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- PDB-3esf: Crystal Structure of the enzyme Fe-superoxide dismutase TbSODB2 f... -

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Basic information

Entry
Database: PDB / ID: 3esf
TitleCrystal Structure of the enzyme Fe-superoxide dismutase TbSODB2 from Trypanosoma brucei
ComponentsIron-containing superoxide dismutase B2
KeywordsOXIDOREDUCTASE / alpha/beta
Function / homology
Function and homology information


superoxide dismutase / superoxide dismutase activity / metal ion binding
Similarity search - Function
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
Similarity search - Domain/homology
: / Superoxide dismutase
Similarity search - Component
Biological speciesTrypanosoma brucei (eukaryote)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.01 Å
AuthorsBachega, J.F.R. / Navarro, M.V.A.S. / Garratt, R.C.
CitationJournal: Proteins / Year: 2009
Title: Systematic structural studies of iron superoxide dismutases from human parasites and a statistical coupling analysis of metal binding specificity
Authors: Bachega, J.F. / Navarro, M.V. / Bleicher, L. / Bortoleto-Bugs, R.K. / Dive, D. / Hoffmann, P. / Viscogliosi, E. / Garratt, R.C.
History
DepositionOct 5, 2008Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 12, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Refinement description / Version format compliance
Revision 1.2Oct 20, 2021Group: Database references / Derived calculations
Category: database_2 / struct_conn ...database_2 / 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
Revision 1.3Sep 6, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model / struct_ncs_dom_lim
Item: _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.end_auth_comp_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Iron-containing superoxide dismutase B2
B: Iron-containing superoxide dismutase B2
C: Iron-containing superoxide dismutase B2
D: Iron-containing superoxide dismutase B2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)88,8198
Polymers88,5954
Non-polymers2234
Water12,719706
1
A: Iron-containing superoxide dismutase B2
B: Iron-containing superoxide dismutase B2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)44,4094
Polymers44,2982
Non-polymers1122
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1790 Å2
ΔGint-13 kcal/mol
Surface area16990 Å2
MethodPISA
2
C: Iron-containing superoxide dismutase B2
D: Iron-containing superoxide dismutase B2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)44,4094
Polymers44,2982
Non-polymers1122
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1790 Å2
ΔGint-13 kcal/mol
Surface area16980 Å2
MethodPISA
Unit cell
Length a, b, c (Å)68.302, 76.504, 76.981
Angle α, β, γ (deg.)90.00, 92.70, 90.00
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
31C
41D

NCS domain segments:

Component-ID: 1 / Ens-ID: 1 / Beg auth comp-ID: MET / Beg label comp-ID: MET / End auth comp-ID: ARG / End label comp-ID: ARG / Refine code: 2 / Auth seq-ID: 1 - 197 / Label seq-ID: 1 - 197

Dom-IDAuth asym-IDLabel asym-ID
1AA
2BB
3CC
4DD

NCS ensembles :
ID
1
2

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Components

#1: Protein
Iron-containing superoxide dismutase B2


Mass: 22148.807 Da / Num. of mol.: 4 / Mutation: A159T
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Trypanosoma brucei (eukaryote) / Gene: sodb2 / Plasmid: pET28a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 (DE3) / References: UniProt: Q2KN30, superoxide dismutase
#2: Chemical
ChemComp-FE / FE (III) ION


Mass: 55.845 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Fe
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 706 / 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: 45.76 %
Crystal growTemperature: 291 K / Method: hanging drop / pH: 8.5
Details: 0.1 M Tris pH 8.5, 24-30% PEG4000 and 0.2 M MgCl2, hanging drop, temperature 291K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.54 Å
DetectorType: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: May 1, 2006
RadiationMonochromator: CONFOCAL MIRROR / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 2→30.3 Å / Num. all: 52771 / Num. obs: 52751 / % possible obs: 98.4 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 4.4 % / Rmerge(I) obs: 0.08 / Rsym value: 0.08
Reflection shellResolution: 2→2.059 Å / Redundancy: 2.9 % / Rmerge(I) obs: 0.298 / Mean I/σ(I) obs: 3.8 / Rsym value: 0.298 / % possible all: 89.7

