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- PDB-1dqi: CRYSTAL STRUCTURE OF SUPEROXIDE REDUCTASE FROM P. FURIOSUS IN THE... -

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Basic information

Entry
Database: PDB / ID: 1dqi
TitleCRYSTAL STRUCTURE OF SUPEROXIDE REDUCTASE FROM P. FURIOSUS IN THE OXIDIZED STATE AT 1.7 ANGSTROMS RESOLUTION
ComponentsSUPEROXIDE REDUCTASE
KeywordsOXIDOREDUCTASE / non-heme iron protein / immunoglobulin-like (Ig) beta barrel fold
Function / homology
Function and homology information


superoxide reductase / superoxide reductase activity / iron ion binding
Similarity search - Function
SOR catalytic domain / Desulfoferrodoxin, ferrous iron-binding domain / Desulfoferrodoxin, ferrous iron-binding domain superfamily / : / Desulfoferrodoxin / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
: / Superoxide reductase
Similarity search - Component
Biological speciesPyrococcus furiosus (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 1.7 Å
AuthorsYeh, A.P. / Hu, Y. / Jenney Jr., F.E. / Adams, M.W.W. / Rees, D.C.
Citation
Journal: Biochemistry / Year: 2000
Title: Structures of the superoxide reductase from Pyrococcus furiosus in the oxidized and reduced states.
Authors: Yeh, A.P. / Hu, Y. / Jenney Jr., F.E. / Adams, M.W. / Rees, D.C.
#1: Journal: Science / Year: 1999
Title: Anaerobic Microbes: Oxygen Detoxification Without Superoxide Dismutase
Authors: Jenney Jr., F.E. / Verhagen, M.F. / Cui, X. / Adams, M.W.W.
History
DepositionJan 4, 2000Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 10, 2000Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 7, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / 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.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _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_asym_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: SUPEROXIDE REDUCTASE
B: SUPEROXIDE REDUCTASE
C: SUPEROXIDE REDUCTASE
D: SUPEROXIDE REDUCTASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)57,6008
Polymers57,3774
Non-polymers2234
Water7,494416
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area12300 Å2
ΔGint-68 kcal/mol
Surface area17760 Å2
MethodPISA
Unit cell
Length a, b, c (Å)49.662, 93.191, 99.505
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein
SUPEROXIDE REDUCTASE / SOR


Mass: 14344.189 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Source: (natural) Pyrococcus furiosus (archaea) / References: UniProt: P82385
#2: Chemical
ChemComp-FE / FE (III) ION


Mass: 55.845 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Fe
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 416 / Source method: isolated from a natural source / Formula: H2O
Compound detailsThis structure of oxidized SOR is different from the 2.0 Angstroms resolution structure of oxidized ...This structure of oxidized SOR is different from the 2.0 Angstroms resolution structure of oxidized SOR in that the data set for this structure was collected under cryogenic temperatures and is at a higher resolution of 1.7 Angstroms

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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: 2.01 Å3/Da / Density % sol: 38.67 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop / pH: 8
Details: PEG4000, Tris-hydrochloride, pH 8.0, glycerol, sodium chloride, ethanol, VAPOR DIFFUSION, SITTING DROP, temperature 295K
Crystal
*PLUS
Density % sol: 44 %
Crystal grow
*PLUS
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
1100 mg/mlprotein1drop
250 mMTris-HCl1drop
322 %PEG40001reservoir
4100 mMTris-HCl1reservoir
510 %(v/v)glycerol1reservoir
6200 mM1reservoirNaCl
72 %(v/v)ethanol1reservoir

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Data collection

DiffractionMean temperature: 90 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL9-1 / Wavelength: 0.98
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Dec 13, 1997
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 1.7→29.6 Å / Num. all: 51080 / Num. obs: 51080 / % possible obs: 99.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4.3 % / Biso Wilson estimate: 19.2 Å2 / Rmerge(I) obs: 0.063 / Net I/σ(I): 21.7
Reflection shellResolution: 1.7→1.73 Å / Redundancy: 4.2 % / Rmerge(I) obs: 0.251 / Num. unique all: 2506 / % possible all: 99.8
Reflection
*PLUS
Num. measured all: 222107
Reflection shell
*PLUS
% possible obs: 99.8 % / Mean I/σ(I) obs: 5.5

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Processing

Software
NameVersionClassification
AMoREphasing
X-PLOR3.851refinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementResolution: 1.7→29.6 Å / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.217 1532 -3% of the 51080 reflections were randomly selected for the test set.
Rwork0.203 ---
all0.204 51080 --
obs0.204 51080 99.5 %-
Refinement stepCycle: LAST / Resolution: 1.7→29.6 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4056 0 4 416 4476
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.004
X-RAY DIFFRACTIONx_angle_deg1.24
Software
*PLUS
Name: X-PLOR / Version: 3.851 / Classification: refinement
Refinement
*PLUS
Highest resolution: 1.7 Å / Lowest resolution: 29.6 Å / σ(F): 0 / % reflection Rfree: 3 % / Rfactor obs: 0.203
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_deg29.6
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg0.55

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