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- PDB-1do6: CRYSTAL STRUCTURE OF SUPEROXIDE REDUCTASE IN THE OXIDIZED STATE A... -

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Basic information

Entry
Database: PDB / ID: 1do6
TitleCRYSTAL STRUCTURE OF SUPEROXIDE REDUCTASE IN THE OXIDIZED STATE AT 2.0 ANGSTROM 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 / Resolution: 2 Å
AuthorsYeh, A.P. / Hu, Y. / Jenney Junior, F.E. / Adams, M.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 Junior, F.E. / Verhagen, M.F. / Cui, X. / Adams, M.W.
History
DepositionDec 19, 1999Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 24, 2000Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: 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 1.4Feb 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_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_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.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_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_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

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Assembly

Deposited unit
A: SUPEROXIDE REDUCTASE
B: SUPEROXIDE REDUCTASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,8004
Polymers28,6882
Non-polymers1122
Water2,306128
1
A: SUPEROXIDE REDUCTASE
B: SUPEROXIDE REDUCTASE
hetero molecules

A: SUPEROXIDE REDUCTASE
B: SUPEROXIDE REDUCTASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)57,6008
Polymers57,3774
Non-polymers2234
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_665-x+1,-y+1,z1
Buried area12210 Å2
ΔGint-41 kcal/mol
Surface area17810 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)50.310, 94.020, 52.900
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212
Components on special symmetry positions
IDModelComponents
11B-267-

HOH

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Components

#1: Protein SUPEROXIDE REDUCTASE / SOR


Mass: 14344.189 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pyrococcus furiosus (archaea) / Production host: Escherichia coli (E. coli) / References: UniProt: P82385
#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.: 128 / 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: 2.18 Å3/Da / Density % sol: 43.57 %
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: 295 K
Diffraction sourceSource: ROTATING ANODE / Type: SIEMENS / Wavelength: 1.5418
DetectorType: XENTRONICS / Detector: AREA DETECTOR / Date: Mar 21, 1997
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2→28.8 Å / Num. all: 16334 / Num. obs: 16334 / % possible obs: 92.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4 % / Biso Wilson estimate: 35.2 Å2 / Rmerge(I) obs: 0.062 / Net I/σ(I): 23.8
Reflection shellResolution: 2→2.2 Å / Redundancy: 2.4 % / Rmerge(I) obs: 0.178 / % possible all: 84.2
Reflection
*PLUS
Num. measured all: 65376
Reflection shell
*PLUS
% possible obs: 84.2 % / Mean I/σ(I) obs: 4.4

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Processing

Software
NameVersionClassification
MLPHAREphasing
X-PLOR3.851refinement
X-GENdata reduction
XDSdata scaling
RefinementResolution: 2→28.8 Å / σ(F): 0 / σ(I): 0 / Stereochemistry target values: ENGH & HUBER
RfactorNum. reflection% reflectionSelection details
Rfree0.189 1038 -6.4% OF 16,334 REFLECTIONS WERE RANDOMLY SELECTED FOR THE TEST SET
Rwork0.16 ---
all0.162 16334 --
obs0.162 16334 92.9 %-
Refinement stepCycle: LAST / Resolution: 2→28.8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2028 0 2 128 2158
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.01
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_deg1.49
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d
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
Name: X-PLOR / Version: 3.851 / Classification: refinement
Refinement
*PLUS
Highest resolution: 2 Å / Lowest resolution: 28.8 Å / σ(F): 0 / % reflection Rfree: 6.4 % / Rfactor obs: 0.16 / Rfactor Rwork: 0.16
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.01
X-RAY DIFFRACTIONx_dihedral_angle_deg29.9
X-RAY DIFFRACTIONx_improper_angle_deg0.73

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