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- PDB-3qvn: Crystal Structure of cytosolic MnSOD3 from Candida albicans -

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Basic information

Entry
Database: PDB / ID: 3qvn
TitleCrystal Structure of cytosolic MnSOD3 from Candida albicans
ComponentsManganese-containing superoxide dismutase
KeywordsOXIDOREDUCTASE / Mn Superoxide Dismutase
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
Similarity search - Component
Biological speciesCandida albicans (yeast)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.6 Å
AuthorsSheng, Y. / Cascio, D. / Valentine, J.S.
CitationJournal: J.Am.Chem.Soc. / Year: 2011
Title: Comparison of two yeast MnSODs: mitochondrial Saccharomyces cerevisiae versus cytosolic Candida albicans.
Authors: Sheng, Y. / Stich, T.A. / Barnese, K. / Gralla, E.B. / Cascio, D. / Britt, R.D. / Cabelli, D.E. / Valentine, J.S.
History
DepositionFeb 25, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 8, 2012Provider: repository / Type: Initial release
Revision 1.1Sep 13, 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_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_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_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: Manganese-containing superoxide dismutase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,8172
Polymers22,7621
Non-polymers551
Water39622
1
A: Manganese-containing superoxide dismutase
hetero molecules

A: Manganese-containing superoxide dismutase
hetero molecules

A: Manganese-containing superoxide dismutase
hetero molecules

A: Manganese-containing superoxide dismutase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)91,2668
Polymers91,0474
Non-polymers2204
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_665-x+1,-y+1,z1
crystal symmetry operation7_556y,x,-z+4/31
crystal symmetry operation10_666-y+1,-x+1,-z+4/31
Buried area10200 Å2
ΔGint-32 kcal/mol
Surface area31130 Å2
MethodPISA
Unit cell
Length a, b, c (Å)77.134, 77.134, 120.080
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number181
Space group name H-MP6422
Components on special symmetry positions
IDModelComponents
11A-211-

HOH

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Components

#1: Protein Manganese-containing superoxide dismutase / Putative uncharacterized protein CaJ7.0018


Mass: 22761.664 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Candida albicans (yeast) / Gene: CaJ7.0018, SOD3 / Plasmid: pVT102U / Production host: Saccharomyces cerevisiae (brewer's yeast) / Strain (production host): EG110 / References: UniProt: Q96UT6
#2: Chemical ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mn
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 22 / 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: 2.27 Å3/Da / Density % sol: 45.7 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 5.5
Details: 0.1M MgCl2, 0.1M NaCl, 0.1M Trisodium Citrate, 30% PEG 400, pH 5.5, vapor diffusion, hanging drop, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU FR-E+ SUPERBRIGHT / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS HTC / Detector: IMAGE PLATE / Date: Nov 19, 2010
RadiationMonochromator: CONFOCAL MIRRORS Varimax HF / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.6→44.654 Å / Num. obs: 6933 / % possible obs: 99 % / Observed criterion σ(I): -3 / Redundancy: 36.4 % / Biso Wilson estimate: 52.8 Å2 / Rmerge(I) obs: 0.179 / Χ2: 1.029 / Net I/σ(I): 8.3
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
2.6-2.6938.20.7436700.9031100
2.69-2.838.50.6496790.9471100
2.8-2.9338.80.4856761.0121100
2.93-3.0838.90.3866791.125199.9
3.08-3.2838.40.2626751.063199.7
3.28-3.5337.70.2126971.124199.9
3.53-3.88370.1686861.131199.1
3.88-4.4533.70.1326861.01197.4
4.45-5.6330.1086990.99197.1
5.6-44.6530.70.0817860.969197.8

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Phasing

PhasingMethod: molecular replacement
Phasing MRRfactor: 45.38 / Model details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation2.6 Å44.65 Å
Translation2.6 Å44.65 Å

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Processing

Software
NameVersionClassificationNB
SCALEPACKdata scaling
PHASER2.1.4phasing
PHENIX1.7_650refinement
PDB_EXTRACT3.1data extraction
CrystalCleardata collection
DENZOdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3LSU

3lsu


Resolution: 2.6→44.65 Å / Occupancy max: 1 / Occupancy min: 1 / FOM work R set: 0.7527 / SU ML: 0.44 / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2726 317 4.78 %RANDOM
Rwork0.2118 ---
obs0.2145 6626 95.09 %-
Solvent computationShrinkage radii: 0.72 Å / VDW probe radii: 1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 45.392 Å2 / ksol: 0.357 e/Å3
Displacement parametersBiso max: 134.74 Å2 / Biso mean: 52.2936 Å2 / Biso min: 24.41 Å2
Baniso -1Baniso -2Baniso -3
1-11.9167 Å2-0 Å2-0 Å2
2--11.9167 Å2-0 Å2
3----23.8334 Å2
Refinement stepCycle: LAST / Resolution: 2.6→44.65 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1593 0 1 22 1616
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0031632
X-RAY DIFFRACTIONf_angle_d0.6872223
X-RAY DIFFRACTIONf_chiral_restr0.05246
X-RAY DIFFRACTIONf_plane_restr0.004285
X-RAY DIFFRACTIONf_dihedral_angle_d12.284569
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 2

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.6-2.690.41211620.27422967312993
3.277-44.66050.22181550.1893342349797
Refinement TLS params.Method: refined / Origin x: 20.5306 Å / Origin y: 19.0058 Å / Origin z: 65.6845 Å
111213212223313233
T0.3398 Å2-0.0708 Å20.0001 Å2-0.2791 Å2-0.0171 Å2--0.2816 Å2
L0.3433 °20.245 °2-0.0814 °2-0.1838 °2-0.1084 °2--0.2901 °2
S-0.0159 Å °0.1132 Å °-0.0048 Å °0.0027 Å °0.0007 Å °0.0167 Å °0.0806 Å °-0.0046 Å °0.0135 Å °
Refinement TLS groupSelection details: ALL

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