr0.084525
X-RAY DIFFRACTIONf_plane_restr0.013538
X-RAY DIFFRACTIONf_dihedral_angle_d17.328874
LS refinement shellResolution: 1.9→29.37 Å
RfactorNum. reflection% reflection
Rwork0.1435 1513 -
obs--98.08 %

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