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- PDB-7azq: Crystal structure of the iron/manganese cambialistic superoxide d... -

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Basic information

Entry
Database: PDB / ID: 7azq
TitleCrystal structure of the iron/manganese cambialistic superoxide dismutase from Rhodobacter capsulatus complex with Fe
ComponentsSuperoxide dismutase [Fe]
KeywordsOXIDOREDUCTASE / superoxide oxidoreductase / SODs / metal ion binding protein.
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 / Manganese/iron superoxide dismutase, N-terminal domain superfamily / Iron/manganese superoxide dismutases, C-terminal domain
Similarity search - Domain/homology
: / Superoxide dismutase [Fe]
Similarity search - Component
Biological speciesRhodobacter capsulatus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsPonce-Salvatierra, A. / Hermoso, J.A.
CitationJournal: To be published
Title: Structural and functional characterization of the cambialistic superoxide dismutase from Rhodobacter capsulatus.
Authors: Ponce-Salvatierra, A. / Di Capua, C. / Gonzalez, J. / Cortez, N. / Hermoso, J.A.
History
DepositionNov 17, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 1, 2021Provider: repository / Type: Initial release
Revision 1.1Jan 31, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Superoxide dismutase [Fe]
E: Superoxide dismutase [Fe]
hetero molecules


Theoretical massNumber of molelcules
Total (without water)44,1855
Polymers44,0332
Non-polymers1523
Water3,603200
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2220 Å2
ΔGint-19 kcal/mol
Surface area16260 Å2
MethodPISA
Unit cell
Length a, b, c (Å)162.790, 162.790, 43.840
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212

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Components

#1: Protein Superoxide dismutase [Fe]


Mass: 22016.709 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rhodobacter capsulatus (bacteria) / Gene: sodB, sod / Production host: Escherichia coli (E. coli) / References: UniProt: O30970, superoxide dismutase
#2: Chemical ChemComp-FE / FE (III) ION


Mass: 55.845 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Fe
#3: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 200 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 3.3 Å3/Da / Density % sol: 62.7 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 7.5 / Details: 58% MPD, 200 mM CaCl2, and 100 mM HEPES

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.97909 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Jun 7, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97909 Å / Relative weight: 1
ReflectionResolution: 2→57.62 Å / Num. obs: 40497 / % possible obs: 99.85 % / Redundancy: 122 % / CC1/2: 0.942 / Net I/σ(I): 17.11
Reflection shellResolution: 2→2.072 Å / Mean I/σ(I) obs: 3.37 / Num. unique obs: 3978 / CC1/2: 0.833 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.8.0258refinement
MOSFLMdata reduction
SCALAdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1dt0

1dt0


Resolution: 2→57.62 Å / Cor.coef. Fo:Fc: 0.959 / Cor.coef. Fo:Fc free: 0.955 / SU B: 5.673 / SU ML: 0.084 / Cross valid method: THROUGHOUT / ESU R: 0.125 / ESU R Free: 0.113 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: U VALUES : WITH TLS ADDED HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : RESIDUAL ONLY
RfactorNum. reflection% reflectionSelection details
Rfree0.1882 2027 5 %RANDOM
Rwork0.1686 ---
obs0.1696 38414 99.86 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.3 Å / Solvent model: MASK
Displacement parametersBiso mean: 33.514 Å2
Baniso -1Baniso -2Baniso -3
1-0.59 Å2-0 Å2-0 Å2
2--0.59 Å20 Å2
3----1.18 Å2
Refinement stepCycle: LAST / Resolution: 2→57.62 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3106 0 3 200 3309
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0193214
X-RAY DIFFRACTIONr_bond_other_d0.0010.022824
X-RAY DIFFRACTIONr_angle_refined_deg1.4221.8534340
X-RAY DIFFRACTIONr_angle_other_deg1.2122.9316569
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.1325398
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.69125.033153
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.37315507
X-RAY DIFFRACTIONr_dihedral_angle_4_deg5.296156
X-RAY DIFFRACTIONr_chiral_restr0.0930.2441
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.023656
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02688
X-RAY DIFFRACTIONr_mcbond_it0.7091.411594
X-RAY DIFFRACTIONr_mcbond_other0.7091.411593
X-RAY DIFFRACTIONr_mcangle_it1.12.1111991
X-RAY DIFFRACTIONr_mcangle_other1.0992.1111992
X-RAY DIFFRACTIONr_scbond_it1.4821.5331618
X-RAY DIFFRACTIONr_scbond_other1.4831.5331616
X-RAY DIFFRACTIONr_scangle_other1.8342.2422347
X-RAY DIFFRACTIONr_long_range_B_refined3.81917.0823770
X-RAY DIFFRACTIONr_long_range_B_other3.7216.7473730
LS refinement shellResolution: 2→2.052 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.243 165 -
Rwork0.227 2767 -
obs--100 %
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)
11.6669-0.3053-0.1894.83571.45692.43050.02080.17460.0836-1.04770.16670.0156-0.42940.1051-0.18760.2596-0.00870.02860.10350.05090.0517-51.1750.54-20.157
22.0043-3.0045-2.49135.21663.25623.79010.0211-0.19760.181-0.1120.263-0.3912-0.20480.3374-0.28410.1621-0.04570.0540.13330.01960.1703-51.08318.735-2.51
30.8594-0.6373-0.10755.38171.5951.7682-0.1218-0.04870.12530.05260.3167-0.0603-0.13660.1227-0.19490.04510.01330.01590.08880.0220.0667-50.7064.938-4.787
42.3743-0.4512-1.93874.5812.20384.8361-0.2134-0.40570.15071.23380.804-0.77110.80640.7757-0.59060.38630.2854-0.24950.2567-0.17870.1769-37.42-17.5323.28
53.8446-0.8066-1.59674.98053.45942.955-0.3029-0.23340.0031.3920.406-0.00981.03690.3337-0.10310.45390.1624-0.01450.09290.00430.0338-49.229-20.8081.679
63.4577-2.77391.4636.95463.24924.8264-0.2541-0.04890.19760.37540.4486-0.49790.16260.4225-0.19460.18290.11250.03430.1968-0.02370.0694-37.821-35.494-16.166
71.3615-1.2802-0.72864.922.07652.084-0.1308-0.0089-0.01920.15940.3636-0.27710.25980.316-0.23270.06790.0761-0.02450.1513-0.04470.0433-43.881-23.449-12.486
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1E2 - 88
2X-RAY DIFFRACTION2E89 - 111
3X-RAY DIFFRACTION3E112 - 200
4X-RAY DIFFRACTION4A2 - 53
5X-RAY DIFFRACTION5A54 - 88
6X-RAY DIFFRACTION6A89 - 111
7X-RAY DIFFRACTION7A112 - 200

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