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- PDB-4br6: Crystal structure of Chaetomium thermophilum MnSOD -

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Basic information

Entry
Database: PDB / ID: 4br6
TitleCrystal structure of Chaetomium thermophilum MnSOD
ComponentsSUPEROXIDE DISMUTASE
KeywordsOXIDOREDUCTASE / DISMUTATION / ANTIOXIDANTS / THERMOSTABILITY / 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
MANGANESE (III) ION / Superoxide dismutase / Superoxide dismutase
Similarity search - Component
Biological speciesCHAETOMIUM THERMOPHILUM (fungus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsHaikarainen, T. / Frioux, C. / Zhnag, L.-Q. / Li, D.-C. / Papageorgiou, A.C.
CitationJournal: Biochim.Biophys.Acta / Year: 2014
Title: Crystal Structure and Biochemical Characterization of a Manganese Superoxide Dismutase from Chaetomium Thermophilum.
Authors: Haikarainen, T. / Frioux, C. / Zhnag, L. / Li, D. / Papageorgiou, A.C.
History
DepositionJun 4, 2013Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 18, 2013Provider: repository / Type: Initial release
Revision 1.1Jan 29, 2014Group: Database references
Revision 1.2Jul 17, 2019Group: Data collection / Category: diffrn_source / Item: _diffrn_source.pdbx_synchrotron_site
Revision 1.3Dec 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / 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_database_status.status_code_sf / _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_auth_comp_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr2_label_atom_id / _pdbx_struct_conn_angle.ptnr2_label_comp_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_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_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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)87,89615
Polymers87,4464
Non-polymers45011
Water22,9871276
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8930 Å2
ΔGint-103.9 kcal/mol
Surface area31100 Å2
MethodPISA
Unit cell
Length a, b, c (Å)69.140, 69.140, 300.430
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number169
Space group name H-MP61

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Components

#1: Protein
SUPEROXIDE DISMUTASE / / MANGANESE SUPEROXIDE DISMUTASE


Mass: 21861.432 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Source: (natural) CHAETOMIUM THERMOPHILUM (fungus)
References: UniProt: A5JTR7, UniProt: F8V325*PLUS, superoxide dismutase
#2: Chemical
ChemComp-MN3 / MANGANESE (III) ION / Manganese


Mass: 54.938 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Mn
#3: Chemical
ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Na
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 1276 / 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: 2.4 Å3/Da / Density % sol: 38.9 % / Description: NONE
Crystal growDetails: 16% PEG3350, 0.2 M NA FORMATE, 10MG/ML PROTEIN IN 10 MM TRIS-HCL BUFFER, PH 8.0

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: X13 / Wavelength: 0.8123
DetectorType: MARRESEARCH / Detector: CCD / Date: Nov 19, 2010
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.8123 Å / Relative weight: 1
ReflectionResolution: 2→20 Å / Num. obs: 54201 / % possible obs: 99 % / Observed criterion σ(I): -3 / Redundancy: 6.1 % / Rmerge(I) obs: 0.06 / Net I/σ(I): 25.4
Reflection shellResolution: 2→2.05 Å / Redundancy: 4.2 % / Rmerge(I) obs: 0.36 / Mean I/σ(I) obs: 4.1 / % possible all: 88.8

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Processing

Software
NameVersionClassification
PHENIX(PHENIX.REFINE: 1.8.2_1309)refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1VAR

1var


Resolution: 2→19.959 Å / σ(F): 2.06 / Phase error: 22.17 / Stereochemistry target values: TWIN_LSQ_F
Details: TYR9 IS MISSING THE OH GROUP OWING TO RADIATION DAMAGE
RfactorNum. reflection% reflection
Rfree0.1777 1988 3.68 %
Rwork0.1196 --
obs0.123 54085 99.31 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2→19.959 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6175 0 16 1276 7467
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0076366
X-RAY DIFFRACTIONf_angle_d18632
X-RAY DIFFRACTIONf_dihedral_angle_d12.9772251
X-RAY DIFFRACTIONf_chiral_restr0.06893
X-RAY DIFFRACTIONf_plane_restr0.0041127
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.0016-2.05160.2481310.16653494X-RAY DIFFRACTION90
2.0516-2.1070.22141410.15473744X-RAY DIFFRACTION96
2.107-2.16890.20941480.15013731X-RAY DIFFRACTION96
2.1689-2.23890.21271390.14613712X-RAY DIFFRACTION96
2.2389-2.31870.22291370.14673741X-RAY DIFFRACTION96
2.3187-2.41140.20811410.14443713X-RAY DIFFRACTION96
2.4114-2.52090.20411430.13943750X-RAY DIFFRACTION96
2.5209-2.65350.20571480.13413753X-RAY DIFFRACTION96
2.6535-2.81920.22521430.1243706X-RAY DIFFRACTION96
2.8192-3.03610.15421440.1233733X-RAY DIFFRACTION96
3.0361-3.34010.17141450.11123752X-RAY DIFFRACTION96
3.3401-3.820.15971380.10363761X-RAY DIFFRACTION96
3.82-4.79980.16271390.0893743X-RAY DIFFRACTION96
4.7998-18.94220.13891490.10953752X-RAY DIFFRACTION96

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