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- PDB-3evk: Crystal structure of the metal-bound superoxide dismutase from Py... -

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Basic information

Entry
Database: PDB / ID: 3evk
TitleCrystal structure of the metal-bound superoxide dismutase from Pyrobaculum aerophilum
ComponentsSuperoxide dismutase [Fe]
KeywordsOXIDOREDUCTASE / alpha-beta / Iron / Metal-binding
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
: / Superoxide dismutase [Fe]
Similarity search - Component
Biological speciesPyrobaculum aerophilum (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.85 Å
AuthorsLee, S.
CitationJournal: Bull.Korean Chem.Soc. / Year: 2008
Title: Crystal Structure of the Metal-bound Superoxide Dismutase from Pyrobaculum aerophilum and Comparison with the Metal-free Form
Authors: Lee, S.
History
DepositionOct 13, 2008Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Aug 25, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2Nov 1, 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_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_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: Superoxide dismutase [Fe]
B: Superoxide dismutase [Fe]
C: Superoxide dismutase [Fe]
D: Superoxide dismutase [Fe]
hetero molecules


Theoretical massNumber of molelcules
Total (without water)102,2648
Polymers102,0444
Non-polymers2204
Water3,189177
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area16310 Å2
ΔGint-57 kcal/mol
Surface area26480 Å2
MethodPISA
Unit cell
Length a, b, c (Å)94.909, 94.909, 171.890
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Space group name H-MP3221

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Components

#1: Protein
Superoxide dismutase [Fe]


Mass: 25511.055 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pyrobaculum aerophilum (archaea) / Gene: sod, PAE0274 / Plasmid: pQE30 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: O93724, superoxide dismutase
#2: Chemical
ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Mn
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 177 / 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: 2.19 Å3/Da / Density % sol: 43.84 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 22% PEG 3000, 0.15M calcium acetate, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 200 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X8C / Wavelength: 1.1 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Jun 7, 2001
RadiationMonochromator: Si 111 channel / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.1 Å / Relative weight: 1
ReflectionResolution: 1.85→47 Å / Num. all: 76717 / Num. obs: 76717 / % possible obs: 99.4 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Rmerge(I) obs: 0.076 / Net I/σ(I): 23.2
Reflection shellResolution: 1.85→1.92 Å / Rmerge(I) obs: 0.518 / Mean I/σ(I) obs: 3.7 / % possible all: 99.6

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Processing

Software
NameVersionClassification
HKL-2000data collection
AMoREphasing
REFMAC5.2.0019refinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1P7G

1p7g


Resolution: 1.85→41.54 Å / Cor.coef. Fo:Fc: 0.954 / Cor.coef. Fo:Fc free: 0.941 / SU B: 7.201 / SU ML: 0.107 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.166 / ESU R Free: 0.145 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS; the region around GLU D 37 is highly flexible and poorly defined
RfactorNum. reflection% reflectionSelection details
Rfree0.23027 7500 10.1 %RANDOM
Rwork0.20159 ---
all0.20446 67009 --
obs0.20446 67009 96.62 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 30.565 Å2
Baniso -1Baniso -2Baniso -3
1-0.06 Å20.03 Å20 Å2
2--0.06 Å20 Å2
3----0.09 Å2
Refinement stepCycle: LAST / Resolution: 1.85→41.54 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6856 0 4 177 7037
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0227048
X-RAY DIFFRACTIONr_angle_refined_deg1.081.9389556
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.0275840
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.31624.607356
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.062151192
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.4511528
X-RAY DIFFRACTIONr_chiral_restr0.0790.2992
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.025452
X-RAY DIFFRACTIONr_nbd_refined0.1880.23402
X-RAY DIFFRACTIONr_nbtor_refined0.2990.24821
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.220.2324
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1980.233
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1290.28
X-RAY DIFFRACTIONr_mcbond_it0.4731.54342
X-RAY DIFFRACTIONr_mcangle_it0.72926704
X-RAY DIFFRACTIONr_scbond_it1.17333177
X-RAY DIFFRACTIONr_scangle_it1.7484.52852
LS refinement shellResolution: 1.85→1.898 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.307 506 -
Rwork0.255 4654 -
obs--91.72 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
12.04190.038-0.20262.23940.78292.2565-0.00370.2017-0.2261-0.15420.1978-0.0790.14910.0726-0.1941-0.1536-0.0147-0.0102-0.189-0.0509-0.1897100.701868.1653-21.5696
21.88430.43020.78182.65961.86283.4263-0.10130.183-0.0538-0.06660.6622-0.8198-0.25260.8473-0.5609-0.1607-0.06630.02740.0405-0.2730.1014123.846793.3193-4.0409
32.01040.55480.92732.63840.96192.411-0.1211-0.17490.2001-0.07630.09640.0889-0.3251-0.07150.0247-0.14710.0357-0.0093-0.2022-0.0302-0.2082100.223694.6506-6.8439
41.85390.23160.12252.84732.03563.8714-0.00640.1747-0.2514-0.19270.794-1.02650.04851.1137-0.7877-0.15840.01940.0580.1855-0.41050.2574124.44369.3008-22.4855
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A12 - 222
2X-RAY DIFFRACTION2B12 - 222
3X-RAY DIFFRACTION3C12 - 222
4X-RAY DIFFRACTION4D12 - 222

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