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- PDB-8ito: Crystal structure of FeRlp from Desulfovibrio vulgaris (Hildenborough) -

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Basic information

Entry
Database: PDB / ID: 8ito
TitleCrystal structure of FeRlp from Desulfovibrio vulgaris (Hildenborough)
ComponentsRubredoxin
KeywordsELECTRON TRANSPORT / iron-sulfur cluster / metallo protein / monomer
Function / homology
Function and homology information


alkane catabolic process / electron transfer activity / iron ion binding
Similarity search - Function
: / Rubredoxin domain / Rubredoxin / Rubredoxin-like domain / Rubredoxin-like domain profile.
Similarity search - Domain/homology
: / PHOSPHATE ION / Rubredoxin
Similarity search - Component
Biological speciesDesulfovibrio vulgaris (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.1 Å
AuthorsNakatsuji, T. / Ogata, H. / Kitamura, M.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: To Be Published
Title: Crystal structure of FeRlp from Desulfovibrio vulgaris (Hildenborough)
Authors: Nakatsuji, T. / Nishikawa, K. / Ogata, H. / Kitamura, M.
History
DepositionMar 22, 2023Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Mar 27, 2024Provider: repository / Type: Initial release
Revision 1.1Oct 23, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Rubredoxin
B: Rubredoxin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)17,4256
Polymers17,1232
Non-polymers3024
Water1,20767
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)36.565, 57.856, 59.198
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Rubredoxin


Mass: 8561.743 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Desulfovibrio vulgaris (bacteria)
Strain: ATCC 29579 / DSM 644 / NCIMB 8303 / VKM B-1760 / Hildenborough
Gene: rdl / Production host: Escherichia coli K-12 (bacteria) / References: UniProt: Q726L3
#2: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: PO4 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-FE / FE (III) ION


Mass: 55.845 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Fe / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 67 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationY

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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: 1.87 Å3/Da / Density % sol: 34.27 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 7
Details: 0.5 M NaHPO4, 0.9 M K2HPO4, 0.8 M Potassium sodium tartrate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU FR-X / Wavelength: 1.54 Å
DetectorType: RIGAKU RAXIS VII / Detector: IMAGE PLATE / Date: Jun 30, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 2.01→18.68 Å / Num. obs: 52024 / % possible obs: 99.6 % / Redundancy: 6 % / Rpim(I) all: 0.039 / Net I/σ(I): 15.9
Reflection shellResolution: 2.01→2.04 Å / Num. unique obs: 425 / Rpim(I) all: 0.207

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Processing

Software
NameVersionClassification
PHENIX(1.19.2_4158: ???)refinement
HKL-2000data reduction
SCALAdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.1→18.68 Å / SU ML: 0.27 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 28.5 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2435 461 6.06 %
Rwork0.1849 --
obs0.1885 7606 98.36 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.1→18.68 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1161 0 12 67 1240
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0081203
X-RAY DIFFRACTIONf_angle_d0.9911633
X-RAY DIFFRACTIONf_dihedral_angle_d6.061161
X-RAY DIFFRACTIONf_chiral_restr0.058157
X-RAY DIFFRACTIONf_plane_restr0.011223
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.1-2.40.36271470.24982266X-RAY DIFFRACTION96
2.4-3.030.28361460.21492402X-RAY DIFFRACTION100
3.03-18.680.20361680.15742477X-RAY DIFFRACTION99

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