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

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Basic information

Entry
Database: PDB / ID: 5sbj
TitleThe crystal structure of METP in complex with Cd at a resolution of 1.29 A.
ComponentsMETP, miniaturized rubredoxin
KeywordsDE NOVO PROTEIN
Function / homology:
Function and homology information
Biological speciessynthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.28 Å
AuthorsDi Costanzo, L. / La Gatta, S. / Pavone, V.
CitationJournal: To be published
Title: Miniaturization process reloaded - structural and functional insights from a miniaturized rubredoxin
Authors: Chino, M. / Di Costanzo, L.
History
DepositionAug 24, 2021Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 15, 2023Provider: repository / Type: Initial release
Revision 1.1Nov 15, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond
Revision 1.2Apr 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)3,0682
Polymers2,9551
Non-polymers1121
Water37821
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)37.070, 56.654, 19.331
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number20
Space group name H-MC2221

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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-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.: 21 / 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: 1.72 Å3/Da / Density % sol: 28.37 %
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: 1.01→31.02 Å / Num. obs: 19836 / % possible obs: 95.7 % / Observed criterion σ(I): -3 / Redundancy: 2.15 % / CC1/2: 0.996 / Rmerge(I) obs: 0.123 / Rrim(I) all: 0.16 / Net I/σ(I): 3.95
Reflection shellResolution: 1.01→1.07 Å / Redundancy: 2 % / Mean I/σ(I) obs: 0.07 / Num. unique obs: 3171 / CC1/2: 0.053 / % possible all: 94.4

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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: 1.28→31.02 Å / SU ML: 0.12 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 13.61 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1703 276 5.05 %
Rwork0.1511 5190 -
obs0.1521 5466 98.75 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 60.34 Å2 / Biso mean: 15.3847 Å2 / Biso min: 8.18 Å2
Refinement stepCycle: final / Resolution: 1.28→31.02 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms204 0 1 21 226
Biso mean--10.73 23.9 -
Num. residues----30
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 2 / % reflection obs: 99 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all
1.2802-1.6130.22941420.224325352677
1.613-31.02880.15171340.129626552789

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