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- PDB-1j30: The crystal structure of sulerythrin, a rubrerythrin-like protein... -

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Basic information

Entry
Database: PDB / ID: 1j30
TitleThe crystal structure of sulerythrin, a rubrerythrin-like protein from a strictly aerobic and thermoacidiphilic archaeon
Components144aa long hypothetical rubrerythrin
KeywordsELECTRON TRANSPORT / rubrerythrin / sulerythrin / Sulfolobus tokodaii strain 7 / four-helix bundle / domain swapping / metal binding site plasticity / STRUCTURAL GENOMICS
Function / homology
Function and homology information


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
: / OXYGEN MOLECULE / Sulerythrin / :
Similarity search - Component
Biological speciesSulfolobus tokodaii (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.7 Å
AuthorsFushinobu, S. / Shoun, H. / Wakagi, T.
Citation
Journal: Biochemistry / Year: 2003
Title: The Crystal Structure of Sulerythrin, A Rubrerythrin-like Protein from A Strictly Aerobic Archaeon, Sulfolobus tokodaii strain 7, shows unexpected domain swapping
Authors: Fushinobu, S. / Shoun, H. / Wakagi, T.
#1: Journal: FEMS Microbiol.Lett. / Year: 2003
Title: Sulerythrin, the smallest member of the rubrerythrin family, from a strictly aerobic and thermoacidophilic archaeon, Sulfolobus tokodaii strain 7
Authors: Wakagi, T.
History
DepositionJan 16, 2003Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Oct 14, 2003Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Source and taxonomy / Version format compliance
Revision 1.3Oct 25, 2023Group: 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 / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_comp_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr2_label_atom_id / _pdbx_struct_conn_angle.ptnr2_label_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _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_conn.ptnr2_label_seq_id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: 144aa long hypothetical rubrerythrin
B: 144aa long hypothetical rubrerythrin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,5038
Polymers32,1962
Non-polymers3076
Water6,323351
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7310 Å2
ΔGint-157 kcal/mol
Surface area12600 Å2
MethodPISA
2
A: 144aa long hypothetical rubrerythrin
B: 144aa long hypothetical rubrerythrin
hetero molecules

A: 144aa long hypothetical rubrerythrin
B: 144aa long hypothetical rubrerythrin
hetero molecules

A: 144aa long hypothetical rubrerythrin
B: 144aa long hypothetical rubrerythrin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)97,50824
Polymers96,5886
Non-polymers92018
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_775-y+2,x-y+2,z1
crystal symmetry operation3_575-x+y,-x+2,z1
Buried area27450 Å2
ΔGint-490 kcal/mol
Surface area32280 Å2
MethodPISA
Unit cell
Length a, b, c (Å)72.428, 72.428, 98.208
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number173
Space group name H-MP63
DetailsThe biological assembly is the dimer in the asymmetric unit.

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Components

#1: Protein 144aa long hypothetical rubrerythrin / SULERYTHRIN / 144AA LONG RUBRERYTHRIN-LIKE PROTEIN


Mass: 16098.076 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Sulfolobus tokodaii (archaea) / Strain: 7 / References: UniProt: Q96XZ7, UniProt: F9VPE5*PLUS
#2: Chemical ChemComp-FE / FE (III) ION / Iron


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


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#4: Chemical ChemComp-OXY / OXYGEN MOLECULE / Oxygen


Mass: 31.999 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: O2
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 351 / 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: 2.08 Å3/Da / Density % sol: 40.41 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 8
Details: ammonium sulfate, HEPES-NaOH, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 298.0K
Crystal grow
*PLUS
Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
150 mg/mlprotein1drop
25 mMTris-HCl1droppH8.0
32.0 Mammonium sulfate1reservoir
410 mMHEPES-NaOH1reservoirpH7.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-6A / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: May 23, 2000 / Details: mirrors
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.7→24.25 Å / Num. all: 32087 / Num. obs: 32087 / % possible obs: 99.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 5.4 % / Biso Wilson estimate: 19.7 Å2 / Rmerge(I) obs: 0.054 / Net I/σ(I): 10.1
Reflection shellResolution: 1.7→1.79 Å / Redundancy: 5.2 % / Rmerge(I) obs: 0.346 / Mean I/σ(I) obs: 2.2 / Num. unique all: 4410 / % possible all: 99.3
Reflection
*PLUS
Num. measured all: 171729
Reflection shell
*PLUS
% possible obs: 99.3 %

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Processing

Software
NameVersionClassification
CNS1.1refinement
MOSFLMdata reduction
CCP4(SCALA)data scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1RYT

1ryt


Resolution: 1.7→24.29 Å / Rfactor Rfree error: 0.006 / Data cutoff high absF: 1564993.67 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
Details: the oxygen molecules are putative. We still don't have any spectroscopic evidence to confirm that the molecule is "dioxygen".
RfactorNum. reflection% reflectionSelection details
Rfree0.223 1593 5 %RANDOM
Rwork0.192 ---
all0.194 32190 --
obs0.192 32061 99.6 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 48.4439 Å2 / ksol: 0.407613 e/Å3
Displacement parametersBiso mean: 19.6 Å2
Baniso -1Baniso -2Baniso -3
1--3.02 Å2-1.06 Å20 Å2
2---3.02 Å20 Å2
3---6.04 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.21 Å0.18 Å
Luzzati d res low-5 Å
Luzzati sigma a0.08 Å0.09 Å
Refinement stepCycle: LAST / Resolution: 1.7→24.29 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2193 0 8 351 2552
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.005
X-RAY DIFFRACTIONc_angle_deg1.1
X-RAY DIFFRACTIONc_dihedral_angle_d17
X-RAY DIFFRACTIONc_improper_angle_d0.74
X-RAY DIFFRACTIONc_mcbond_it2.161.5
X-RAY DIFFRACTIONc_mcangle_it2.472
X-RAY DIFFRACTIONc_scbond_it3.662
X-RAY DIFFRACTIONc_scangle_it4.752.5
LS refinement shellResolution: 1.7→1.81 Å / Rfactor Rfree error: 0.015 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.247 256 4.8 %
Rwork0.22 5050 -
obs--99.1 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2WATER_REP.PARAMWATER.TOP
X-RAY DIFFRACTION3ION.PARAMION.TOP
X-RAY DIFFRACTION4O2.PARAMO2.TOP
Refinement
*PLUS
% reflection Rfree: 5 %
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg17
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg0.74

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