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- PDB-2pya: Ultra-high resolution structure of P. abyssi rubredoxin W4L/R5S/A44S -

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Basic information

Entry
Database: PDB / ID: 2pya
TitleUltra-high resolution structure of P. abyssi rubredoxin W4L/R5S/A44S
ComponentsRubredoxin
KeywordsELECTRON TRANSPORT / O-H...S-Fe hydrogen bond
Function / homology
Function and homology information


electron transfer activity / iron ion binding
Similarity search - Function
Rubredoxin / Rubredoxin, iron-binding site / Rubredoxin signature. / Rubrerythrin, domain 2 - #10 / Rubredoxin domain / Rubredoxin / Rubredoxin-like domain / Rubredoxin-like domain profile. / Rubrerythrin, domain 2 / Single Sheet / Mainly Beta
Similarity search - Domain/homology
Biological speciesPyrococcus abyssi (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / AB INITIO PHASING / Resolution: 0.86 Å
AuthorsBoenisch, H. / Ladenstein, R.
CitationJournal: J.Biol.Inorg.Chem. / Year: 2007
Title: Ultrahigh-resolution study on Pyrococcus abyssi rubredoxin: II. Introduction of an O-H...Sgamma-Fe hydrogen bond increased the reduction potential by 65 mV.
Authors: Bonisch, H. / Schmidt, C.L. / Bianco, P. / Ladenstein, R.
History
DepositionMay 16, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 29, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Oct 20, 2021Group: Data collection / Database references / Derived calculations
Category: database_2 / diffrn_source ...database_2 / diffrn_source / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _diffrn_source.pdbx_synchrotron_site / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.3Feb 21, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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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)5,8904
Polymers5,7881
Non-polymers1023
Water1,69394
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)25.385, 39.812, 45.117
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 / / Rd


Mass: 5788.364 Da / Num. of mol.: 1 / Mutation: W4L,R5S,A44S
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pyrococcus abyssi (archaea) / Strain: GE5/Orsay / Gene: rub / Plasmid: pet15b / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21-DE3 / References: UniProt: Q9V099
#2: Chemical ChemComp-FE / FE (III) ION / Iron


Mass: 55.845 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Fe
#3: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Na
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 94 / Source method: isolated from a natural source / Formula: H2O

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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: 1.97 Å3/Da / Density % sol: 37.49 %
Crystal growTemperature: 293 K / pH: 6
Details: 3.7 - 4.0 M Sodium Malonate, pH 6.0, VAPOR DIFFUSION, SITTING DROP, temperature 293K, pH 6.00

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: BW7B / Wavelength: 0.85
DetectorType: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: Dec 9, 2003
RadiationMonochromator: SI [111], HORIZONTALLY FOCUSSING / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.85 Å / Relative weight: 1
ReflectionResolution: 0.86→30 Å / Num. obs: 38349 / % possible obs: 96.7 % / Observed criterion σ(I): -3 / Redundancy: 5.6 % / Biso Wilson estimate: 2.9 Å2 / Rsym value: 0.053 / Net I/σ(I): 41.3
Reflection shellResolution: 0.86→0.87 Å / Redundancy: 4.7 % / Mean I/σ(I) obs: 9.64 / Rsym value: 0.148 / % possible all: 95.6

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Processing

Software
NameClassification
MAR345dtbdata collection
SHELXDphasing
SHELXL-97refinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: AB INITIO PHASING / Resolution: 0.86→30 Å / Num. parameters: 4966 / Num. restraintsaints: 1399 / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: ENGH & HUBER
RfactorNum. reflection% reflectionSelection details
Rfree0.105 3516 5 %RANDOM
all0.098 70239 --
obs0.098 -96.7 %-
Solvent computationSolvent model: DIFFUSE SOLVENT MODEL
Displacement parametersBiso mean: 7.39 Å2
Refine analyzeNum. disordered residues: 12 / Occupancy sum hydrogen: 367 / Occupancy sum non hydrogen: 499
Refinement stepCycle: LAST / Resolution: 0.86→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms851 0 3 100 954
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONs_bond_d0.033
X-RAY DIFFRACTIONs_angle_d0.062
X-RAY DIFFRACTIONs_similar_dist
X-RAY DIFFRACTIONs_from_restr_planes0.65
X-RAY DIFFRACTIONs_zero_chiral_vol0.139
X-RAY DIFFRACTIONs_non_zero_chiral_vol0.161
X-RAY DIFFRACTIONs_anti_bump_dis_restr
X-RAY DIFFRACTIONs_rigid_bond_adp_cmpnt
X-RAY DIFFRACTIONs_similar_adp_cmpnt
X-RAY DIFFRACTIONs_approx_iso_adps
LS refinement shellHighest resolution: 0.86 Å

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