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- PDB-1e5d: RUBREDOXIN OXYGEN:OXIDOREDUCTASE (ROO) FROM ANAEROBE DESULFOVIBRI... -

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Basic information

Entry
Database: PDB / ID: 1e5d
TitleRUBREDOXIN OXYGEN:OXIDOREDUCTASE (ROO) FROM ANAEROBE DESULFOVIBRIO GIGAS
ComponentsRUBREDOXIN\:OXYGEN OXIDOREDUCTASE
KeywordsOXIDOREDUCTASE / OXYGENREDUCTASE / DIIRON-CENTRE / FLAVOPROTEINS / LACTAMASE-FOLD
Function / homology
Function and homology information


Oxidoreductases / respiratory electron transport chain / FMN binding / electron transfer activity / oxidoreductase activity / metal ion binding
Similarity search - Function
Rubredoxin-oxygen oxidoreductase / ODP domain / ODP family beta lactamase / Flavodoxin domain / Metallo-beta-lactamase superfamily / Ribonuclease Z/Hydroxyacylglutathione hydrolase-like / Metallo-beta-lactamase; Chain A / Metallo-beta-lactamase superfamily / Metallo-beta-lactamase / Flavodoxin ...Rubredoxin-oxygen oxidoreductase / ODP domain / ODP family beta lactamase / Flavodoxin domain / Metallo-beta-lactamase superfamily / Ribonuclease Z/Hydroxyacylglutathione hydrolase-like / Metallo-beta-lactamase; Chain A / Metallo-beta-lactamase superfamily / Metallo-beta-lactamase / Flavodoxin / Flavodoxin-like domain profile. / Flavodoxin/nitric oxide synthase / Ribonuclease Z/Hydroxyacylglutathione hydrolase-like / Flavoprotein-like superfamily / 4-Layer Sandwich / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
MU-OXO-DIIRON / FLAVIN MONONUCLEOTIDE / OXYGEN MOLECULE / Rubredoxin-oxygen oxidoreductase
Similarity search - Component
Biological speciesDESULFOVIBRIO GIGAS (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.5 Å
AuthorsFrazao, C. / Silva, G. / Gomes, C.M. / Matias, P. / Coelho, R. / Sieker, L. / Macedo, S. / Liu, M.Y. / Oliveira, S. / Teixeira, M. ...Frazao, C. / Silva, G. / Gomes, C.M. / Matias, P. / Coelho, R. / Sieker, L. / Macedo, S. / Liu, M.Y. / Oliveira, S. / Teixeira, M. / Xavier, A.V. / Rodrigues-Pousada, C. / Carrondo, M.A. / Le Gall, J.
Citation
#1: Journal: Acta Crystallogr. D Biol. Crystallogr. / Year: 1999
Title: Crystallization and preliminary diffraction data analysis of both single and pseudo-merohedrally twinned crystals of rubredoxin oxygen oxidoreductase from Desulfovibrio gigas.
Authors: Frazao, C. / Sieker, L. / Coelho, R. / Morais, J. / Pacheco, I. / Chen, L. / LeGall, J. / Dauter, Z. / Wilson, K. / Carrondo, M.A.
#2: Journal: J.Biol.Chem. / Year: 1997
Title: Studies on the Redox Centres of the Terminal Oxidase from Desulfovibrio Gigas and Evidence for its Interaction with Rubredoxin
Authors: Gomes, C.M. / Silva, G. / Oliveira, S. / Le Gall, J. / Liu, M.-Y. / Xavier, A.V. / Rodrigues-Pousada, C. / Teixeira, M.
#3: Journal: Biochem.Biophys.Res.Comm. / Year: 1993
Title: Rubredoxin Oxidase, a New Flavo-Heme-Protein, is the Site of Oxygen Reduction to Water by the " Strictly Anaerobe" Desulfovibrio Gigas
Authors: Chen, L. / Liu, M.-Y. / Le Gall, J. / Fareleira, P. / Santos, H. / Xavier, A.V.
History
DepositionJul 24, 2000Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 17, 2000Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Apr 18, 2018Group: Data collection / Database references / Category: citation / citation_author / diffrn_source
Item: _citation.journal_abbrev / _citation.journal_volume ..._citation.journal_abbrev / _citation.journal_volume / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.name / _diffrn_source.pdbx_synchrotron_site
Revision 1.4May 8, 2019Group: Data collection / Experimental preparation / Category: exptl_crystal_grow / Item: _exptl_crystal_grow.method
Revision 1.5May 22, 2019Group: Data collection / Refinement description / Category: refine / Item: _refine.pdbx_ls_cross_valid_method
Revision 1.6Jul 10, 2019Group: Data collection / Category: diffrn_source / Item: _diffrn_source.pdbx_synchrotron_site
Revision 1.7Jul 24, 2019Group: Data collection / Category: diffrn_source / Item: _diffrn_source.pdbx_synchrotron_site
Revision 1.8May 8, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / 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_database_status.status_code_sf / _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.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_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: RUBREDOXIN\:OXYGEN OXIDOREDUCTASE
B: RUBREDOXIN\:OXYGEN OXIDOREDUCTASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)90,9318
Polymers89,6982
Non-polymers1,2326
Water3,063170
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)98.240, 101.250, 90.800
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212
Noncrystallographic symmetry (NCS)NCS oper: (Code: given
Matrix: (-0.1195, 0.9928, -0.002), (0.9928, 0.1195, -0.0013), (-0.001, -0.0021, -1)
Vector: 4.776, -4.107, 89.563)

