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- PDB-1b2o: CLOSTRIDIUM PASTEURIANUM RUBREDOXIN G10VG43A MUTANT -

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Basic information

Entry
Database: PDB / ID: 1b2o
TitleCLOSTRIDIUM PASTEURIANUM RUBREDOXIN G10VG43A MUTANT
ComponentsPROTEIN (RUBREDOXIN)
KeywordsELECTRON TRANSPORT / METALLOPROTEIN / IRON SULFUR / ELECTRON TRANSFER
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 / MOLECULAR REPLACEMENT / Resolution: 1.9 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 30, 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

Downloads & links

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Assembly

Deposited unit
A: PROTEIN (RUBREDOXIN)
B: PROTEIN (RUBREDOXIN)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)12,3274
Polymers12,2152
Non-polymers1122
Water2,450136
1
A: PROTEIN (RUBREDOXIN)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)6,1642
Polymers6,1081
Non-polymers561
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: PROTEIN (RUBREDOXIN)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)6,1642
Polymers6,1081
Non-polymers561
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)61.850, 61.850, 80.450
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212

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Components

#1: Protein PROTEIN (RUBREDOXIN)


Mass: 6107.716 Da / Num. of mol.: 2 / Mutation: G10V, G43A
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


Mass: 55.845 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Fe
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 136 / 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: 3.1 Å3/Da / Density % sol: 60.04 %
Crystal growpH: 5
Details: PROTEIN WAS CRYSTALLISED FROM 70% SATURATED AMMONIUM SULFATE IN SODIUM ACETATE BUFFER (50 MM) AT PH 5.0.
Components of the solutions
IDNameCrystal-IDSol-ID
170% SATURATED AMMONIUM SULFATE12
2SODIUM ACETATE BUFFER (50 MM) AT PH 5.012
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: 1.9→30 Å / Num. obs: 12136 / % possible obs: 94 % / Redundancy: 2.8 % / Rmerge(I) obs: 0.092 / Net I/σ(I): 10.9
Reflection shellResolution: 1.94→2.03 Å / Redundancy: 2.8 % / Rmerge(I) obs: 0.28 / Mean I/σ(I) obs: 3.7 / % possible all: 95.6
Reflection
*PLUS
Num. measured all: 54730
Reflection shell
*PLUS
% possible obs: 96 % / Rmerge(I) obs: 0.28

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Processing

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

5rxn


Resolution: 1.9→30 Å / σ(F): 0 / Details: ESD FROM CRUIKSHANK (A): 0.08
RfactorNum. reflection% reflectionSelection details
Rfree0.237 607 0.05 %RANDOM
Rwork0.194 ---
obs-12136 94 %-
Displacement parametersBiso mean: 27 Å2
Refinement stepCycle: LAST / Resolution: 1.9→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms850 0 2 136 988
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONp_bond_d0.0140.025
X-RAY DIFFRACTIONp_angle_d0.0260.04
X-RAY DIFFRACTIONp_angle_deg
X-RAY DIFFRACTIONp_planar_d0.0260.045
X-RAY DIFFRACTIONp_hb_or_metal_coord
X-RAY DIFFRACTIONp_mcbond_it2.3483
X-RAY DIFFRACTIONp_mcangle_it3.3885
X-RAY DIFFRACTIONp_scbond_it5.1436
X-RAY DIFFRACTIONp_scangle_it7.3258
X-RAY DIFFRACTIONp_plane_restr
X-RAY DIFFRACTIONp_chiral_restr
X-RAY DIFFRACTIONp_singtor_nbd0.170.3
X-RAY DIFFRACTIONp_multtor_nbd0.2710.3
X-RAY DIFFRACTIONp_xhyhbond_nbd
X-RAY DIFFRACTIONp_xyhbond_nbd
X-RAY DIFFRACTIONp_planar_tor4.77
X-RAY DIFFRACTIONp_staggered_tor17.415
X-RAY DIFFRACTIONp_orthonormal_tor
X-RAY DIFFRACTIONp_transverse_tor14.920
X-RAY DIFFRACTIONp_special_tor015
Software
*PLUS
Name: REFMAC / Classification: refinement
Refinement
*PLUS
Highest resolution: 1.9 Å / Rfactor obs: 0.194
Solvent computation
*PLUS
Displacement parameters
*PLUS
Biso mean: 27 Å2
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal target
X-RAY DIFFRACTIONp_angle_d0.04
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: 0.245 / Rfactor obs: 0.18

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