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

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Basic information

Entry
Database: PDB / ID: 7azr
TitleCrystal structure of the iron/manganese cambialistic superoxide dismutase from Rhodobacter capsulatus complex with Mn
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: 2.1 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)44,2236
Polymers44,0332
Non-polymers1904
Water2,666148
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2300 Å2
ΔGint-25 kcal/mol
Surface area16320 Å2
MethodPISA
Unit cell
Length a, b, c (Å)162.650, 162.650, 44.000
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-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mn
#3: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ca
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 148 / 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: 62.78 %
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: 2.1→45.15 Å / Num. obs: 35121 / % possible obs: 99.98 % / Redundancy: 34.8 % / CC1/2: 0.999 / Net I/σ(I): 26.24
Reflection shellResolution: 2.1→2.175 Å / Mean I/σ(I) obs: 3.54 / Num. unique obs: 3405 / CC1/2: 0.881

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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: 2.1→45.15 Å / Cor.coef. Fo:Fc: 0.958 / Cor.coef. Fo:Fc free: 0.953 / SU B: 7.263 / SU ML: 0.1 / Cross valid method: THROUGHOUT / ESU R: 0.148 / ESU R Free: 0.129 / 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
Rfree0.19255 1764 5 %RANDOM
Rwork0.17303 ---
obs0.17404 33410 99.84 %-
Solvent computationIon probe radii: 0.7 Å / Shrinkage radii: 0.7 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 38.742 Å2
Baniso -1Baniso -2Baniso -3
1--0.07 Å2-0 Å2-0 Å2
2---0.07 Å20 Å2
3---0.14 Å2
Refinement stepCycle: LAST / Resolution: 2.1→45.15 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3106 0 4 148 3258
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0193214
X-RAY DIFFRACTIONr_bond_other_d0.0030.022826
X-RAY DIFFRACTIONr_angle_refined_deg1.2821.8534356
X-RAY DIFFRACTIONr_angle_other_deg1.1632.9316578
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.0285400
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.02425.065154
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.89215510
X-RAY DIFFRACTIONr_dihedral_angle_4_deg6.794156
X-RAY DIFFRACTIONr_chiral_restr0.0880.2442
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.023674
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02684
X-RAY DIFFRACTIONr_mcbond_it1.2691.7571599
X-RAY DIFFRACTIONr_mcbond_other1.2681.7571598
X-RAY DIFFRACTIONr_mcangle_it1.8692.6281999
X-RAY DIFFRACTIONr_mcangle_other1.8692.6282000
X-RAY DIFFRACTIONr_scbond_it1.9061.9191613
X-RAY DIFFRACTIONr_scbond_other1.9061.9191613
X-RAY DIFFRACTIONr_scangle_other3.0472.7982356
X-RAY DIFFRACTIONr_long_range_B_refined4.45820.6923728
X-RAY DIFFRACTIONr_long_range_B_other4.39220.5113705
LS refinement shellResolution: 2.1→2.153 Å
RfactorNum. reflection% reflection
Rfree0.271 126 -
Rwork0.259 2359 -
obs--98.07 %
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)
10.6521-0.8655-0.18126.18622.06832.04370.0040.04910.1157-0.60030.1724-0.0155-0.34010.1041-0.17650.0903-0.01470.01310.08220.05310.0798-50.8934.476-11.215
21.0852-1.0986-0.84786.10642.76762.1694-0.2715-0.0890.01030.87530.5203-0.44410.54740.4409-0.24880.17980.1378-0.06210.1559-0.04660.0541-42.446-22.879-6.34
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1E2 - 200
2X-RAY DIFFRACTION2A2 - 200

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