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- PDB-1dxg: CRYSTAL STRUCTURE OF DESULFOREDOXIN FROM DESULFOVIBRIO GIGAS AT 1... -

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Basic information

Entry
Database: PDB / ID: 1dxg
TitleCRYSTAL STRUCTURE OF DESULFOREDOXIN FROM DESULFOVIBRIO GIGAS AT 1.8 A RESOLUTION
ComponentsDESULFOREDOXIN
KeywordsNON-HEME IRON PROTEIN / RUBREDOXIN TYPE METAL CENTER / ELECTRON TRANSPORT
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 / SIRAS / Resolution: 1.8 Å
AuthorsArcher, M. / Huber, R. / Romao, M.J.
CitationJournal: 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
DepositionJul 4, 1997Processing site: BNL
Revision 1.0Nov 12, 1997Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 7, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.process_site / _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: DESULFOREDOXIN
B: DESULFOREDOXIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)7,7264
Polymers7,6152
Non-polymers1122
Water1,24369
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1710 Å2
ΔGint-36 kcal/mol
Surface area3930 Å2
MethodPISA
Unit cell
Length a, b, c (Å)42.180, 42.180, 72.220
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Space group name H-MP3221
Noncrystallographic symmetry (NCS)NCS oper: (Code: given
Matrix: (0.204527, -0.683513, -0.700699), (-0.692437, -0.606992, 0.389989), (-0.691881, 0.405427, -0.597436)
Vector: 24.68513, 30.97293, 11.8294)

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Components

#1: Protein/peptide DESULFOREDOXIN


Mass: 3807.350 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Details: ANAEROBIC, SULPHATE REDUCING BACTERIA / Source: (natural) Desulfovibrio gigas (bacteria) / References: UniProt: P00273
#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.: 69 / 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: 2.4 Å3/Da / Density % sol: 50 %
Crystal growpH: 4.5 / Details: 10% PEG 4K, 0.1M SODIUM ACETATE (PH 4.5)
Crystal grow
*PLUS
pH: 7.6 / Method: vapor diffusion
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
18 mg/mlprotein1drop
210 mMTris-HCl1drop
310 %PEG40001reservoir
40.1 Msodium acetate1reservoir
50.8 Mlithium sulfate1reservoir
60.1 Msodium acetate1reservoir

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Data collection

DiffractionMean temperature: 269 K
Diffraction sourceSource: ROTATING ANODE / Type: ENRAF-NONIUS FR571 / Wavelength: 1.5418
DetectorType: MARRESEARCH / Detector: IMAGE PLATE
RadiationMonochromator: GRAPHITE(002) / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.8→11.4 Å / Num. obs: 6529 / % possible obs: 94.2 % / Redundancy: 4.8 % / Rmerge(I) obs: 0.083
Reflection shellResolution: 1.83→1.87 Å / % possible all: 82.4
Reflection
*PLUS
Num. measured all: 31254
Reflection shell
*PLUS
% possible obs: 82.4 %

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Processing

Software
NameVersionClassification
PROTEINmodel building
X-PLOR3.1refinement
MOSFLMdata reduction
CCP4data scaling
PROTEINphasing
RefinementMethod to determine structure: SIRAS / Resolution: 1.8→8 Å / Cross valid method: R-FREE / σ(F): 2
RfactorNum. reflection% reflectionSelection details
Rfree0.187 785 7.5 %RANDOM
Rwork0.169 ---
obs0.169 10346 94.6 %-
Displacement parametersBiso mean: 14.2 Å2
Refinement stepCycle: LAST / Resolution: 1.8→8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms594 0 2 69 665
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.012
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_deg2.3
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d27.3
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d0.84
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it3
X-RAY DIFFRACTIONx_mcangle_it5
X-RAY DIFFRACTIONx_scbond_it3
X-RAY DIFFRACTIONx_scangle_it5
LS refinement shellResolution: 1.83→1.91 Å / Total num. of bins used: 8
RfactorNum. reflection% reflection
Rfree0.264 84 -
Rwork0.219 972 -
obs--83.7 %
Software
*PLUS
Name: X-PLOR / Version: 3.1 / Classification: refinement
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_deg27.3
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg0.84

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