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- PDB-4jyy: Crystal structure of the azide and iron substituted Clostrium dif... -

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Basic information

Entry
Database: PDB / ID: 4jyy
TitleCrystal structure of the azide and iron substituted Clostrium difficile SOD2 complex
ComponentsSuperoxide dismutase
KeywordsOXIDOREDUCTASE / Rossmann Fold / superoxide dismutase / METAL ION Binding / cytosol
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
AZIDE ION / : / Superoxide dismutase
Similarity search - Component
Biological speciesClostridium difficile (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.101 Å
AuthorsLi, W. / Ying, T.L. / Wang, C.L. / Zhao, Y. / Wang, H.F. / Tan, X.S.
CitationJournal: To be Published
Title: Crystal structure of the azide and iron substituted Clostrium difficile SOD2 complex
Authors: Li, W. / Ying, T.L. / Wang, C.L. / Zhao, Y. / Wang, H.F. / Tan, X.S.
History
DepositionApr 1, 2013Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Apr 2, 2014Provider: repository / Type: Initial release
Revision 1.1Nov 8, 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: Superoxide dismutase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,3783
Polymers24,2801
Non-polymers982
Water2,432135
1
A: Superoxide dismutase
hetero molecules

A: Superoxide dismutase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,7566
Polymers48,5602
Non-polymers1964
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation12_544x,x-y-1,-z-1/61
Buried area2110 Å2
ΔGint-9 kcal/mol
Surface area18300 Å2
MethodPISA
Unit cell
Length a, b, c (Å)80.375, 80.375, 250.532
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number179
Space group name H-MP6522
Components on special symmetry positions
IDModelComponents
11A-401-

HOH

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Components

#1: Protein Superoxide dismutase /


Mass: 24280.244 Da / Num. of mol.: 1 / Fragment: UNP residues 27-234
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Clostridium difficile (bacteria) / Strain: 630 / Gene: CD630_16310, sodA / Plasmid: pMAL-c2x / Production host: Escherichia coli (E. coli) / Strain (production host): Rosseta(DE3)Plys S / References: UniProt: Q186I6, superoxide dismutase
#2: Chemical ChemComp-FE / FE (III) ION / Iron


Mass: 55.845 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Fe
#3: Chemical ChemComp-AZI / AZIDE ION / Azide


Mass: 42.020 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: N3
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 135 / 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: 4.81 Å3/Da / Density % sol: 74.43 %
Crystal growTemperature: 289 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 60% (v/v) tacsimateTM, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 289K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 0.9795 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Jan 3, 2012 / Details: mirrors
RadiationMonochromator: Si 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 2.1→40.2 Å / Num. obs: 28940 / % possible obs: 99.9 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 3 / Redundancy: 41.9 % / Biso Wilson estimate: 35 Å2 / Rmerge(I) obs: 0.083 / Rsym value: 0.094 / Net I/σ(I): 69.6
Reflection shellResolution: 2.1→2.14 Å / Redundancy: 43.2 % / Rmerge(I) obs: 0.703 / Mean I/σ(I) obs: 9 / Rsym value: 0.671 / % possible all: 100

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Processing

Software
NameVersionClassification
ADSCQuantumdata collection
PHASESphasing
PHENIX(phenix.refine: 1.5_2)refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3TJT

3tjt


Resolution: 2.101→40.187 Å / Occupancy max: 1 / Occupancy min: 1 / FOM work R set: 0.8788 / SU ML: 0.2 / Isotropic thermal model: Isotropic / σ(F): 1 / σ(I): 1 / Phase error: 18.25 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.1977 1962 6.93 %RANDOM
Rwork0.182 ---
all0.219 28940 --
obs0.1831 28331 97.78 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 48.017 Å2 / ksol: 0.385 e/Å3
Displacement parametersBiso max: 81.75 Å2 / Biso mean: 35 Å2 / Biso min: 22.62 Å2
Baniso -1Baniso -2Baniso -3
1--1.1415 Å20 Å20 Å2
2---1.1415 Å2-0 Å2
3---2.2831 Å2
Refinement stepCycle: LAST / Resolution: 2.101→40.187 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1669 0 4 135 1808
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0071719
X-RAY DIFFRACTIONf_angle_d0.9762331
X-RAY DIFFRACTIONf_dihedral_angle_d17.114616
X-RAY DIFFRACTIONf_chiral_restr0.072241
X-RAY DIFFRACTIONf_plane_restr0.004300
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 14

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.1005-2.1530.24691320.2067176094
2.153-2.21120.22341310.2011177995
2.2112-2.27630.23161320.2042179696
2.2763-2.34980.24561360.2085183297
2.3498-2.43370.25331380.1946183997
2.4337-2.53120.1871390.1943184398
2.5312-2.64640.24181350.1959185199
2.6464-2.78580.20421410.2054188198
2.7858-2.96030.27671400.1996187998
2.9603-3.18880.2281430.1914190199
3.1888-3.50960.1861420.1806192299
3.5096-4.0170.17091470.15621955100
4.017-5.05940.14581470.14871986100
5.0594-40.19480.18181590.18792145100

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