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- PDB-4rvp: Crystal structure of superoxide dismutase from sedum alfredii -

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Basic information

Entry
Database: PDB / ID: 4rvp
TitleCrystal structure of superoxide dismutase from sedum alfredii
Componentssuperoxide dismutase
KeywordsOXIDOREDUCTASE
Function / homology
Function and homology information


superoxide dismutase / superoxide dismutase activity / metal ion binding
Similarity search - Function
Superoxide dismutase, copper/zinc binding domain / Copper/Zinc superoxide dismutase signature 1. / Superoxide dismutase, copper/zinc, binding site / Copper/Zinc superoxide dismutase signature 2. / Superoxide dismutase, copper/zinc binding domain / Superoxide dismutase (Cu/Zn) / superoxide dismutase copper chaperone / Copper/zinc superoxide dismutase (SODC) / Superoxide dismutase-like, copper/zinc binding domain superfamily / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
Superoxide dismutase [Cu-Zn]
Similarity search - Component
Biological speciesSedum alfredii (plant)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.6 Å
AuthorsQiu, R. / Li, C. / Zhai, J. / Tang, L. / Zhang, H. / Yuan, M. / Hu, X.
CitationJournal: To be Published
Title: The positive effects of Cd and Cd-Zn relationship in the Zn-related physiological processes involved in growth in the Zn/Cd hyperaccumulator Sedum alfredii
Authors: Qiu, R. / Li, C. / Zhai, J. / Tang, L. / Zhang, H. / Yuan, M. / Hu, X.
History
DepositionNov 27, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 16, 2015Provider: repository / Type: Initial release
Revision 1.1Sep 20, 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 / 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_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_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 dismutase
B: superoxide dismutase
C: superoxide dismutase
D: superoxide dismutase
E: superoxide dismutase
F: superoxide dismutase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)97,15512
Polymers96,7626
Non-polymers3926
Water1,62190
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)49.979, 85.781, 105.312
Angle α, β, γ (deg.)90.00, 99.84, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
superoxide dismutase /


Mass: 16127.049 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Sedum alfredii (plant) / Production host: Escherichia coli (E. coli) / References: UniProt: A0A0A0QA66*PLUS, superoxide dismutase
#2: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Zn
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 90 / 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: 2.3 Å3/Da / Density % sol: 46.49 %
Crystal growTemperature: 289 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 25%PEG4000,0.1M sodium cacodylate, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 289K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SEALED TUBE / Type: OXFORD DIFFRACTION ENHANCE ULTRA / Wavelength: 1.5418 Å
DetectorType: OXFORD ONYX CCD / Detector: CCD / Date: Nov 22, 2014
RadiationMonochromator: multilayer optics / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.6→25.069 Å / Num. all: 27050 / Num. obs: 27050 / % possible obs: 99.89 % / Observed criterion σ(F): 1.34 / Observed criterion σ(I): 1.34
Reflection shell
Resolution (Å)Diffraction-ID% possible all
2.6-2.692811
5.5829-25.070411

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Processing

Software
NameVersionClassification
CrysalisProdata collection
MOLREPphasing
PHENIX(phenix.refine: 1.9_1692)refinement
CrysalisProdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3KM1

3km1


Resolution: 2.6→25.069 Å / SU ML: 0.44 / σ(F): 1.34 / Phase error: 33.17 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2904 1338 4.95 %random
Rwork0.2239 ---
all0.2272 27050 --
obs0.2272 27050 99.89 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.6→25.069 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6608 0 6 90 6704
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0116734
X-RAY DIFFRACTIONf_angle_d1.8269177
X-RAY DIFFRACTIONf_dihedral_angle_d13.8482362
X-RAY DIFFRACTIONf_chiral_restr0.0741082
X-RAY DIFFRACTIONf_plane_restr0.0081247
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.6-2.69280.36841380.30982559X-RAY DIFFRACTION100
2.6928-2.80050.41851360.3112538X-RAY DIFFRACTION100
2.8005-2.92780.3381300.29852591X-RAY DIFFRACTION100
2.9278-3.08190.38671310.28582555X-RAY DIFFRACTION100
3.0819-3.27460.36411250.27992551X-RAY DIFFRACTION100
3.2746-3.52680.27131300.25182583X-RAY DIFFRACTION100
3.5268-3.88050.27861450.21852569X-RAY DIFFRACTION100
3.8805-4.43940.26431490.18962531X-RAY DIFFRACTION100
4.4394-5.58290.22861290.16942606X-RAY DIFFRACTION100
5.5829-25.07040.22551250.15732629X-RAY DIFFRACTION99

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