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- PDB-1r0i: cadmium-substituted rubredoxin -

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Basic information

Entry
Database: PDB / ID: 1r0i
Titlecadmium-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: 1.5 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)6,1642
Polymers6,0521
Non-polymers1121
Water73941
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)64.294, 64.294, 32.567
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-CD / CADMIUM ION


Mass: 112.411 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cd
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 41 / 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: 37.7 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 4
Details: sodium acetate, ammonium sulfate, 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: 1.5→50 Å / Num. all: 7544 / Num. obs: 7544 / % possible obs: 93.9 % / Redundancy: 3.9 % / Rmerge(I) obs: 0.111 / Net I/σ(I): 14.5
Reflection shellHighest resolution: 1.5 Å / Redundancy: 1.6 % / Rmerge(I) obs: 0.12 / Mean I/σ(I) obs: 1.5 / % possible all: 66.4
Reflection
*PLUS
Num. measured all: 29513
Reflection shell
*PLUS
% possible obs: 66.4 % / Rmerge(I) obs: 0.12

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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: 1.5→18.57 Å / Cor.coef. Fo:Fc: 0.968 / Cor.coef. Fo:Fc free: 0.972 / SU B: 0.991 / SU ML: 0.038 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.066 / ESU R Free: 0.057 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. The Rfree set was correctly assigned. The R(work) and R(free) values were 0.315 and 0.348, respectively at the commencement of the ...Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. The Rfree set was correctly assigned. The R(work) and R(free) values were 0.315 and 0.348, respectively at the commencement of the refinement. They converged during the refinement. Author has no explanation as to why the value for R(free) is lower than that for R(work).
RfactorNum. reflection% reflectionSelection details
Rfree0.14561 347 4.6 %RANDOM
Rwork0.14627 ---
obs0.14624 7194 100 %-
all-7541 --
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: 14.633 Å2
Baniso -1Baniso -2Baniso -3
1--0.75 Å2-0.38 Å20 Å2
2---0.75 Å20 Å2
3---1.13 Å2
Refinement stepCycle: LAST / Resolution: 1.5→18.57 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms423 0 1 41 465
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.022440
X-RAY DIFFRACTIONr_bond_other_d0.0020.02371
X-RAY DIFFRACTIONr_angle_refined_deg1.2521.978600
X-RAY DIFFRACTIONr_angle_other_deg0.7753924
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.788552
X-RAY DIFFRACTIONr_dihedral_angle_2_deg
X-RAY DIFFRACTIONr_chiral_restr0.0830.263
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.02489
X-RAY DIFFRACTIONr_gen_planes_other0.0020.0274
X-RAY DIFFRACTIONr_nbd_refined0.2030.274
X-RAY DIFFRACTIONr_nbd_other0.2310.2379
X-RAY DIFFRACTIONr_nbtor_other0.0850.2226
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.0960.220
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2030.28
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2570.214
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.0910.27
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_mcbond_it0.6241.5267
X-RAY DIFFRACTIONr_mcangle_it1.2092440
X-RAY DIFFRACTIONr_scbond_it1.8323173
X-RAY DIFFRACTIONr_scangle_it2.994.5158
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.502→1.54 Å / Total num. of bins used: 20
RfactorNum. reflection
Rfree0.206 21
Rwork0.147 366
obs-366
Refinement TLS params.Method: refined / Origin x: 18.9662 Å / Origin y: 25.184 Å / Origin z: 17.9664 Å
111213212223313233
T0.0245 Å2-0.0001 Å20.0029 Å2-0.0103 Å2-0.0053 Å2--0.0031 Å2
L2.0505 °2-0.201 °2-0.2977 °2-1.0729 °2-0.081 °2--0.8804 °2
S-0.0177 Å °0.0801 Å °0.0545 Å °-0.0356 Å °0.0229 Å °0.0512 Å °-0.0107 Å °-0.0259 Å °-0.0052 Å °
Refinement
*PLUS
Highest resolution: 1.5 Å / Lowest resolution: 19 Å / Num. reflection obs: 7541 / % reflection Rfree: 5 % / Rfactor Rfree: 0.146 / Rfactor Rwork: 0.146
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONr_bond_d0.007
X-RAY DIFFRACTIONr_angle_d
X-RAY DIFFRACTIONr_angle_deg1.2

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