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- PDB-3qvd: Exposure of rubrerythrin from Pyrococcus furiosus to peroxide, fi... -

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Basic information

Entry
Database: PDB / ID: 3qvd
TitleExposure of rubrerythrin from Pyrococcus furiosus to peroxide, fifteen second time point.
ComponentsRubrerythrin
KeywordsOXIDOREDUCTASE / Rubrerythrin / Peroxide reduction / removal of reactive oxygen species
Function / homology
Function and homology information


oxidoreductase activity / iron ion binding
Similarity search - Function
: / Rubrerythrin, rubredoxin-like domain / Rubrerythrin, diiron-binding domain / Rubrerythrin / Rubrerythrin, domain 2 - #10 / Rubredoxin-like domain / Rubredoxin-like domain profile. / Rubrerythrin, domain 2 / Ferritin, core subunit, four-helix bundle / Ferritin ...: / Rubrerythrin, rubredoxin-like domain / Rubrerythrin, diiron-binding domain / Rubrerythrin / Rubrerythrin, domain 2 - #10 / Rubredoxin-like domain / Rubredoxin-like domain profile. / Rubrerythrin, domain 2 / Ferritin, core subunit, four-helix bundle / Ferritin / Ferritin-like diiron domain / Ferritin-like diiron domain profile. / Ferritin-like / Single Sheet / Ferritin-like superfamily / Up-down Bundle / Mainly Beta / Mainly Alpha
Similarity search - Domain/homology
: / : / HYDROGEN PEROXIDE / Rubrerythrin
Similarity search - Component
Biological speciesPyrococcus furiosus (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsDillard, B.D. / Demick, J.M. / Adams, M.W.W. / Lanzilotta, W.N.
CitationJournal: J.Biol.Inorg.Chem. / Year: 2011
Title: A cryo-crystallographic time course for peroxide reduction by rubrerythrin from Pyrococcus furiosus.
Authors: Dillard, B.D. / Demick, J.M. / Adams, M.W. / Lanzilotta, W.N.
History
DepositionFeb 25, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 22, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Aug 10, 2011Group: Database references
Revision 1.3Feb 21, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / 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_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: Rubrerythrin
B: Rubrerythrin
C: Rubrerythrin
D: Rubrerythrin
E: Rubrerythrin
F: Rubrerythrin
G: Rubrerythrin
H: Rubrerythrin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)156,88640
Polymers155,1878
Non-polymers1,70032
Water6,269348
1
A: Rubrerythrin
B: Rubrerythrin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,22210
Polymers38,7972
Non-polymers4258
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9150 Å2
ΔGint-137 kcal/mol
Surface area15120 Å2
MethodPISA
2
C: Rubrerythrin
D: Rubrerythrin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,22210
Polymers38,7972
Non-polymers4258
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9140 Å2
ΔGint-135 kcal/mol
Surface area15100 Å2
MethodPISA
3
E: Rubrerythrin
F: Rubrerythrin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,22210
Polymers38,7972
Non-polymers4258
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9140 Å2
ΔGint-135 kcal/mol
Surface area15110 Å2
MethodPISA
4
G: Rubrerythrin
H: Rubrerythrin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,22210
Polymers38,7972
Non-polymers4258
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9180 Å2
ΔGint-134 kcal/mol
Surface area15100 Å2
MethodPISA
5
A: Rubrerythrin
B: Rubrerythrin
G: Rubrerythrin
H: Rubrerythrin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)78,44320
Polymers77,5934
Non-polymers85016
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area21550 Å2
ΔGint-292 kcal/mol
Surface area27000 Å2
MethodPISA
6
C: Rubrerythrin
D: Rubrerythrin
E: Rubrerythrin
F: Rubrerythrin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)78,44320
Polymers77,5934
Non-polymers85016
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area21540 Å2
ΔGint-293 kcal/mol
Surface area26950 Å2
MethodPISA
Unit cell
Length a, b, c (Å)79.589, 104.458, 104.512
Angle α, β, γ (deg.)90.00, 90.51, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
Rubrerythrin /


Mass: 19398.340 Da / Num. of mol.: 8 / Source method: isolated from a natural source / Source: (natural) Pyrococcus furiosus (archaea) / References: UniProt: Q9UWP7
#2: Chemical
ChemComp-PEO / HYDROGEN PEROXIDE / Hydrogen peroxide


Mass: 34.015 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: H2O2
#3: Chemical...
ChemComp-FE2 / FE (II) ION


Mass: 55.845 Da / Num. of mol.: 24 / Source method: obtained synthetically / Formula: Fe
#4: Chemical
ChemComp-FE / FE (III) ION / Iron


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


Mass: 18.015 Da / Num. of mol.: 348 / 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: 2.8 Å3/Da / Density % sol: 56.06 %
Crystal growTemperature: 298 K / Method: capillary batch / pH: 7.2
Details: Performed in an anaerobic chamber with less than 1 ppm oxygen at all times. 0.02 M TRIS, 30% PEG 2K MME, pH 7.2, Capillary batch, temperature 298K

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Data collection

DiffractionMean temperature: 115 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1 Å
DetectorType: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: Nov 21, 2010
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2→50 Å / Num. all: 115349 / Num. obs: 111550 / % possible obs: 96.7 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 4.1 % / Biso Wilson estimate: 26.9 Å2 / Rmerge(I) obs: 0.1 / Rsym value: 0.09 / Net I/σ(I): 21.9

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Processing

Software
NameClassification
HKL-2000data collection
CNSrefinement
HKL-2000data reduction
HKL-2000data scaling
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2→46.73 Å / Rfactor Rfree error: 0.003 / Data cutoff high absF: 220179.79 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber / Details: BULK SOLVENT MODEL USED
RfactorNum. reflection% reflectionSelection details
Rfree0.235 5629 5 %RANDOM
Rwork0.211 ---
obs0.211 111550 96.7 %-
all-115349 --
Solvent computationSolvent model: FLAT MODEL / Bsol: 68.5632 Å2 / ksol: 0.4 e/Å3
Displacement parametersBiso mean: 39.3 Å2
Baniso -1Baniso -2Baniso -3
1-11.12 Å20 Å20.01 Å2
2---5.76 Å20 Å2
3----5.36 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.27 Å0.23 Å
Luzzati d res low-5 Å
Luzzati sigma a0.1 Å-0.02 Å
Refinement stepCycle: LAST / Resolution: 2→46.73 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10904 0 36 348 11288
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.006
X-RAY DIFFRACTIONc_angle_deg1.1
X-RAY DIFFRACTIONc_dihedral_angle_d18.9
X-RAY DIFFRACTIONc_improper_angle_d0.69
X-RAY DIFFRACTIONc_mcbond_it1.231.5
X-RAY DIFFRACTIONc_mcangle_it1.782
X-RAY DIFFRACTIONc_scbond_it2.252
X-RAY DIFFRACTIONc_scangle_it3.392.5
Refine LS restraints NCSNCS model details: NONE
LS refinement shellResolution: 2→2.13 Å / Rfactor Rfree error: 0.009 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.262 932 5.3 %
Rwork0.221 16708 -
obs--92.2 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2water_rep.paramion.top
X-RAY DIFFRACTION3ion.paramwater.top
X-RAY DIFFRACTION4ligand.paramligand.top
X-RAY DIFFRACTION5feo.paramfeo.top

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