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- PDB-1b13: CLOSTRIDIUM PASTEURIANUM RUBREDOXIN G10A MUTANT -

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Basic information

Entry
Database: PDB / ID: 1b13
TitleCLOSTRIDIUM PASTEURIANUM RUBREDOXIN G10A MUTANT
ComponentsPROTEIN (RUBREDOXIN)
KeywordsELECTRON TRANSPORT / METALLOPROTEIN / IRON SULFUR / ELECTRON TRANSFER
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 speciesClostridium pasteurianum (bacteria)
MethodX-RAY DIFFRACTION / OTHER / Resolution: 1.5 Å
AuthorsMaher, M.J. / Guss, J.M. / Wilce, M.C.J. / Wedd, A.G.
CitationJournal: Acta Crystallogr.,Sect.D / Year: 1999
Title: Rubredoxin from Clostridium pasteurianum. Structures of G10A, G43A and G10VG43A mutant proteins. Mutation of conserved glycine 10 to valine causes the 9-10 peptide link to invert.
Authors: Maher, M.J. / Xiao, Z. / Wilce, M.C. / Guss, J.M. / Wedd, A.G.
History
DepositionNov 26, 1998Deposition site: BNL / Processing site: RCSB
Revision 1.0May 27, 1999Provider: repository / Type: Initial release
Revision 1.1Oct 16, 2007Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Nov 3, 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 9, 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: PROTEIN (RUBREDOXIN)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)6,1212
Polymers6,0661
Non-polymers561
Water72140
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)64.270, 64.270, 32.920
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 PROTEIN (RUBREDOXIN)


Mass: 6065.637 Da / Num. of mol.: 1 / Mutation: G10A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Clostridium pasteurianum (bacteria) / Strain: JM109 / Cellular location: CYTOPLASM / Gene: CLORUB / Plasmid: PKK223-3 / Gene (production host): CLORUB / Production host: Escherichia coli (E. coli) / Strain (production host): JM109 / References: UniProt: P00268
#2: Chemical ChemComp-FE / FE (III) ION / Iron


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


Mass: 18.015 Da / Num. of mol.: 40 / 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: 2.44 Å3/Da / Density % sol: 49.1 %
Crystal growpH: 4.6
Details: PROTEIN WAS CRYSTALLISED FROM 50-60% SATURATED AMMONIUM SULFATE IN SODIUM ACETATE BUFFER (50 MM) AT PH 4.6.
Components of the solutions
IDNameCrystal-IDSol-ID
150-60% SATURATED AMMONIUM SULFATE12
2SODIUM ACETATE BUFFER (50 MM) AT PH 4.6.12
Crystal
*PLUS
Crystal grow
*PLUS
Temperature: 277 K / Method: vapor diffusion, hanging drop / PH range low: 5 / PH range high: 4
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
17-20 mg/mlprotein1drop
22-35 %ammonium sulfate1drop
350 mMsodium acetate1drop
450-70 %ammonium sulfate1reservoir
550 mMsodium acetate1reservoir

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Data collection

DiffractionMean temperature: 293 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418
DetectorType: RIGAKU RU200 / Detector: IMAGE PLATE / Date: Jul 1, 1996 / Details: MIRRORS
RadiationMonochromator: NI FILTER 0.00015" / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.5→30 Å / Num. obs: 6061 / % possible obs: 94.5 % / Redundancy: 3.3 % / Biso Wilson estimate: 15.74 Å2 / Rmerge(I) obs: 0.08 / Net I/σ(I): 12.5
Reflection shellResolution: 1.5→1.55 Å / Redundancy: 1.5 % / Rmerge(I) obs: 0.245 / Mean I/σ(I) obs: 2.2 / % possible all: 58.8
Reflection
*PLUS
Num. obs: 7662 / Num. measured all: 29561
Reflection shell
*PLUS
% possible obs: 59 %

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Processing

Software
NameClassification
REFMACrefinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: OTHER
Starting model: 5RXN

5rxn


Resolution: 1.5→30 Å / σ(F): 0 / Details: ESD FROM CRUIKSHANK (A): 0.08
RfactorNum. reflection% reflectionSelection details
Rfree0.191 383 0.05 %RANDOM
Rwork0.171 ---
obs-7662 94.5 %-
Displacement parametersBiso mean: 19 Å2
Refinement stepCycle: LAST / Resolution: 1.5→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms423 0 1 40 464
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONp_bond_d0.0150.04
X-RAY DIFFRACTIONp_angle_d0.0180.04
X-RAY DIFFRACTIONp_angle_deg
X-RAY DIFFRACTIONp_planar_d0.0210.05
X-RAY DIFFRACTIONp_hb_or_metal_coord
X-RAY DIFFRACTIONp_mcbond_it1.4763
X-RAY DIFFRACTIONp_mcangle_it2.3775
X-RAY DIFFRACTIONp_scbond_it3.1476
X-RAY DIFFRACTIONp_scangle_it4.7648
X-RAY DIFFRACTIONp_plane_restr
X-RAY DIFFRACTIONp_chiral_restr
X-RAY DIFFRACTIONp_singtor_nbd0.170.3
X-RAY DIFFRACTIONp_multtor_nbd0.2450.3
X-RAY DIFFRACTIONp_xhyhbond_nbd
X-RAY DIFFRACTIONp_xyhbond_nbd
X-RAY DIFFRACTIONp_planar_tor4.77
X-RAY DIFFRACTIONp_staggered_tor1815
X-RAY DIFFRACTIONp_orthonormal_tor
X-RAY DIFFRACTIONp_transverse_tor14.720
X-RAY DIFFRACTIONp_special_tor015
Software
*PLUS
Name: REFMAC / Classification: refinement
Refinement
*PLUS
Highest resolution: 1.5 Å / Rfactor obs: 0.171
Solvent computation
*PLUS
Displacement parameters
*PLUS
Biso mean: 19 Å2
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal target
X-RAY DIFFRACTIONp_bond_d0.04
X-RAY DIFFRACTIONp_angle_d0.04
X-RAY DIFFRACTIONp_planar_d0.05
X-RAY DIFFRACTIONp_mcbond_it3
X-RAY DIFFRACTIONp_scbond_it6
X-RAY DIFFRACTIONp_mcangle_it5
X-RAY DIFFRACTIONp_scangle_it8
LS refinement shell
*PLUS
Rfactor Rfree: 0.432 / Rfactor obs: 0.389

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