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- PDB-1p7g: Crystal structure of superoxide dismutase from Pyrobaculum aerophilum -

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Basic information

Entry
Database: PDB / ID: 1p7g
TitleCrystal structure of superoxide dismutase from Pyrobaculum aerophilum
ComponentsSuperoxide dismutase
KeywordsOXIDOREDUCTASE / ALPHA-BETA
Function / homology
Function and homology information


superoxide dismutase / superoxide dismutase activity / metal ion binding
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
ACETATE ION / BETA-MERCAPTOETHANOL / Superoxide dismutase [Fe]
Similarity search - Component
Biological speciesPyrobaculum aerophilum (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsLee, S. / Sawaya, M.R. / Eisenberg, D.
CitationJournal: Acta Crystallogr.,Sect.D / Year: 2003
Title: Structure of superoxide dismutase from Pyrobaculum aerophilum presents a challenging case in molecular replacement with multiple molecules, pseudo-symmetry and twinning.
Authors: Lee, S. / Sawaya, M.R. / Eisenberg, D.
History
DepositionMay 1, 2003Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 2, 2003Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Aug 16, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / 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 / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Nov 15, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond / Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_2

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Superoxide dismutase
B: Superoxide dismutase
C: Superoxide dismutase
D: Superoxide dismutase
E: Superoxide dismutase
F: Superoxide dismutase
G: Superoxide dismutase
H: Superoxide dismutase
I: Superoxide dismutase
J: Superoxide dismutase
K: Superoxide dismutase
L: Superoxide dismutase
M: Superoxide dismutase
N: Superoxide dismutase
O: Superoxide dismutase
P: Superoxide dismutase
Q: Superoxide dismutase
R: Superoxide dismutase
S: Superoxide dismutase
T: Superoxide dismutase
U: Superoxide dismutase
V: Superoxide dismutase
W: Superoxide dismutase
X: Superoxide dismutase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)617,70155
Polymers615,64224
Non-polymers2,05931
Water45,6862536
1
A: Superoxide dismutase
B: Superoxide dismutase
C: Superoxide dismutase
D: Superoxide dismutase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)102,8818
Polymers102,6074
Non-polymers2744
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area17090 Å2
ΔGint-57 kcal/mol
Surface area25170 Å2
MethodPISA
2
E: Superoxide dismutase
F: Superoxide dismutase
G: Superoxide dismutase
H: Superoxide dismutase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)102,9409
Polymers102,6074
Non-polymers3335
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area17440 Å2
ΔGint-61 kcal/mol
Surface area25510 Å2
MethodPISA
3
I: Superoxide dismutase
J: Superoxide dismutase
K: Superoxide dismutase
L: Superoxide dismutase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)102,8818
Polymers102,6074
Non-polymers2744
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area17170 Å2
ΔGint-59 kcal/mol
Surface area25420 Å2
MethodPISA
4
M: Superoxide dismutase
N: Superoxide dismutase
O: Superoxide dismutase
P: Superoxide dismutase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)102,99910
Polymers102,6074
Non-polymers3926
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area17470 Å2
ΔGint-60 kcal/mol
Surface area25460 Å2
MethodPISA
5
Q: Superoxide dismutase
R: Superoxide dismutase
S: Superoxide dismutase
T: Superoxide dismutase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)102,99910
Polymers102,6074
Non-polymers3926
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area17470 Å2
ΔGint-59 kcal/mol
Surface area25390 Å2
MethodPISA
6
U: Superoxide dismutase
V: Superoxide dismutase
W: Superoxide dismutase
X: Superoxide dismutase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)102,99910
Polymers102,6074
Non-polymers3926
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area17680 Å2
ΔGint-62 kcal/mol
Surface area25070 Å2
MethodPISA
Unit cell
Length a, b, c (Å)163.429, 163.429, 172.169
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number145
Space group name H-MP32
DetailsThe biological assembly is a tetramer. There are six tetramers in the asymmetric unit.

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Components

#1: Protein ...
Superoxide dismutase /


Mass: 25651.740 Da / Num. of mol.: 24
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pyrobaculum aerophilum (archaea) / Gene: SOD OR PAE0274 / Plasmid: pQE-30 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: O93724, superoxide dismutase
#2: Chemical
ChemComp-ACT / ACETATE ION / Acetate


Mass: 59.044 Da / Num. of mol.: 19 / Source method: obtained synthetically / Formula: C2H3O2
#3: Chemical
ChemComp-BME / BETA-MERCAPTOETHANOL / 2-Mercaptoethanol


Mass: 78.133 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: C2H6OS
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 2536 / 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: 2.14 Å3/Da / Density % sol: 42.8 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: PEG 3000, calcium acetate, hepes, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal grow
*PLUS
Temperature: 295 K / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
110-15 %(v/v)PEG30001reservoir
20.1 MHEPES1reservoirpH7.5
30.15 Mcalcium acetate1reservoir
422 mg/mlprotein1drop

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X8C / Wavelength: 0.9785, 0.9708, 0.9787, 0.9863
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Jun 11, 1999 / Details: MIRRORS
RadiationMonochromator: MIRRORS / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.97851
20.97081
30.97871
40.98631
ReflectionResolution: 1.8→36.51 Å / Num. all: 476704 / Num. obs: 465126 / % possible obs: 97.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4.3 % / Biso Wilson estimate: 18.2 Å2 / Rmerge(I) obs: 0.076 / Net I/σ(I): 20.1
Reflection shellResolution: 1.8→1.86 Å / Redundancy: 1.5 % / Rmerge(I) obs: 0.302 / Mean I/σ(I) obs: 3.3 / Num. unique all: 39384 / % possible all: 82.6
Reflection
*PLUS
Highest resolution: 1.8 Å / Lowest resolution: 36.4 Å / Num. measured all: 2013670
Reflection shell
*PLUS
% possible obs: 82.6 %

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Processing

Software
NameVersionClassification
DENZOdata reduction
SCALEPACKdata scaling
GLRFphasing
CNS1refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1SSS

1sss
PDB Unreleased entry


Resolution: 1.8→36.45 Å / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
Details: Partial twinning incorporated with the twinning fraction being 0.463.
RfactorNum. reflection% reflectionSelection details
Rfree0.217 37229 -RANDOM
Rwork0.162 ---
all0.162 476704 --
obs0.162 460759 96.7 %-
Displacement parametersBiso mean: 21 Å2
Baniso -1Baniso -2Baniso -3
1-0.329 Å2-0.717 Å20 Å2
2--0.329 Å20 Å2
3----0.659 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.23 Å0.18 Å
Luzzati d res low-5 Å
Luzzati sigma a0.17 Å0.18 Å
Refinement stepCycle: LAST / Resolution: 1.8→36.45 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms41127 0 124 2536 43787
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.007
X-RAY DIFFRACTIONc_angle_deg1.4
X-RAY DIFFRACTIONc_dihedral_angle_d21.1
X-RAY DIFFRACTIONc_improper_angle_d0.86
LS refinement shellResolution: 1.8→1.86 Å
RfactorNum. reflection% reflection
Rfree0.265 3093 -
Rwork0.243 --
obs-36629 82.6 %
Refinement
*PLUS
Highest resolution: 1.8 Å
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg21.1
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg0.86
LS refinement shell
*PLUS
Rfactor Rfree: 0.263 / Rfactor Rwork: 0.241

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