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- PDB-5cw9: Crystal structure of De novo designed ferredoxin-ferredoxin domai... -

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Basic information

Entry
Database: PDB / ID: 5cw9
TitleCrystal structure of De novo designed ferredoxin-ferredoxin domain insertion protein
ComponentsDe novo designed ferredoxin-ferredoxin domain insertion protein
KeywordsDE NOVO PROTEIN / designed / de novo / ferredoxin / domain insertion
Biological speciessynthetic construct (others)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 3.108 Å
AuthorsDiMaio, F. / King, I.C. / Gleixner, J. / Doyle, L. / Stoddard, B. / Baker, D.
Funding support United States, 1items
OrganizationGrant numberCountry
Defense Threat Reduction Agency (DTRA)N00024-10-D-6318/0024 United States
CitationJournal: Elife / Year: 2015
Title: Precise assembly of complex beta sheet topologies from de novo designed building blocks.
Authors: King, I.C. / Gleixner, J. / Doyle, L. / Kuzin, A. / Hunt, J.F. / Xiao, R. / Montelione, G.T. / Stoddard, B.L. / DiMaio, F. / Baker, D.
History
DepositionJul 28, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 23, 2015Provider: repository / Type: Initial release
Revision 1.1Dec 23, 2015Group: Database references
Revision 1.2Nov 1, 2017Group: Author supporting evidence / Derived calculations
Category: pdbx_struct_assembly_auth_evidence / pdbx_struct_oper_list
Item: _pdbx_struct_oper_list.symmetry_operation
Revision 1.3Jan 1, 2020Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.4Mar 6, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: De novo designed ferredoxin-ferredoxin domain insertion protein


Theoretical massNumber of molelcules
Total (without water)16,8391
Polymers16,8391
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)80.563, 80.563, 222.683
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number98
Space group name H-MI4122
Detailsmonomer according to gel filtration

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Components

#1: Protein De novo designed ferredoxin-ferredoxin domain insertion protein


Mass: 16838.682 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) synthetic construct (others) / Production host: Escherichia coli (E. coli)

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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: 5.36 Å3/Da / Density % sol: 77.07 %
Crystal growTemperature: 298 K / Method: vapor diffusion / Details: 0.1 M HEPES pH 7.5, 3.5 M NaCl

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Data collection

DiffractionMean temperature: 95 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.54 Å
DetectorType: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Jul 31, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 3.1→40.282 Å / Num. obs: 6783 / % possible obs: 99.5 % / Redundancy: 13.1 % / Rmerge(I) obs: 0.077 / Net I/σ(I): 18.4
Reflection shellResolution: 3.1→3.42 Å / Redundancy: 11.4 % / Mean I/σ(I) obs: 5.1 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIXrefinement
PDB_EXTRACT3.15data extraction
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3.108→40.282 Å / FOM work R set: 0.4538 / SU ML: 0.46 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 53.72 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.3488 675 9.95 %
Rwork0.3332 6108 -
obs0.3349 6783 97.18 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 428.27 Å2 / Biso mean: 219.11 Å2 / Biso min: 154.8 Å2
Refinement stepCycle: final / Resolution: 3.108→40.282 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1181 0 0 0 1181
Num. residues----146
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0191194
X-RAY DIFFRACTIONf_angle_d1.7111607
X-RAY DIFFRACTIONf_chiral_restr0.089192
X-RAY DIFFRACTIONf_plane_restr0.007204
X-RAY DIFFRACTIONf_dihedral_angle_d10.25469
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 5

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
3.1082-3.34810.44441240.45831121124592
3.3481-3.68490.48891320.46041204133698
3.6849-4.21760.53631360.45951218135499
4.2176-5.31180.36121380.37111250138899
5.3118-40.28490.28981450.26921315146098

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