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- PDB-1b71: RUBRERYTHRIN -

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Basic information

Entry
Database: PDB / ID: 1b71
TitleRUBRERYTHRIN
ComponentsPROTEIN (RUBRERYTHRIN)
KeywordsELECTRON TRANSPORT / IRON / FERROXIDASE
Function / homology
Function and homology information


oxidoreductase activity / iron ion binding / cytoplasm
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
Biological speciesDesulfovibrio vulgaris subsp. vulgaris str. Hildenborough (bacteria)
MethodX-RAY DIFFRACTION / OTHER / Resolution: 1.9 Å
AuthorsSieker, L.C. / Holmes, M. / Le Trong, I. / Turley, S. / Santarsiero, B.D. / Liu, M.-Y. / Legall, J. / Stenkamp, R.E.
CitationJournal: Nat.Struct.Biol. / Year: 1999
Title: Alternative metal-binding sites in rubrerythrin.
Authors: Sieker, L.C. / Holmes, M. / Le Trong, I. / Turley, S. / Santarsiero, B.D. / Liu, M.Y. / LeGall, J. / Stenkamp, R.E.
History
DepositionJan 26, 1999Processing site: RCSB
Revision 1.0Jan 26, 2000Provider: repository / Type: Initial release
Revision 1.1Apr 26, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Oct 29, 2014Group: Derived calculations
Revision 1.4Oct 4, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 1.5Aug 9, 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_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_alt_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_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_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_alt_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.pdbx_ptnr1_label_alt_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_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: PROTEIN (RUBRERYTHRIN)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,7544
Polymers21,5771
Non-polymers1773
Water3,081171
1
A: PROTEIN (RUBRERYTHRIN)
hetero molecules

A: PROTEIN (RUBRERYTHRIN)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,5098
Polymers43,1552
Non-polymers3546
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_555-x,y,-z1
Buried area3200 Å2
ΔGint-65 kcal/mol
Surface area18030 Å2
MethodPISA
2
A: PROTEIN (RUBRERYTHRIN)
hetero molecules

A: PROTEIN (RUBRERYTHRIN)
hetero molecules

A: PROTEIN (RUBRERYTHRIN)
hetero molecules

A: PROTEIN (RUBRERYTHRIN)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)87,01816
Polymers86,3094
Non-polymers70812
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,-y,z1
crystal symmetry operation3_555-x,y,-z1
crystal symmetry operation4_555x,-y,-z1
Buried area12690 Å2
ΔGint-156 kcal/mol
Surface area29780 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)49.300, 81.300, 100.100
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number23
Space group name H-MI222
Components on special symmetry positions
IDModelComponents
11A-327-

HOH

21A-360-

HOH

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Components

#1: Protein PROTEIN (RUBRERYTHRIN)


Mass: 21577.281 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Desulfovibrio vulgaris subsp. vulgaris str. Hildenborough (bacteria)
Species: Desulfovibrio vulgaris / Strain: HILDENBOROUGH / References: UniProt: P24931
#2: Chemical ChemComp-FE / FE (III) ION


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.: 1 / Source method: obtained synthetically / Formula: Zn
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 171 / 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: 2.32 Å3/Da / Density % sol: 47.07 %
Crystal growpH: 8 / Details: pH 8
Crystal
*PLUS
Density % sol: 48 %
Crystal grow
*PLUS
Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
10.1 MTRIZMA hydrochloride1reservoir
215 %PEG14501reservoir

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Data collection

DiffractionMean temperature: 298 K
Diffraction sourceWavelength: 1.5418
DetectorType: XUONG-HAMLIN MULTIWIRE / Detector: AREA DETECTOR
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.9→30 Å / Num. obs: 15420 / % possible obs: 94.8 % / Observed criterion σ(I): 0 / Redundancy: 15.3 % / Rmerge(I) obs: 0.093 / Net I/σ(I): 9.4

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Processing

SoftwareName: SHELXL-97 / Classification: refinement
RefinementMethod to determine structure: OTHER
Starting model: PDB IDENTIFIER 1RYT

1ryt


Resolution: 1.9→30 Å / Cross valid method: AT BEGINNING, THEN NONE / σ(F): 0 / Stereochemistry target values: ENGH AND HUBER
RfactorNum. reflection% reflection
obs0.195 -94.8 %
all-15420 -
Solvent computationSolvent model: MOEWS AND KRETSINGER
Refinement stepCycle: LAST / Resolution: 1.9→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1522 0 3 171 1696
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONs_bond_d0.006
X-RAY DIFFRACTIONs_angle_d
X-RAY DIFFRACTIONs_similar_dist
X-RAY DIFFRACTIONs_from_restr_planes
X-RAY DIFFRACTIONs_zero_chiral_vol
X-RAY DIFFRACTIONs_non_zero_chiral_vol
X-RAY DIFFRACTIONs_anti_bump_dis_restr
X-RAY DIFFRACTIONs_rigid_bond_adp_cmpnt
X-RAY DIFFRACTIONs_similar_adp_cmpnt
X-RAY DIFFRACTIONs_approx_iso_adps

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