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- PDB-1dcd: DESULFOREDOXIN COMPLEXED WITH CD2+ -

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Basic information

Entry
Database: PDB / ID: 1dcd
TitleDESULFOREDOXIN COMPLEXED WITH CD2+
ComponentsPROTEIN (DESULFOREDOXIN)
KeywordsELECTRON TRANSPORT / RUBREDOXIN TYPE PROTEIN
Function / homologyDesulforedoxin / Desulfoferrodoxin, N-terminal domain / Desulfoferrodoxin, N-terminal domain superfamily / Desulfoferrodoxin, N-terminal domain / iron ion binding / : / Desulforedoxin
Function and homology information
Biological speciesDesulfovibrio gigas (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsArcher, M. / Carvalho, A.L. / Teixeira, S. / Romao, M.J.
Citation
Journal: Protein Sci. / Year: 1999
Title: Structural studies by X-ray diffraction on metal substituted desulforedoxin, a rubredoxin-type protein.
Authors: Archer, M. / Carvalho, A.L. / Teixeira, S. / Moura, I. / Moura, J.J. / Rusnak, F. / Romao, M.J.
#1: Journal: J.Mol.Biol. / Year: 1995
Title: Crystal structure of desulforedoxin from Desulfovibrio gigas determined at 1.8 A resolution: a novel non-heme iron protein structure.
Authors: Archer, M. / Huber, R. / Tavares, P. / Moura, I. / Moura, J.J. / Carrondo, M.A. / Sieker, L.C. / LeGall, J. / Romao, M.J.
History
DepositionMar 20, 1999Deposition site: PDBE / Processing site: RCSB
Revision 1.0Jul 9, 1999Provider: repository / Type: Initial release
Revision 1.1Oct 16, 2007Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Oct 4, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 1.4Nov 13, 2019Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_last ..._citation.journal_volume / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.name
Revision 1.5Aug 9, 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: PROTEIN (DESULFOREDOXIN)
B: PROTEIN (DESULFOREDOXIN)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)7,8404
Polymers7,6152
Non-polymers2252
Water95553
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1630 Å2
ΔGint-23 kcal/mol
Surface area4020 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)27.950, 27.950, 130.940
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number152
Cell settingtrigonal
Space group name H-MP3121
Components on special symmetry positions
IDModelComponents
11A-118-

HOH

21A-126-

HOH

Noncrystallographic symmetry (NCS)NCS oper: (Code: given
Matrix: (-0.939027, -0.226955, -0.258303), (-0.228768, -0.148457, 0.962094), (-0.256699, 0.962524, 0.087485)
Vector: 47.1295, -24.8573, 33.3616)

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Components

#1: Protein/peptide PROTEIN (DESULFOREDOXIN)


Mass: 3807.350 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Desulfovibrio gigas (bacteria) / Cellular location: CYTOPLASM / Cellular location (production host): CYTOPLASM / Gene (production host): DSR / Production host: Escherichia coli (E. coli) / References: UniProt: P00273
#2: Chemical ChemComp-CD / CADMIUM ION


Mass: 112.411 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cd
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 53 / 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: 1.9 Å3/Da / Density % sol: 35 %
Crystal growpH: 5
Details: 30% ETHANOL, 0.1 M SODIUM ACETATE PH 5, 0.2 M CACL2, pH 5.0
Crystal grow
*PLUS
pH: 7.6 / Method: vapor diffusion
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
17 mg/mlprotein1drop
210 mMTris-HCl1drop
330 %ethanol1reservoir
40.1 Msodium acetate1reservoir
50.2 M1reservoirCaCl2

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Data collection

DiffractionMean temperature: 277 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.5418
DetectorType: MARRESEARCH / Detector: IMAGE PLATE
RadiationMonochromator: NI FILTER / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.98→14.8 Å / Num. all: 4403 / Num. obs: 4403 / % possible obs: 97.5 % / Observed criterion σ(I): 0 / Redundancy: 6.4 % / Rsym value: 0.115 / Net I/σ(I): 8
Reflection shellResolution: 1.98→2.05 Å / Mean I/σ(I) obs: 2.5 / Rsym value: 0.432 / % possible all: 96.4
Reflection
*PLUS
Num. measured all: 28142 / Rmerge(I) obs: 0.115
Reflection shell
*PLUS
% possible obs: 96.4 % / Rmerge(I) obs: 0.359

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Processing

Software
NameClassification
AMoREphasing
SHELXLrefinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1DXG

1dxg


Resolution: 2→14.8 Å / Num. parameters: 2325 / Num. restraintsaints: 2656 / σ(F): 0 / Stereochemistry target values: ENGH & HUBER
Details: GEOMETRIC RESTRAINTS WERE APPLIED TO THE METAL CENTER (DFIX CD S 2.55 A)
RfactorNum. reflection% reflection
obs0.189 4342 97.7 %
all-4342 -
Solvent computationSolvent model: MOEWS & KRETSINGER, J.MOL.BIOL.91(1973)201-228
Refine analyzeNum. disordered residues: 2 / Occupancy sum hydrogen: 0 / Occupancy sum non hydrogen: 576
Refinement stepCycle: LAST / Resolution: 2→14.8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms522 0 2 53 577
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONs_bond_d0.005
X-RAY DIFFRACTIONs_angle_d0.018
X-RAY DIFFRACTIONs_similar_dist
X-RAY DIFFRACTIONs_from_restr_planes
X-RAY DIFFRACTIONs_zero_chiral_vol
X-RAY DIFFRACTIONs_non_zero_chiral_vol
X-RAY DIFFRACTIONs_anti_bump_dis_restr
X-RAY DIFFRACTIONs_rigid_bond_adp_cmpnt
X-RAY DIFFRACTIONs_similar_adp_cmpnt
X-RAY DIFFRACTIONs_approx_iso_adps

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