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- PDB-1iu5: X-ray Crystal Structure of the rubredoxin mutant from Pyrococcus ... -

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Basic information

Entry
Database: PDB / ID: 1iu5
TitleX-ray Crystal Structure of the rubredoxin mutant from Pyrococcus Furiosus
Componentsrubredoxin
KeywordsELECTRON TRANSPORT / rubredoxin / mutant / thermostability
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. / Rubrerythrin, domain 2 - #10 / Rubredoxin domain / Rubredoxin / Rubredoxin-like domain / Rubredoxin-like domain profile. / Rubrerythrin, domain 2 ...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
DEUTERATED WATER / : / Rubredoxin
Similarity search - Component
Biological speciesPyrococcus furiosus (archaea)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.5 Å
AuthorsChatake, T. / Kurihara, K. / Tanaka, I. / Tsyba, I. / Bau, R. / Jenney, F.E. / Adams, M.W.W. / Niimura, N.
CitationJournal: Acta Crystallogr.,Sect.D / Year: 2004
Title: A neutron crystallographic analysis of a rubredoxin mutant at 1.6 A resolution.
Authors: Chatake, T. / Kurihara, K. / Tanaka, I. / Tsyba, I. / Bau, R. / Jenney, F.E. / Adams, M.W. / Niimura, N.
History
DepositionFeb 27, 2002Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Aug 27, 2002Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Non-polymer description / Version format compliance
Revision 1.3Nov 10, 2021Group: Database references / Derived calculations
Category: database_2 / struct_conn ...database_2 / struct_conn / 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 / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Oct 25, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: rubredoxin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)5,9192
Polymers5,8631
Non-polymers561
Water95553
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)34.480, 35.700, 43.160
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: 5863.470 Da / Num. of mol.: 1 / Mutation: W3Y, I23V, L32I
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pyrococcus furiosus (archaea) / Production host: Escherichia coli (E. coli) / References: UniProt: P24297
#2: Chemical ChemComp-FE / FE (III) ION


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


Mass: 18.015 Da / Num. of mol.: 53 / Source method: isolated from a natural source / Formula: D2O

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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: 2.26 Å3/Da / Density % sol: 45.65 %
Crystal growMethod: vapor diffusion / Details: Na/K phosphate, VAPOR DIFFUSION
Crystal grow
*PLUS
pH: 8 / Method: vapor diffusion, hanging drop
Details: used macroseeding, Bau, R., (1998) J.BIOL.INORG.CHEM., 3, 484.
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
140 mg/mlprotein1drop
250 mMTris-HCl1drop
30.3 M1dropNaCl
43.6 Msodium potassium phosphate1reservoir

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Data collection

DiffractionMean temperature: 293 K
Diffraction sourceSource: ROTATING ANODE / Type: MACSCIENCE / Wavelength: 1.5418 Å
DetectorType: MAC Science DIP-2000 / Detector: IMAGE PLATE / Date: May 29, 2001
RadiationMonochromator: graphite / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.5→50 Å / Num. all: 8876 / Num. obs: 8876 / % possible obs: 98.6 % / Redundancy: 4.4 % / Biso Wilson estimate: 13.9 Å2 / Rmerge(I) obs: 0.077 / Net I/σ(I): 25.2
Reflection shellResolution: 1.5→1.55 Å / Redundancy: 4.3 % / Rmerge(I) obs: 0.19 / % possible all: 97.7
Reflection
*PLUS
Num. measured all: 38773
Reflection shell
*PLUS
% possible obs: 97.7 % / Rmerge(I) obs: 0.19

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Processing

Software
NameClassification
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
CNSrefinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1BRF

1brf


Resolution: 1.5→10 Å / Isotropic thermal model: isotropic / σ(F): 3
RfactorNum. reflectionSelection details
Rfree0.203 909 RANDOM
Rwork0.187 --
obs-8456 -
Displacement parametersBiso mean: 15.9 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.18 Å0.16 Å
Luzzati d res low-5 Å
Luzzati sigma a0.11 Å0.06 Å
Refinement stepCycle: LAST / Resolution: 1.5→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms392 0 1 53 446
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.007
X-RAY DIFFRACTIONc_angle_deg1.4
LS refinement shellResolution: 1.5→1.59 Å
RfactorNum. reflection% reflection
Rfree0.259 --
Rwork0.243 --
obs-1140 88.2 %
Refinement
*PLUS
Lowest resolution: 10 Å / Rfactor Rfree: 0.204 / Rfactor Rwork: 0.189
Solvent computation
*PLUS
Displacement parameters
*PLUS

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