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- PDB-1b06: SUPEROXIDE DISMUTASE FROM SULFOLOBUS ACIDOCALDARIUS -

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Basic information

Entry
Database: PDB / ID: 1b06
TitleSUPEROXIDE DISMUTASE FROM SULFOLOBUS ACIDOCALDARIUS
ComponentsPROTEIN (SUPEROXIDE DISMUTASE)
KeywordsOXIDOREDUCTASE / SUPEROXIDE DISMUTASE
Function / homology
Function and homology information


superoxide dismutase / superoxide dismutase activity / metal ion binding / cytoplasm
Similarity search - Function
Iron/manganese superoxide dismutase, C-terminal domain / Fe,Mn superoxide dismutase (SOD) domain / minor pseudopilin epsh fold / 3-Layer(bab) Sandwich / Manganese/iron superoxide dismutase, binding site / Manganese and iron superoxide dismutases signature. / Manganese/iron superoxide dismutase / Manganese/iron superoxide dismutase, N-terminal / Iron/manganese superoxide dismutases, alpha-hairpin domain / Manganese/iron superoxide dismutase, C-terminal ...Iron/manganese superoxide dismutase, C-terminal domain / Fe,Mn superoxide dismutase (SOD) domain / minor pseudopilin epsh fold / 3-Layer(bab) Sandwich / Manganese/iron superoxide dismutase, binding site / Manganese and iron superoxide dismutases signature. / Manganese/iron superoxide dismutase / Manganese/iron superoxide dismutase, N-terminal / Iron/manganese superoxide dismutases, alpha-hairpin domain / Manganese/iron superoxide dismutase, C-terminal / Manganese/iron superoxide dismutase, C-terminal domain superfamily / Iron/manganese superoxide dismutases, C-terminal domain / Manganese/iron superoxide dismutase, N-terminal domain superfamily / Helix Hairpins / Orthogonal Bundle / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
: / Superoxide dismutase [Fe]
Similarity search - Component
Biological speciesSulfolobus acidocaldarius (acidophilic)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.2 Å
AuthorsKnapp, S. / Kardinahl, S. / Niklas, H. / Tibbelin, G. / Schafer, G. / Ladenstein, R.
CitationJournal: J.Mol.Biol. / Year: 1999
Title: Refined crystal structure of a superoxide dismutase from the hyperthermophilic archaeon Sulfolobus acidocaldarius at 2.2 A resolution.
Authors: Knapp, S. / Kardinahl, S. / Hellgren, N. / Tibbelin, G. / Schafer, G. / Ladenstein, R.
History
DepositionNov 16, 1998Deposition site: BNL / Processing site: RCSB
Revision 1.0Nov 18, 1999Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Source and taxonomy / Version format compliance
Revision 1.3Dec 27, 2023Group: 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_ref_seq_dif / 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_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.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_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_ref_seq_dif.details / _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 (SUPEROXIDE DISMUTASE)
B: PROTEIN (SUPEROXIDE DISMUTASE)
C: PROTEIN (SUPEROXIDE DISMUTASE)
D: PROTEIN (SUPEROXIDE DISMUTASE)
E: PROTEIN (SUPEROXIDE DISMUTASE)
F: PROTEIN (SUPEROXIDE DISMUTASE)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)145,33212
Polymers144,9976
Non-polymers3356
Water5,783321
1
A: PROTEIN (SUPEROXIDE DISMUTASE)
B: PROTEIN (SUPEROXIDE DISMUTASE)
hetero molecules

A: PROTEIN (SUPEROXIDE DISMUTASE)
B: PROTEIN (SUPEROXIDE DISMUTASE)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)96,8888
Polymers96,6654
Non-polymers2234
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_656-x+1,y,-z+11
2
C: PROTEIN (SUPEROXIDE DISMUTASE)
D: PROTEIN (SUPEROXIDE DISMUTASE)
E: PROTEIN (SUPEROXIDE DISMUTASE)
F: PROTEIN (SUPEROXIDE DISMUTASE)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)96,8888
Polymers96,6654
Non-polymers2234
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area14250 Å2
ΔGint-59 kcal/mol
Surface area28540 Å2
MethodPISA
Unit cell
Length a, b, c (Å)168.100, 91.300, 85.700
Angle α, β, γ (deg.)90.00, 91.40, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11B-362-

HOH

21B-365-

HOH

Noncrystallographic symmetry (NCS)NCS oper: (Code: given
Matrix: (-0.506638, 0.005294, 0.862142), (-0.006206, -0.999978, 0.002493), (0.862136, -0.004088, 0.50666)
Vector: 88.40617, 90.81549, -50.50517)

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Components

#1: Protein
PROTEIN (SUPEROXIDE DISMUTASE)


Mass: 24166.236 Da / Num. of mol.: 6 / Source method: isolated from a natural source / Details: GERMAN COLLECTION OF MICROORGANISMS / Source: (natural) Sulfolobus acidocaldarius (acidophilic) / Cellular location: CYTOSOL / Strain: DSM 639 / References: UniProt: Q08713, superoxide dismutase
#2: Chemical
ChemComp-FE / FE (III) ION / Iron


Mass: 55.845 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Fe
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 321 / 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: 2.44 Å3/Da / Density % sol: 45.73 %
Crystal growpH: 7.5 / Details: pH 7.5
Crystal grow
*PLUS
Temperature: 20 ℃ / Method: vapor diffusion
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
116.25 %PEG40001reservoir
20.2 Mammonium sulfate1reservoir
35 %(w/v)2-propanol1reservoir
40.1 MHEPES1reservoir

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Data collection

DiffractionMean temperature: 286 K
Diffraction sourceSource: ROTATING ANODE / Wavelength: 1.5418
DetectorType: MARRESEARCH / Detector: IMAGE PLATE
RadiationMonochromator: NI FILTER / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.2→30 Å / Num. obs: 69271 / % possible obs: 99 % / Observed criterion σ(I): 2 / Redundancy: 3.6 % / Rmerge(I) obs: 0.101
Reflection
*PLUS
% possible obs: 99.5 % / Num. measured all: 248523
Reflection shell
*PLUS
Highest resolution: 2.2 Å / Lowest resolution: 2.25 Å / % possible obs: 95 %

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Processing

Software
NameVersionClassification
X-PLORmodel building
X-PLOR3.8refinement
DENZOdata reduction
SCALEPACKdata scaling
X-PLORphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.2→8 Å / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 2
RfactorNum. reflection% reflectionSelection details
Rfree0.223 -10 %RANDOM
Rwork0.174 ---
obs0.174 69271 99 %-
Displacement parametersBiso mean: 23 Å2
Refinement stepCycle: LAST / Resolution: 2.2→8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10176 0 6 321 10503
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.006
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_deg1.16
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d24.36
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d0.59
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
Refine LS restraints NCSNCS model details: RESTRAINTS
Xplor fileSerial no: 1 / Param file: PARAM19X.PRO / Topol file: TOPH19X.PRO
Software
*PLUS
Name: X-PLOR / Version: 3.8 / Classification: refinement
Refinement
*PLUS
Highest resolution: 2.2 Å / Lowest resolution: 8 Å / σ(F): 2 / % reflection Rfree: 10 %
Solvent computation
*PLUS
Displacement parameters
*PLUS
Biso mean: 23 Å2
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_deg24.36
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg0.59

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