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- PDB-1jyb: Crystal structure of Rubrerythrin -

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Basic information

Entry
Database: PDB / ID: 1jyb
TitleCrystal structure of Rubrerythrin
ComponentsRubrerythrin
KeywordsELECTRON TRANSPORT / alpha helix bundle
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 (bacteria)
MethodX-RAY DIFFRACTION / FOURIER SYNTHESIS / Resolution: 2.2 Å
AuthorsChang, W.R. / Li, M. / Liu, M.Y.
CitationJournal: J.Biol.Inorg.Chem. / Year: 2003
Title: Crystal structure studies on rubrerythrin: enzymatic activity in relation to the zinc movement.
Authors: Li, M. / Liu, M.Y. / LeGall, J. / Gui, L.L. / Liao, J. / Jiang, T. / Zhang, J.P. / Liang, D.C. / Chang, W.R.
History
DepositionSep 11, 2001Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Sep 11, 2002Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Mar 13, 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_seq_id / _pdbx_struct_conn_angle.ptnr1_label_atom_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_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_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: Rubrerythrin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,7544
Polymers21,5771
Non-polymers1773
Water1,24369
1
A: Rubrerythrin
hetero molecules

A: 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 operation2_555-x,-y,z1
Buried area3660 Å2
ΔGint-117 kcal/mol
Surface area18130 Å2
MethodPISA
2
A: Rubrerythrin
hetero molecules

A: Rubrerythrin
hetero molecules

A: Rubrerythrin
hetero molecules

A: 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 area13170 Å2
ΔGint-269 kcal/mol
Surface area30400 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)49.670, 81.552, 99.754
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number23
Space group name H-MI222
DetailsThe second part of the biological assembly is generated by the two fold axis: -x, -y, z

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Components

#1: Protein Rubrerythrin


Mass: 21577.281 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Desulfovibrio vulgaris (bacteria) / 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.: 69 / 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: 2.34 Å3/Da / Density % sol: 47.45 %
Crystal growTemperature: 298 K / Method: vapor diffusion / pH: 7
Details: PEG1500, Tris, pH 7.0, VAPOR DIFFUSION, temperature 298K
Crystal grow
*PLUS
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
110 mg/mlprotein1drop
25 %PEG15001drop
350 mMTris-Cl1droppH7.0
410 %PEG15001reservoir
5100 mMTris-Cl1reservoir

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Data collection

DiffractionMean temperature: 298 K
Diffraction sourceSource: SEALED TUBE / Type: CONVENTIONAL Cu / Wavelength: 1.5418 Å
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Mar 1, 1999
RadiationMonochromator: graphite / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2→30 Å / Num. all: 14352 / Num. obs: 14352 / % possible obs: 100 % / Observed criterion σ(I): 0 / Rmerge(I) obs: 0.09
Reflection shellResolution: 2.22→2.39 Å / Rmerge(I) obs: 0.376 / % possible all: 100
Reflection
*PLUS
Lowest resolution: 15 Å / Num. obs: 10576 / % possible obs: 99.9 % / Redundancy: 11.5 %

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Processing

Software
NameClassification
DENZOdata reduction
SCALEPACKdata scaling
X-PLORmodel building
X-PLORrefinement
X-PLORphasing
RefinementMethod to determine structure: FOURIER SYNTHESIS / Resolution: 2.2→8 Å / σ(F): 2 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.231 867 10 %random
Rwork0.182 ---
all-10032 --
obs-8671 86.4 %-
Refinement stepCycle: LAST / Resolution: 2.2→8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1514 0 3 69 1586
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.017
X-RAY DIFFRACTIONx_angle_deg2.8
Refinement
*PLUS
Lowest resolution: 8 Å / σ(F): 2
Solvent computation
*PLUS
Displacement parameters
*PLUS

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