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
MOSFLMdata reduction
SCALAdata scaling
MOLREPphasing
REFMAC5.2.0019refinement
PDB_EXTRACT3.006data extraction
MAR345dtbdata collection
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 2GPC

2gpc


Resolution: 2.01→30.18 Å / Cor.coef. Fo:Fc: 0.946 / Cor.coef. Fo:Fc free: 0.921 / Occupancy max: 1 / Occupancy min: 0 / SU B: 8.961 / SU ML: 0.114 / TLS residual ADP flag: LIKELY RESIDUAL / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / ESU R: 0.202 / ESU R Free: 0.168 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.21911 2666 5.1 %RANDOM
Rwork0.17499 ---
obs0.17721 50085 99.44 %-
all-50082 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 20.698 Å2
Baniso -1Baniso -2Baniso -3
1--0.02 Å20 Å2-0.01 Å2
2--0.02 Å20 Å2
3----0.01 Å2
Refinement stepCycle: LAST / Resolution: 2.01→30.18 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6272 0 4 706 6982
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0226516
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.4181.9078870
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg10.3125792
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.74924.438320
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.87315985
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.1241517
X-RAY DIFFRACTIONr_chiral_restr0.1030.2904
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.025133
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.20.23295
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3020.24464
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1570.2552
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1920.252
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1440.216
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.5641.54034
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it0.88126310
X-RAY DIFFRACTIONr_scbond_it1.75332931
X-RAY DIFFRACTIONr_scangle_it2.6864.52558
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Ens-ID: 1 / Refine-ID: X-RAY DIFFRACTION

Dom-IDAuth asym-IDNumberTypeRms dev position (Å)Weight position
1A778tight positional0.050.05
2B778tight positional0.060.05
3C778tight positional0.070.05
4D778tight positional0.060.05
1A758medium positional0.430.5
2B758medium positional0.380.5
3C758medium positional0.640.5
4D758medium positional0.40.5
1A778tight thermal0.150.5
2B778tight thermal0.160.5
3C778tight thermal0.150.5
4D778tight thermal0.130.5
1A758medium thermal0.722
2B758medium thermal0.832
3C758medium thermal0.752
4D758medium thermal0.672
LS refinement shellResolution: 2.01→2.059 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.258 211 -
Rwork0.198 3432 -
obs--94.23 %
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)
10.8473-0.4385-0.08181.68470.15311.8516-0.0229-0.0987-0.07810.3585-0.01450.15080.12910.030.0374-0.0167-0.04220.0667-0.0882-0.0017-0.10822.172-5.783132.8563
20.9115-0.0987-0.35761.89441.25172.29910.01320.16760.0095-0.1495-0.11080.0872-0.1446-0.13610.0977-0.14350.0003-0.0193-0.0573-0.005-0.138223.72025.82844.7689
31.3412-0.02620.20111.8983-0.47481.47750.0056-0.06280.15310.24320.004-0.2658-0.18180.0041-0.0096-0.10980.0053-0.0506-0.0905-0.0119-0.048957.039216.027424.8105
41.1576-0.1334-0.0682.83730.64351.72550.05760.0316-0.1565-0.16980.0317-0.40670.15510.0539-0.0893-0.1139-0.0082-0.0089-0.0936-0.00430.011156.8682-12.020113.0792
50.50930.0249-0.06080.590.10510.2749-0.01730.0133-0.02320.0517-0.0154-0.04440.018-0.01130.03260.01310.0032-0.00360.0355-0.0027-0.031438.32142.016418.6842
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 197
2X-RAY DIFFRACTION2B1 - 197
3X-RAY DIFFRACTION3C1 - 197
4X-RAY DIFFRACTION4D1 - 197
5X-RAY DIFFRACTION5A204 - 900
6X-RAY DIFFRACTION5C203 - 904
7X-RAY DIFFRACTION5B205 - 902
8X-RAY DIFFRACTION5D208 - 897

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