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- PDB-4yip: X-ray structure of the iron/manganese cambialistic superoxide dis... -

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Basic information

Entry
Database: PDB / ID: 4yip
TitleX-ray structure of the iron/manganese cambialistic superoxide dismutase from Streptococcus mutans
ComponentsSuperoxide dismutase [Mn/Fe]
KeywordsOXIDOREDUCTASE / cambialistic
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
: / Superoxide dismutase [Mn/Fe]
Similarity search - Component
Biological speciesStreptococcus mutans (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.15 Å
AuthorsRusso Krauss, I. / Merlino, A. / Pica, A. / Sica, F.
CitationJournal: Rsc Adv / Year: 2015
Title: Fine tuning of metal-specific activity in the Mn-like group of cambialistic superoxide dismutases
Authors: Russo Krauss, I. / Merlino, A. / Pica, A. / Rullo, R. / Bertoni, A. / Capasso, A. / Amato, M. / Riccitiello, F. / De Vendittis, E. / Sica, F.
History
DepositionMar 2, 2015Deposition site: RCSB / Processing site: PDBE
Revision 1.0Jan 13, 2016Provider: repository / Type: Initial release
Revision 1.1Jan 10, 2024Group: 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 / struct_conn
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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Superoxide dismutase [Mn/Fe]
B: Superoxide dismutase [Mn/Fe]
C: Superoxide dismutase [Mn/Fe]
D: Superoxide dismutase [Mn/Fe]
hetero molecules


Theoretical massNumber of molelcules
Total (without water)94,5858
Polymers94,3624
Non-polymers2234
Water4,990277
1
A: Superoxide dismutase [Mn/Fe]
B: Superoxide dismutase [Mn/Fe]
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,2934
Polymers47,1812
Non-polymers1122
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
C: Superoxide dismutase [Mn/Fe]
D: Superoxide dismutase [Mn/Fe]
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,2934
Polymers47,1812
Non-polymers1122
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)67.964, 82.879, 72.779
Angle α, β, γ (deg.)90.00, 94.25, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
Superoxide dismutase [Mn/Fe]


Mass: 23590.414 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptococcus mutans (bacteria) / Production host: Escherichia coli (E. coli) / References: UniProt: P09738, superoxide dismutase
#2: Chemical
ChemComp-FE / FE (III) ION / Iron


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


Mass: 18.015 Da / Num. of mol.: 277 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.17 Å3/Da / Density % sol: 43.22 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: 28-33% PEG 8000, 0.1 M sodium cacodylate buffer at pH 6.0, 3% acetonitrile

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.54 Å
DetectorType: RIGAKU SATURN 944 / Detector: CCD / Date: Jan 21, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 2.15→50 Å / Num. obs: 43458 / % possible obs: 99.7 % / Redundancy: 5.7 % / Rmerge(I) obs: 0.135 / Net I/σ(I): 8.4
Reflection shellResolution: 2.15→2.23 Å / Rmerge(I) obs: 0.647 / Mean I/σ(I) obs: 2.6 / % possible all: 99.7

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Processing

Software
NameVersionClassification
REFMAC5.7.0029refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3LIO

3lio


Resolution: 2.15→31.39 Å / Cor.coef. Fo:Fc: 0.952 / Cor.coef. Fo:Fc free: 0.911 / SU B: 6.424 / SU ML: 0.165 / Cross valid method: THROUGHOUT / ESU R: 0.29 / ESU R Free: 0.229 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
RfactorNum. reflection% reflectionSelection details
Rfree0.25854 2181 5 %RANDOM
Rwork0.19346 ---
obs0.19671 41189 98.99 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 32.367 Å2
Baniso -1Baniso -2Baniso -3
1--1.4 Å20 Å2-0.62 Å2
2--1.11 Å20 Å2
3---0.33 Å2
Refinement stepCycle: LAST / Resolution: 2.15→31.39 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6395 0 4 277 6676
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.0196593
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.7311.9359026
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.675814
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.725.016321
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.977151001
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.2041520
X-RAY DIFFRACTIONr_chiral_restr0.120.21014
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.0215112
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.152→2.207 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.348 156 -
Rwork0.262 2842 -
obs--92.87 %

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