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- PDB-9bkl: Cobalt substituted rubredoxin from Pyrococcus furiosus solved by ... -

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Basic information

Entry
Database: PDB / ID: 9bkl
TitleCobalt substituted rubredoxin from Pyrococcus furiosus solved by Co/S-SAD
ComponentsRubredoxin
KeywordsELECTRON TRANSPORT / Cobalt 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: 1.7 Å
AuthorsZhou, D. / Chen, L. / Rose, J.P. / Wang, B.C.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: To Be Published
Title: Cobalt substituted rubredoxin from Pyrococcus furiosus solved by Co/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)6,0912
Polymers6,0321
Non-polymers591
Water1,982110
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area3470 Å2
Unit cell
Length a, b, c (Å)34.016, 34.645, 43.347
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-CO / COBALT (II) ION


Mass: 58.933 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Co / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 110 / 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: 2.12 Å3/Da / Density % sol: 41.91 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / Details: 3.8M NaH2PO4, 3.8M K2HPO4 (1:1, v/v)

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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 9, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.7→50 Å / Num. obs: 9458 / % possible obs: 90.8 % / Redundancy: 9.8 % / Biso Wilson estimate: 7.62 Å2 / Rmerge(I) obs: 0.049 / Net I/σ(I): 64.98
Reflection shellResolution: 1.7→1.73 Å / Rmerge(I) obs: 0.066 / Num. unique obs: 101

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Processing

Software
NameVersionClassification
PHENIX1.21_5207refinement
HKL-3000data reduction
HKL-3000data scaling
AutoSolphasing
RefinementMethod to determine structure: SAD / Resolution: 1.7→27.06 Å / SU ML: 0.1166 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 16.6474
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.1829 932 9.85 %
Rwork0.1422 8526 -
obs0.146 9458 86.57 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 11.85 Å2
Refinement stepCycle: LAST / Resolution: 1.7→27.06 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms420 0 1 110 531
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0061432
X-RAY DIFFRACTIONf_angle_d0.7969586
X-RAY DIFFRACTIONf_chiral_restr0.053258
X-RAY DIFFRACTIONf_plane_restr0.004478
X-RAY DIFFRACTIONf_dihedral_angle_d10.9823160
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.7-1.790.2232470.1821437X-RAY DIFFRACTION30.63
1.79-1.90.18321320.14931063X-RAY DIFFRACTION77.1
1.9-2.050.14331560.13341390X-RAY DIFFRACTION99.42
2.05-2.250.16441530.13391398X-RAY DIFFRACTION99.94
2.25-2.580.20561510.14381414X-RAY DIFFRACTION99.94
2.58-3.250.19121390.15341421X-RAY DIFFRACTION100
3.25-27.060.18881540.13531403X-RAY DIFFRACTION99.87

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