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- PDB-5sbg: The crystal structure of METP in complex with Zn at a resolution ... -

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Basic information

Entry
Database: PDB / ID: 5sbg
TitleThe crystal structure of METP in complex with Zn at a resolution of 1.34 A.
ComponentsMETP, miniaturized rubredoxin
KeywordsDE NOVO PROTEIN
Biological speciessynthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.338 Å
AuthorsDi Costanzo, L. / La Gatta, S. / Chino, M.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: Nat Commun / Year: 2023
Title: Designed Rubredoxin miniature in a fully artificial electron chain triggered by visible light
Authors: Chino, M. / Di Costanzo, L.F. / Leone, L. / La Gatta, S. / Famulari, A. / Chiesa, M. / Lombardi, A. / Pavone, V.
History
DepositionAug 24, 2021Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 15, 2023Provider: repository / Type: Initial release
Revision 1.1May 17, 2023Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.pdbx_database_id_DOI / _citation.title / _citation.year
Revision 1.2Nov 15, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond
Revision 1.3Apr 3, 2024Group: Refinement description / Category: pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
C: METP, miniaturized rubredoxin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)3,0212
Polymers2,9551
Non-polymers651
Water41423
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)37.663, 55.978, 19.128
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number20
Space group name H-MC2221
Components on special symmetry positions
IDModelComponents
11C-202-

HOH

21C-205-

HOH

31C-220-

HOH

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Components

#1: Protein/peptide METP, miniaturized rubredoxin


Mass: 2955.254 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: chemically synthesized / Source: (synth.) synthetic construct (others)
#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 23 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 1.71 Å3/Da / Density % sol: 27.89 %
Crystal growTemperature: 300 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 0.1 M HEPES, 1.4 M sodium citrate tribasic dihydrate

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ELETTRA / Beamline: 5.2R / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 2M / Detector: CCD / Date: Dec 24, 2020 / Details: mirrors
RadiationMonochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.338→31.249 Å / Num. obs: 8463 / % possible obs: 95.8 % / Observed criterion σ(I): -3 / Redundancy: 2.18 % / CC1/2: 0.995 / Rmerge(I) obs: 0.066 / Rrim(I) all: 0.086 / Net I/σ(I): 7.55
Reflection shellResolution: 1.338→1.42 Å / Redundancy: 2.05 % / Rmerge(I) obs: 0.443 / Mean I/σ(I) obs: 1.48 / Num. unique obs: 1320 / CC1/2: 0.755 / Rrim(I) all: 0.579 / % possible all: 93.5

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Processing

Software
NameVersionClassificationNB
PHENIX1.16_3549refinement
PDB_EXTRACT3.27data extraction
XDSdata reduction
XDSdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: Rosetta, computational model

Resolution: 1.338→31.249 Å / SU ML: 0.07 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 9.81 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1737 266 5.58 %
Rwork0.1309 4504 -
obs0.1328 4770 98.51 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 56.23 Å2 / Biso mean: 17.9366 Å2 / Biso min: 9.85 Å2
Refinement stepCycle: final / Resolution: 1.338→31.249 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms204 0 1 23 228
Biso mean--12.91 26.83 -
Num. residues----30
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 2

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.3377-1.68530.19691400.14682184232498
1.6853-31.2570.16471260.12662320244699

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