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Components

#1: Protein RUBREDOXIN\:OXYGEN OXIDOREDUCTASE


Mass: 44849.227 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) DESULFOVIBRIO GIGAS (bacteria) / References: UniProt: Q9F0J6*PLUS
#2: Chemical ChemComp-FMN / FLAVIN MONONUCLEOTIDE / RIBOFLAVIN MONOPHOSPHATE


Mass: 456.344 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C17H21N4O9P
#3: Chemical ChemComp-FEO / MU-OXO-DIIRON


Mass: 127.689 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Fe2O
#4: Chemical ChemComp-OXY / OXYGEN MOLECULE


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


Mass: 18.015 Da / Num. of mol.: 170 / 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: 2.15 Å3/Da / Density % sol: 42.9 %
Description: TWO DATA SETS WERE COLLECTED. A MAD DATA SET TO 2.7A CORRESPONDING TO FOUR WAVELENGTHS NEAR THE FE ABSORPTION EDGE WAS COLLECTED AT ESRF, BM14, AND USED TO SOLVE THE PHASE PROBLEM. A ...Description: TWO DATA SETS WERE COLLECTED. A MAD DATA SET TO 2.7A CORRESPONDING TO FOUR WAVELENGTHS NEAR THE FE ABSORPTION EDGE WAS COLLECTED AT ESRF, BM14, AND USED TO SOLVE THE PHASE PROBLEM. A SECOND, SINGLE WAVELENGTH DATA SET TO 2.5A WAS COLLECTED AT DESY/ EMBL, X11, AND USED IN STRCUTURE REFINEMENT
Crystal growMethod: vapor diffusion, sitting drop / pH: 6
Details: VAPOUR DIFFUSION IN SITTING DROP. DROPS OF PROTEIN SOLUTION 10MG/ML AND ALIQUOTS OF PRECIPITANT SOLUTION COMPOSED OF PEG 6 K 10%, TRIS-MALEIC BUFFER 0.1 M PH 6.0
Crystal grow
*PLUS
Temperature: 4-10 ℃ / Method: vapor diffusion, sitting drop / pH: 6
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
110 mg/mlprotein1drop
210 %(v/v)PEG60001reservoir
3100 mMTris-maleate1reservoirpH6.0

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Data collection

DiffractionMean temperature: 110 K
Diffraction sourceSource: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: X11 / Wavelength: 1.0331
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Nov 15, 1993
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0331 Å / Relative weight: 1
ReflectionResolution: 2.5→29.4 Å / Num. obs: 31676 / % possible obs: 99.6 % / Redundancy: 3.5 % / Rmerge(I) obs: 0.066 / Net I/σ(I): 17.5
Reflection shellResolution: 2.5→2.54 Å / Redundancy: 3.3 % / Rmerge(I) obs: 0.265 / Mean I/σ(I) obs: 4.7 / % possible all: 87.3
Reflection
*PLUS
Num. measured all: 123925
Reflection shell
*PLUS
% possible obs: 96.9 %

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Processing

Software
NameClassification
SHELXL-97refinement
HKLdata reduction
HKLdata scaling
SHELXL-97phasing
RefinementMethod to determine structure: MAD / Resolution: 2.5→15 Å / Num. parameters: 26292 / Num. restraintsaints: 33720 / Cross valid method: FREE R-VALUE / σ(F): 0
StereochEM target val spec case: DIIRON SITES REFINED WITHOUT TARGET VALUES BUT RESTRAINED TO A COMMON GEOMETRY. NCS APPLIED BY RESTRAINING HOMOLOGOUS 1-4 DISTANCES TO THEIR COMMON VALUES. SOLVENT ...StereochEM target val spec case: DIIRON SITES REFINED WITHOUT TARGET VALUES BUT RESTRAINED TO A COMMON GEOMETRY. NCS APPLIED BY RESTRAINING HOMOLOGOUS 1-4 DISTANCES TO THEIR COMMON VALUES. SOLVENT WATERS WITH HOMOLOGOUS H- BONDING PATTERN TO EACH MONOMER WERE RESTRAINED TO THEIR COMMON ISOTROPIC DISPLACEMENT PARAMETERS.
Stereochemistry target values: ENGH AND HUBER
Details: ANISOTROPIC SCALING APPLIED BY THE METHOD OF PARKIN, MOEZZI & HOPE, J.APPL.CRYST.28 (1995)53-56
RfactorNum. reflection% reflectionSelection details
Rfree0.2477 1919 6.1 %RANDOM
all0.1794 31671 --
obs0.1805 -98.8 %-
Solvent computationSolvent model: MOEWS & KRETSINGER, J.MOL.BIOL.91(1973)201-2
Refine analyzeNum. disordered residues: 7 / Occupancy sum hydrogen: 0 / Occupancy sum non hydrogen: 6532
Refinement stepCycle: LAST / Resolution: 2.5→15 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6290 0 72 170 6532
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONs_bond_d0.005
X-RAY DIFFRACTIONs_angle_d0.019
X-RAY DIFFRACTIONs_similar_dist0.033
X-RAY DIFFRACTIONs_from_restr_planes0.0241
X-RAY DIFFRACTIONs_zero_chiral_vol0.026
X-RAY DIFFRACTIONs_non_zero_chiral_vol0.032
X-RAY DIFFRACTIONs_anti_bump_dis_restr0.007
X-RAY DIFFRACTIONs_rigid_bond_adp_cmpnt0
X-RAY DIFFRACTIONs_similar_adp_cmpnt0.071
X-RAY DIFFRACTIONs_approx_iso_adps0
Software
*PLUS
Name: SHELXL-97 / Classification: refinement
Refinement
*PLUS
σ(I): 2 / Rfactor obs: 0.1618 / Rfactor Rwork: 0.1805
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONs_plane_restr0.0241
X-RAY DIFFRACTIONs_chiral_restr0.026

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