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- PDB-1r0h: cobalt-substituted rubredoxin -

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Basic information

Entry
Database: PDB / ID: 1r0h
Titlecobalt-substituted rubredoxin
ComponentsRubredoxin
KeywordsELECTRON TRANSPORT / rubredoxin / iron-sulfur / Clostridium pasteurianum
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 / FOURIER SYNTHESIS / Resolution: 1.7 Å
AuthorsMaher, M. / Cross, M. / Wilce, M.C.J. / Guss, J.M. / Wedd, A.G.
CitationJournal: Acta Crystallogr.,Sect.D / Year: 2004
Title: Metal-substituted derivatives of the rubredoxin from Clostridium pasteurianum.
Authors: Maher, M. / Cross, M. / Wilce, M.C. / Guss, J.M. / Wedd, A.G.
History
DepositionSep 22, 2003Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Feb 10, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 25, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_conn / 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_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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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)6,1112
Polymers6,0521
Non-polymers591
Water82946
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)64.247, 64.247, 32.854
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: 6051.611 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Clostridium pasteurianum (bacteria) / Plasmid: pkk223-3 / Production host: Escherichia coli (E. coli) / Strain (production host): JM109 / References: UniProt: P00268
#2: Chemical ChemComp-CO / COBALT (II) ION


Mass: 58.933 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Co
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 46 / 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: 1.99 Å3/Da / Density % sol: 37.76 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 4
Details: ammonium sulfate, sodium acetate, pH 4.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal grow
*PLUS
Temperature: 277 K / Method: vapor diffusion, hanging drop / PH range low: 4.6 / PH range high: 4
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
17-20 mg/mlprotein1drop
250-67 %satammonium sulfate1reservoir
30.05 Msodium acetate1reservoirpH4.0-4.6

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Data collection

DiffractionMean temperature: 298 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS IIC / Detector: IMAGE PLATE / Details: mirror
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.7→50 Å / Num. all: 5552 / Num. obs: 5552 / % possible obs: 99.7 % / Redundancy: 2.3 % / Rmerge(I) obs: 0.064 / Net I/σ(I): 11.6
Reflection shellResolution: 1.7→1.76 Å / Redundancy: 2.2 % / Rmerge(I) obs: 0.393 / Mean I/σ(I) obs: 2.3 / Num. unique all: 565 / % possible all: 99.8
Reflection
*PLUS
Num. measured all: 16277
Reflection shell
*PLUS
% possible obs: 99.8 %

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Processing

Software
NameVersionClassification
REFMAC5.1.24refinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: FOURIER SYNTHESIS
Starting model: 1iro

1iro


Resolution: 1.7→20 Å / Cor.coef. Fo:Fc: 0.98 / Cor.coef. Fo:Fc free: 0.966 / SU B: 2.485 / SU ML: 0.076 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.093 / ESU R Free: 0.101 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.19676 248 4.5 %RANDOM
Rwork0.14498 ---
obs0.14722 5276 100 %-
all-5524 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 20.57 Å2
Baniso -1Baniso -2Baniso -3
1--1.19 Å2-0.59 Å20 Å2
2---1.19 Å20 Å2
3---1.78 Å2
Refinement stepCycle: LAST / Resolution: 1.7→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms421 0 1 46 468
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.022433
X-RAY DIFFRACTIONr_bond_other_d0.0020.02352
X-RAY DIFFRACTIONr_angle_refined_deg1.4091.974590
X-RAY DIFFRACTIONr_angle_other_deg0.8573841
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.323552
X-RAY DIFFRACTIONr_dihedral_angle_2_deg
X-RAY DIFFRACTIONr_chiral_restr0.0930.261
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.02489
X-RAY DIFFRACTIONr_gen_planes_other0.0020.0274
X-RAY DIFFRACTIONr_nbd_refined0.2350.287
X-RAY DIFFRACTIONr_nbd_other0.2450.2380
X-RAY DIFFRACTIONr_nbtor_other0.0940.2219
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1480.235
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2310.29
X-RAY DIFFRACTIONr_symmetry_vdw_other0.220.222
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1460.24
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_mcbond_it0.7451.5266
X-RAY DIFFRACTIONr_mcangle_it1.442435
X-RAY DIFFRACTIONr_scbond_it2.23167
X-RAY DIFFRACTIONr_scangle_it3.5494.5155
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.7→1.744 Å / Total num. of bins used: 20
RfactorNum. reflection
Rfree0.206 14
Rwork0.256 371
obs-371
Refinement TLS params.Method: refined / Origin x: 18.9308 Å / Origin y: 25.0439 Å / Origin z: 18.082 Å
111213212223313233
T0.0335 Å20.004 Å20.0037 Å2-0.015 Å2-0.0055 Å2--0.0029 Å2
L3.0872 °2-0.3564 °2-0.5057 °2-1.6536 °2-0.0172 °2--1.1415 °2
S-0.0225 Å °0.0448 Å °0.1157 Å °-0.0486 Å °0.0285 Å °0.0816 Å °-0.0294 Å °-0.0684 Å °-0.006 Å °
Refinement
*PLUS
Highest resolution: 1.7 Å / Lowest resolution: 20 Å / Num. reflection obs: 5524 / % reflection Rfree: 5 % / Rfactor Rfree: 0.197 / Rfactor Rwork: 0.145
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONr_bond_d0.011
X-RAY DIFFRACTIONr_angle_d
X-RAY DIFFRACTIONr_angle_deg1.4

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