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- PDB-1oa1: REDUCED HYBRID CLUSTER PROTEIN (HCP) FROM DESULFOVIBRIO VULGARIS ... -

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Basic information

Entry
Database: PDB / ID: 1oa1
TitleREDUCED HYBRID CLUSTER PROTEIN (HCP) FROM DESULFOVIBRIO VULGARIS HILDENBOROUGH STRUCTURE AT 1.55A RESOLUTION USING SYNCHROTRON RADIATION.
ComponentsHYDROXYLAMINE REDUCTASE
KeywordsOXIDOREDUCTASE / REDUCED FORMS
Function / homology
Function and homology information


hydroxylamine reductase / hydroxylamine reductase activity / peroxidase activity / response to hydrogen peroxide / 4 iron, 4 sulfur cluster binding / metal ion binding / cytoplasm
Similarity search - Function
Substrate Binding Domain Of Dnak; Chain:A; Domain 2 - #20 / Hydroxylamine reductase / Prismane, alpha-bundle / Rossmann fold - #2030 / Hydroxylamine reductase/Ni-containing CO dehydrogenase / Prismane/CO dehydrogenase family / Prismane-like, alpha/beta-sandwich / Prismane-like superfamily / Substrate Binding Domain Of Dnak; Chain:A; Domain 2 / Up-down Bundle ...Substrate Binding Domain Of Dnak; Chain:A; Domain 2 - #20 / Hydroxylamine reductase / Prismane, alpha-bundle / Rossmann fold - #2030 / Hydroxylamine reductase/Ni-containing CO dehydrogenase / Prismane/CO dehydrogenase family / Prismane-like, alpha/beta-sandwich / Prismane-like superfamily / Substrate Binding Domain Of Dnak; Chain:A; Domain 2 / Up-down Bundle / Rossmann fold / 3-Layer(aba) Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
FE4-S3 CLUSTER / IRON/SULFUR CLUSTER / Hydroxylamine reductase
Similarity search - Component
Biological speciesDESULFOVIBRIO VULGARIS (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.55 Å
AuthorsAragao, D. / Macedo, S. / Mitchell, E.P. / Romao, C.V. / Liu, M.Y. / Frazao, C. / Saraiva, L.M. / Xavier, A.V. / Legall, J. / Van Dongen, W.M.A.M. ...Aragao, D. / Macedo, S. / Mitchell, E.P. / Romao, C.V. / Liu, M.Y. / Frazao, C. / Saraiva, L.M. / Xavier, A.V. / Legall, J. / Van Dongen, W.M.A.M. / Hagen, W.R. / Teixeira, M. / Carrondo, M.A. / Lindley, P.F.
CitationJournal: J.Biol.Inorg.Chem. / Year: 2003
Title: Reduced Hybrid Cluster Proteins (Hcp) from Desulfovibrio Desulfuricans Atcc 27774 and Desulfovibrio Vulgaris (Hildenborough): X-Ray Structures at High Resolution Using Synchrotron Radiation
Authors: Aragao, D. / Macedo, S. / Mitchell, E.P. / Romao, C.V. / Liu, M.Y. / Frazao, C. / Saraiva, L.M. / Xavier, A.V. / Legall, J. / Van Dongen, W.M.A.M. / Hagen, W.R. / Teixeira, M. / Carrondo, M.A. / Lindley, P.F.
History
DepositionDec 23, 2002Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 8, 2003Provider: repository / Type: Initial release
Revision 1.1Mar 27, 2013Group: Derived calculations / Non-polymer description ...Derived calculations / Non-polymer description / Other / Structure summary / Version format compliance
Revision 1.2Mar 6, 2019Group: Data collection / Experimental preparation / Other
Category: exptl_crystal_grow / pdbx_database_proc / pdbx_database_status
Item: _exptl_crystal_grow.temp / _pdbx_database_status.recvd_author_approval
Revision 1.3Mar 29, 2023Group: Database references / Derived calculations ...Database references / Derived calculations / Other / Structure summary
Category: audit_author / database_2 ...audit_author / database_2 / pdbx_database_status / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _audit_author.identifier_ORCID / _database_2.pdbx_DOI ..._audit_author.identifier_ORCID / _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.ptnr2_label_atom_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
Revision 1.4May 1, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: HYDROXYLAMINE REDUCTASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)60,8985
Polymers60,0431
Non-polymers8554
Water14,754819
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)64.053, 67.464, 134.955
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein HYDROXYLAMINE REDUCTASE / PRISMANE PROTEIN / HYBRID CLUSTER PROTEIN / HCP


