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- PDB-1dqk: CRYSTAL STRUCTURE OF SUPEROXIDE REDUCTASE IN THE REDUCED STATE AT... -

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Basic information

Entry
Database: PDB / ID: 1dqk
TitleCRYSTAL STRUCTURE OF SUPEROXIDE REDUCTASE IN THE REDUCED STATE AT 2.0 ANGSTROMS RESOLUTION
ComponentsSUPEROXIDE REDUCTASE
KeywordsOXIDOREDUCTASE / non-heme mononuclear 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 / Resolution: 2 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 / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _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_seq_id / _struct_conn.ptnr2_label_asym_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
Water5,945330
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area12450 Å2
ΔGint-78 kcal/mol
Surface area17390 Å2
MethodPISA
Unit cell
Length a, b, c (Å)49.840, 93.210, 99.970
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-FE2 / FE (II) ION


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


Mass: 18.015 Da / Num. of mol.: 330 / 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: 2.02 Å3/Da / Density % sol: 39.19 %
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: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418
DetectorType: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: May 1, 1998
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2→22.7 Å / Num. all: 31825 / Num. obs: 31825 / % possible obs: 98.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 2.9 % / Biso Wilson estimate: 25.9 Å2 / Rmerge(I) obs: 0.06 / Net I/σ(I): 19.2
Reflection shellResolution: 2→2.07 Å / Redundancy: 2.5 % / Rmerge(I) obs: 0.242 / Num. unique all: 3038 / % possible all: 95.7
Reflection
*PLUS
Num. measured all: 92775 / Rmerge(I) obs: 0.06
Reflection shell
*PLUS
% possible obs: 95.7 % / Mean I/σ(I) obs: 4.7

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Processing

Software
NameVersionClassification
X-PLORmodel building
X-PLOR3.851refinement
DENZOdata reduction
SCALEPACKdata scaling
X-PLORphasing
RefinementResolution: 2→22.7 Å / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
Details: Since SOR contains iron and the data set was collected at a wavelength near the iron edge, an anomalous signal was expected. Therefore, the structure was refined against the separate Friedel mates
RfactorNum. reflection% reflectionSelection details
Rfree0.247 947 -3% of the 31,825 reflections were randomly selected for the test set
Rwork0.222 ---
all0.224 31825 --
obs0.224 31825 98.7 %-
Refinement stepCycle: LAST / Resolution: 2→22.7 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4056 0 4 330 4390
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.006
X-RAY DIFFRACTIONx_angle_deg1.58
Software
*PLUS
Name: X-PLOR / Version: 3.851 / Classification: refinement
Refinement
*PLUS
Highest resolution: 2 Å / Lowest resolution: 22.7 Å / σ(F): 0 / % reflection Rfree: 3 % / Rfactor obs: 0.222
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_deg29.3
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg0.68

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