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- PDB-9bkt: Crystal structure of rubredoxin from Pyrococcus furiosus reconsti... -

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Basic information

Entry
Database: PDB / ID: 9bkt
TitleCrystal structure of rubredoxin from Pyrococcus furiosus reconstituted with FeSO4 solved by Fe/S-SAD
ComponentsRubredoxin
KeywordsELECTRON TRANSPORT / FeSO4 substituted / native SAD
Function / homology
Function and homology information


alkane catabolic process / electron transfer activity / iron ion binding
Similarity search - Function
Rubredoxin / : / Rubredoxin, iron-binding site / Rubredoxin signature. / Rubredoxin domain / Rubredoxin / Rubredoxin-like domain / Rubredoxin-like domain profile.
Similarity search - Domain/homology
Biological speciesPyrococcus furiosus (archaea)
MethodX-RAY DIFFRACTION / SAD / Resolution: 1.8 Å
AuthorsZhou, D. / Chen, L. / Rose, J.P. / Wang, B.C.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: To Be Published
Title: Crystal structure of rubredoxin from Pyrococcus furiosus reconstituted with FeSO4 solved by Fe/S-SAD
Authors: Zhou, D. / Chen, L. / Rose, J.P. / Wang, B.C.
History
DepositionApr 29, 2024Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 5, 2024Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Rubredoxin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)6,0882
Polymers6,0321
Non-polymers561
Water2,234124
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area3500 Å2
Unit cell
Length a, b, c (Å)33.828, 34.507, 43.302
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Space group name HallP2ac2ab
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x,y+1/2,-z+1/2
#4: -x+1/2,-y,z+1/2

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Components

#1: Protein Rubredoxin / Rd


Mass: 6031.728 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pyrococcus furiosus (archaea) / Gene: rub, PF1282 / Production host: Escherichia coli (E. coli) / References: UniProt: P24297
#2: Chemical ChemComp-FE2 / FE (II) ION


Mass: 55.845 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Fe / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 124 / 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: 2.1 Å3/Da / Density % sol: 41.29 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / Details: 0.1M tris pH 8.4 2.2 M ammonium sulfate 30% MPD

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-002 / Wavelength: 1.5418 Å
DetectorType: DECTRIS PILATUS 200K / Detector: PIXEL / Date: Aug 17, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.8→50 Å / Num. obs: 8697 / % possible obs: 97.1 % / Redundancy: 10.6 % / Biso Wilson estimate: 7.29 Å2 / Rmerge(I) obs: 0.038 / Net I/σ(I): 75.56
Reflection shellResolution: 1.8→1.83 Å / Rmerge(I) obs: 0.063 / Num. unique obs: 181

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Processing

Software
NameVersionClassification
PHENIX1.21_5207refinement
HKL-3000data reduction
HKL-3000data scaling
AutoSolphasing
RefinementMethod to determine structure: SAD / Resolution: 1.8→26.99 Å / SU ML: 0.138 / Cross valid method: FREE R-VALUE / σ(F): 1.48 / Phase error: 15.0836
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.1662 893 10.27 %
Rwork0.135 7804 -
obs0.1382 8697 96.07 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 9.98 Å2
Refinement stepCycle: LAST / Resolution: 1.8→26.99 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms420 0 1 124 545
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0071432
X-RAY DIFFRACTIONf_angle_d0.8818586
X-RAY DIFFRACTIONf_chiral_restr0.056458
X-RAY DIFFRACTIONf_plane_restr0.004878
X-RAY DIFFRACTIONf_dihedral_angle_d17.8064160
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.8-1.910.20341150.13791052X-RAY DIFFRACTION77.23
1.91-2.060.15541540.11731341X-RAY DIFFRACTION99.34
2.06-2.270.16021470.1251351X-RAY DIFFRACTION100
2.27-2.60.14731620.14821360X-RAY DIFFRACTION100
2.6-3.270.17711530.14521349X-RAY DIFFRACTION100
3.27-26.990.16871620.13241351X-RAY DIFFRACTION100

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