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- PDB-3mps: Peroxide Bound Oxidized Rubrerythrin from Pyrococcus furiosus -

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Basic information

Entry
Database: PDB / ID: 3mps
TitlePeroxide Bound Oxidized Rubrerythrin from Pyrococcus furiosus
ComponentsRubrerythrin
KeywordsOXIDOREDUCTASE / Diiron / rubrerythrin / peroxidase / peroxide / oxidized
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
: / MU-OXO-DIIRON / HYDROGEN PEROXIDE / Rubrerythrin
Similarity search - Component
Biological speciesPyrococcus furiosus (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2 Å
AuthorsDillard, B.D. / 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
DepositionApr 27, 2010Deposition 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 3, 2011Group: Database references
Revision 1.3Jul 17, 2019Group: Data collection / Refinement description / Category: software
Item: _software.contact_author / _software.contact_author_email ..._software.contact_author / _software.contact_author_email / _software.location / _software.name / _software.type
Revision 1.4Feb 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_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: Rubrerythrin
B: Rubrerythrin
D: Rubrerythrin
F: Rubrerythrin
G: Rubrerythrin
H: Rubrerythrin
I: Rubrerythrin
K: Rubrerythrin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)156,62529
Polymers155,1878
Non-polymers1,43821
Water7,476415
1
A: Rubrerythrin
B: Rubrerythrin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,1646
Polymers38,7972
Non-polymers3674
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8880 Å2
ΔGint-109 kcal/mol
Surface area15060 Å2
MethodPISA
2
D: Rubrerythrin
I: Rubrerythrin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,1487
Polymers38,7972
Non-polymers3515
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8910 Å2
ΔGint-115 kcal/mol
Surface area15560 Å2
MethodPISA
3
F: Rubrerythrin
K: Rubrerythrin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,1828
Polymers38,7972
Non-polymers3856
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8960 Å2
ΔGint-109 kcal/mol
Surface area15370 Å2
MethodPISA
4
G: Rubrerythrin
H: Rubrerythrin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,1328
Polymers38,7972
Non-polymers3356
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8940 Å2
ΔGint-126 kcal/mol
Surface area15630 Å2
MethodPISA
5
A: Rubrerythrin
B: Rubrerythrin
G: Rubrerythrin
H: Rubrerythrin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)78,29514
Polymers77,5934
Non-polymers70210
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area21130 Å2
ΔGint-256 kcal/mol
Surface area27380 Å2
MethodPISA
6
D: Rubrerythrin
F: Rubrerythrin
I: Rubrerythrin
K: Rubrerythrin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)78,33015
Polymers77,5934
Non-polymers73611
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area21130 Å2
ΔGint-248 kcal/mol
Surface area27670 Å2
MethodPISA
Unit cell
Length a, b, c (Å)80.398, 105.164, 105.220
Angle α, β, γ (deg.)90.00, 90.13, 90.00
Int Tables number4
Space group name H-MP1211
Detailsdimer

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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-FE / FE (III) ION / Iron


Mass: 55.845 Da / Num. of mol.: 16 / Source method: obtained synthetically / Formula: Fe
#3: Chemical
ChemComp-FEO / MU-OXO-DIIRON


Mass: 127.689 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Fe2O
#4: Chemical ChemComp-PEO / HYDROGEN PEROXIDE / Hydrogen peroxide


Mass: 34.015 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: H2O2
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 415 / 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: 2.87 Å3/Da / Density % sol: 57.09 %
Crystal growTemperature: 297 K / Method: evaporation / pH: 6.5
Details: 0.1M Bis-Tris, 28% w/v polyethylene glycol monomethyl ether 2,000 , pH 6.5, EVAPORATION, temperature 297K

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Data collection

Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1.54 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD
Details: Si 220. Rosenbaum-Rock double-crystal monochromator: liquid nitrogen cooled; sagitally focusing 2nd crystal, Rosenbaum-Rock vertical focusing mirror
RadiationMonochromator: Si 220. Rosenbaum-Rock double-crystal monochromator: liquid nitrogen cooled; sagitally focusing 2nd crystal, Rosenbaum-Rock vertical focusing mirror
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 2→105.41 Å / Num. obs: 117636 / % possible obs: 99.58 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 6.2 / Redundancy: 7 % / Rsym value: 0.121

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
REFMACrefinement
CNSrefinement
PDB_EXTRACT3.1data extraction
HKL-2000data collection
HKL-2000data reduction
HKL-2000data scaling
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2→105.41 Å / Cor.coef. Fo:Fc: 0.896 / Cor.coef. Fo:Fc free: 0.86 / Occupancy max: 1 / Occupancy min: 1 / SU B: 5.019 / SU ML: 0.146 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.203 / ESU R Free: 0.189 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.291 5897 5 %RANDOM
Rwork0.242 ---
all0.245 ---
obs0.245 117636 99.58 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 304.87 Å2 / Biso mean: 24.062 Å2 / Biso min: 9.74 Å2
Baniso -1Baniso -2Baniso -3
1-1.51 Å20 Å2-0.16 Å2
2---0.59 Å20 Å2
3----0.92 Å2
Refinement stepCycle: LAST / Resolution: 2→105.41 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10844 0 30 415 11289
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.02211188
X-RAY DIFFRACTIONr_angle_refined_deg1.2151.96414899
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.47351352
X-RAY DIFFRACTIONr_dihedral_angle_2_deg40.5724.674522
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.28151996
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.1851539
X-RAY DIFFRACTIONr_chiral_restr0.0840.21559
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.028423
X-RAY DIFFRACTIONr_nbd_refined0.2130.25850
X-RAY DIFFRACTIONr_nbtor_refined0.3030.27643
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1660.2557
X-RAY DIFFRACTIONr_metal_ion_refined0.0170.21
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1790.265
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2610.217
X-RAY DIFFRACTIONr_mcbond_it0.5771.57012
X-RAY DIFFRACTIONr_mcangle_it0.917210824
X-RAY DIFFRACTIONr_scbond_it1.60434749
X-RAY DIFFRACTIONr_scangle_it2.424.54075
LS refinement shellResolution: 2→2.052 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.32 404 -
Rwork0.252 7903 -
all-8307 -
obs--95.37 %

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