Mass: 60042.641 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: CUBANE CLUSTER [4FE-4S] HYBRID CLUSTER [4FE-3S] / Source: (gene. exp.) DESULFOVIBRIO VULGARIS (bacteria) / Strain: HILDENBOROUGH NCIMB8303 / Plasmid: PJSP104 / Production host: DESULFOVIBRIO VULGARIS (bacteria) / Strain (production host): HILDENBOROUGH NCIMB8303
References: UniProt: P31101, Oxidoreductases; Acting on other nitrogenous compounds as donors
#2: Chemical ChemComp-SF4 / IRON/SULFUR CLUSTER


Mass: 351.640 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Fe4S4
#3: Chemical ChemComp-SF3 / FE4-S3 CLUSTER


Mass: 319.575 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Fe4S3
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 819 / Source method: isolated from a natural source / Formula: H2O
Compound detailsCATALYZES THE REDUCTION OF HYDROXYLAMINE TO FORM AMMONIA AND WATER.

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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: 2.04 Å3/Da / Density % sol: 40 %
Crystal growTemperature: 277 K / pH: 6.5
Details: 25 PEG 4000 0.1M MES PH 6.5, TEMPERATURE 277 KELVIN
Crystal grow
*PLUS
Temperature: 277 K / Method: vapor diffusion, sitting drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetailsChemical formula
125 %PEG40001reservoir
20.1 MMES1reservoirpH6.5
325 mg/mlprotein1drop
420 mMTris-HCl1droppH7.6
50.05 M1dropNaCl

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-2 / Wavelength: 0.933
DetectorType: ADSC CCD / Detector: CCD / Date: May 15, 2002 / Details: TOROIDAL MIRROR MIRROR
RadiationMonochromator: DIAMOND (111) CRYSTAL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.933 Å / Relative weight: 1
ReflectionResolution: 1.55→19.5 Å / Num. obs: 81856 / % possible obs: 95.7 % / Redundancy: 3.2 % / Biso Wilson estimate: 19.3 Å2 / Rmerge(I) obs: 0.071 / Net I/σ(I): 13.2
Reflection shellResolution: 1.55→1.59 Å / Redundancy: 3.8 % / Rmerge(I) obs: 0.254 / Mean I/σ(I) obs: 3.6 / % possible all: 93.5
Reflection
*PLUS
Num. measured all: 262651
Reflection shell
*PLUS
% possible obs: 93.5 %

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Processing

Software
NameClassification
REFMACrefinement
DENZOdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB FROM ANAEROBILLY AS-ISOLATED HCP PROTEIN 1.35A (D.ARAGAO, PRIVATE COMMUNICATION)

Resolution: 1.55→19.5 Å / SU B: 1.035 / SU ML: 0.038 / Cross valid method: THROUGHOUT / ESU R: 0.063 / ESU R Free: 0.063 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.153 4074 5 %RANDOM
Rwork0.131 ---
obs0.132 77786 95.74 %-
Displacement parametersBiso mean: 15.1 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refinement stepCycle: LAST / Resolution: 1.55→19.5 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4217 0 27 819 5063
Refinement
*PLUS
Num. reflection all: 77786 / Num. reflection obs: 73710
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONp_bond_d0.011
X-RAY DIFFRACTIONp_angle_d
X-RAY DIFFRACTIONp_angle_deg1.292
X-RAY DIFFRACTIONp_plane_restr0.006
X-RAY DIFFRACTIONp_chiral_restr0.09
LS refinement shell
*PLUS
Rfactor Rfree: 0.199 / Num. reflection Rfree: 295 / Rfactor Rwork: 0.168 / Num. reflection Rwork: 5497

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