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- PDB-1dhg: HG-SUBSTITUTED DESULFOREDOXIN -

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Basic information

Entry
Database: PDB / ID: 1dhg
TitleHG-SUBSTITUTED DESULFOREDOXIN
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: 2.5 Å
AuthorsArcher, M. / Carvalho, A.L. / Teixeira, S. / Moura, I. / Moura, J.J.G. / Rusnak, F. / Romao, M.J.
CitationJournal: 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.
History
DepositionMar 22, 1999Deposition site: PDBE / Processing site: RCSB
Revision 1.0Jul 9, 1999Provider: repository / Type: Initial release
Revision 1.1Apr 26, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Aug 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)8,0164
Polymers7,6152
Non-polymers4012
Water23413
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1800 Å2
ΔGint-68 kcal/mol
Surface area3910 Å2
MethodPISA
Unit cell
Length a, b, c (Å)27.900, 27.900, 130.900
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number152
Cell settingtrigonal
Space group name H-MP3121
Noncrystallographic symmetry (NCS)NCS oper: (Code: given
Matrix: (-0.93226, -0.24064, -0.27016), (-0.23546, -0.1634, 0.95805), (-0.27469, 0.95676, 0.09567)
Vector: 46.89063, -24.97602, 33.53525)

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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
Details: MERCURY SUBSTITUTED / 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-HG / MERCURY (II) ION


Mass: 200.590 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Hg
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 13 / 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: 1.93 Å3/Da / Density % sol: 36.32 %
Crystal growpH: 7.5 / Details: pH 7.50
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: 110 K
Diffraction sourceSource: ROTATING ANODE / Type: ENRAF-NONIUS / Wavelength: 1.5418
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.5→23.5 Å / Num. obs: 2199 / % possible obs: 94.1 % / Redundancy: 11.4 % / Rsym value: 0.103 / Net I/σ(I): 3.2
Reflection
*PLUS
Highest resolution: 2.5 Å / Lowest resolution: 23.5 Å / % possible obs: 94.1 % / Num. measured all: 25156 / Rmerge(I) obs: 0.103
Reflection shell
*PLUS
Highest resolution: 2.5 Å / Lowest resolution: 2.59 Å / % possible obs: 93.1 % / Rmerge(I) obs: 0.359

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Processing

SoftwareName: X-PLOR / Version: 3.1 / Classification: refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1DXG

1dxg


Resolution: 2.5→23.5 Å / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflection
Rwork0.182 --
all-2199 -
obs-2199 94.1 %
Refinement stepCycle: LAST / Resolution: 2.5→23.5 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms522 0 2 13 537
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.009
X-RAY DIFFRACTIONx_bond_d_na
X-RAY DIFFRACTIONx_bond_d_prot
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_angle_d_na
X-RAY DIFFRACTIONx_angle_d_prot
X-RAY DIFFRACTIONx_angle_deg1.61
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d25.9
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d0.98
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it
X-RAY DIFFRACTIONx_mcangle_it
X-RAY DIFFRACTIONx_scbond_it
X-RAY DIFFRACTIONx_scangle_it
Software
*PLUS
Version: 3.1 / Classification: refinement
Refinement
*PLUS
Highest resolution: 2.5 Å / Lowest resolution: 23.5 Å / Rfactor obs: 0.182
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_deg25.9
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg0.98

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