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- PDB-3qhc: Crystal structure of Symerythrin from Cyanophora paradoxa, reduce... -

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Basic information

Entry
Database: PDB / ID: 3qhc
TitleCrystal structure of Symerythrin from Cyanophora paradoxa, reduced with dithionite
ComponentsSymerythrin
KeywordsOXIDOREDUCTASE / four-helix bundle / rubrerythrin-like / carboxylate bridged-diiron / ferritin-like / ferritin-like superfamily
Function / homology
Function and homology information


cyanelle / oxidoreductase activity / metal ion binding
Similarity search - Function
Rubrerythrin, diiron-binding domain / Rubrerythrin / Ferritin, core subunit, four-helix bundle / Ferritin / Ferritin-like diiron domain / Ferritin-like diiron domain profile. / Ferritin-like / Ferritin-like superfamily / Up-down Bundle / Mainly Alpha
Similarity search - Domain/homology
: / Uncharacterized protein in petA-psaM intergenic region
Similarity search - Component
Biological speciesCyanophora paradoxa (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.25 Å
AuthorsCooley, R.B. / Arp, D.J. / Karplus, P.A.
CitationJournal: J.Mol.Biol. / Year: 2011
Title: Symerythrin structures at atomic resolution and the origins of rubrerythrins and the ferritin-like superfamily.
Authors: Cooley, R.B. / Arp, D.J. / Karplus, P.A.
History
DepositionJan 25, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 31, 2011Provider: repository / Type: Initial release
Revision 1.1Oct 12, 2011Group: Database references

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Symerythrin
B: Symerythrin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)40,0998
Polymers39,7642
Non-polymers3356
Water9,998555
1
A: Symerythrin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)20,0504
Polymers19,8821
Non-polymers1683
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Symerythrin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)20,0504
Polymers19,8821
Non-polymers1683
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)81.499, 81.499, 46.341
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number145
Space group name H-MP32

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Components

#1: Protein Symerythrin / ORF180


Mass: 19882.162 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Cyanophora paradoxa (eukaryote) / Cellular location: Plastid; Cyanelle / Gene: ORF180 / Plasmid: pT7-7 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P48329
#2: Chemical
ChemComp-FE / FE (III) ION


Mass: 55.845 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Fe
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 555 / 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: 2.23 Å3/Da / Density % sol: 44.95 %
Crystal growTemperature: 279 K / Method: hanging drop / pH: 5.5
Details: PEG3350, NH4Cl, BisTris, dithionite, pH 5.5, hanging drop, temperature 279K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.1 / Wavelength: 0.976 Å
DetectorType: ADSC Q315R / Detector: CCD / Date: Sep 23, 2010
RadiationMonochromator: Si(220) Asymmetric cut single crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.976 Å / Relative weight: 1
ReflectionResolution: 1.25→30.6 Å / Num. all: 95243 / Num. obs: 95243 / % possible obs: 100 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 11.9 % / Biso Wilson estimate: 11 Å2 / Rmerge(I) obs: 0.101 / Rsym value: 0.101 / Net I/σ(I): 15
Reflection shellResolution: 1.25→1.31 Å / Redundancy: 10.4 % / Rmerge(I) obs: 0.405 / Mean I/σ(I) obs: 5.4 / Num. unique all: 13875 / Rsym value: 0.405 / % possible all: 100

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Processing

Software
NameVersionClassificationNB
SCALAdata scaling
REFMAC5.5.0110refinement
PDB_EXTRACT3.1data extraction
ADSCQuantumdata collection
MOSFLMdata reduction
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.25→26.68 Å / Cor.coef. Fo:Fc: 0.982 / Cor.coef. Fo:Fc free: 0.977 / Occupancy max: 1 / Occupancy min: 0.2 / SU B: 1.093 / SU ML: 0.022 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.036 / Stereochemistry target values: Engh & Huber
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.1414 4767 5 %RANDOM
Rwork0.1147 ---
all0.116 95243 --
obs0.116 95216 99.99 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso max: 58.57 Å2 / Biso mean: 16.7486 Å2 / Biso min: 4.85 Å2
Baniso -1Baniso -2Baniso -3
1--0.73 Å2-0.36 Å2-0 Å2
2---0.73 Å2-0 Å2
3---1.09 Å2
Refinement stepCycle: LAST / Resolution: 1.25→26.68 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2764 0 6 555 3325
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0220.0223066
X-RAY DIFFRACTIONr_bond_other_d0.0010.022020
X-RAY DIFFRACTIONr_angle_refined_deg2.8371.9564194
X-RAY DIFFRACTIONr_angle_other_deg1.35834988
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.5045424
X-RAY DIFFRACTIONr_dihedral_angle_2_deg40.23325.526152
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.14615551
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.5561516
X-RAY DIFFRACTIONr_chiral_restr0.1710.2471
X-RAY DIFFRACTIONr_gen_planes_refined0.0150.023587
X-RAY DIFFRACTIONr_gen_planes_other0.0030.02613
X-RAY DIFFRACTIONr_mcbond_it2.811.51935
X-RAY DIFFRACTIONr_mcbond_other1.6511.5774
X-RAY DIFFRACTIONr_mcangle_it3.81523129
X-RAY DIFFRACTIONr_scbond_it5.71631131
X-RAY DIFFRACTIONr_scangle_it8.0414.51043
X-RAY DIFFRACTIONr_rigid_bond_restr2.8635086
X-RAY DIFFRACTIONr_sphericity_free17.9353561
X-RAY DIFFRACTIONr_sphericity_bonded10.27935008
LS refinement shellResolution: 1.25→1.282 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.246 332 -
Rwork0.206 6700 -
all-7032 -
obs--100 %

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