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- PDB-1smm: Crystal Structure of Cp Rd L41A mutant in oxidized state -

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Basic information

Entry
Database: PDB / ID: 1smm
TitleCrystal Structure of Cp Rd L41A mutant in oxidized state
ComponentsRubredoxin
KeywordsELECTRON TRANSPORT
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
Biological speciesClostridium pasteurianum (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.36 Å
AuthorsPark, I.Y. / Youn, B. / Harley, J.L. / Eidsness, M.K. / Smith, E. / Ichiye, T. / Kang, C.
CitationJournal: J.BIOL.INORG.CHEM. / Year: 2004
Title: The unique hydrogen bonded water in the reduced form of Clostridium pasteurianum rubredoxin and its possible role in electron transfer
Authors: Park, I.Y. / Youn, B. / Harley, J.L. / Eidsness, M.K. / Smith, E. / Ichiye, T. / Kang, C.
History
DepositionMar 9, 2004Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 16, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 27, 2021Group: Database references / Derived calculations / Category: database_2 / 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_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Aug 23, 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

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Assembly

Deposited unit
A: Rubredoxin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)6,1613
Polymers6,0101
Non-polymers1522
Water66737
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)62.788, 62.788, 32.797
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number146
Space group name H-MH3

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Components

#1: Protein Rubredoxin / Rd


Mass: 6009.531 Da / Num. of mol.: 1 / Mutation: L41A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Clostridium pasteurianum (bacteria) / Production host: Escherichia coli (E. coli) / References: UniProt: P00268
#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-FE / FE (III) ION


Mass: 55.845 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Fe
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 37 / 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: 2.07 Å3/Da / Density % sol: 40.54 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 4
Details: ammonium sulfate, sodium chloride, pH 4.0, VAPOR DIFFUSION, HANGING DROP, temperature 277K
Crystal grow
*PLUS
pH: 4 / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetailsChemical formula
12.3 Mammonium sulfate1reservoir
20.1 %(w/v)satsodium acetate1reservoirpH4.0
310 mM1reservoirNaCl

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Data collection

DiffractionMean temperature: 113 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.2.1 / Wavelength: 1.0332 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Jul 31, 2003
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0332 Å / Relative weight: 1
ReflectionResolution: 1.36→20 Å / Num. all: 10231 / Num. obs: 10231 / % possible obs: 99 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 1.4
Reflection shellResolution: 1.36→1.45 Å / % possible all: 96.6
Reflection
*PLUS
Rmerge(I) obs: 0.029
Reflection shell
*PLUS
Rmerge(I) obs: 0.139 / Mean I/σ(I) obs: 1.9

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Processing

Software
NameVersionClassification
ADSCdata collection
CrystalCleardata reduction
AMoREphasing
X-PLOR3.851refinement
CrystalClear(MSC/RIGAKU)data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1FHH

1fhh


Resolution: 1.36→20 Å / Cross valid method: THROUGHOUT / σ(F): 0.001 / Stereochemistry target values: Engh & Huber
RfactorNum. reflectionSelection details
Rfree0.189 512 RANDOM
Rwork0.18 --
obs0.18 10231 -
all-10231 -
Refinement stepCycle: LAST / Resolution: 1.36→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms787 0 6 37 830
Refinement
*PLUS
Rfactor Rwork: 0.18
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONbond_d0.021
X-RAY DIFFRACTIONangle_d
X-RAY DIFFRACTIONangle_deg2.7

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