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- PDB-1oa0: REDUCED HYBRID CLUSTER PROTEIN FROM DESULFOVIBRIO DESULFURICANS X... -

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Basic information

Entry
Database: PDB / ID: 1oa0
TitleREDUCED HYBRID CLUSTER PROTEIN FROM DESULFOVIBRIO DESULFURICANS X-RAY STRUCTURE AT 1.25A RESOLUTION
ComponentsPRISMANE PROTEIN
KeywordsHYBRID CLUSTER PROTEIN / HYBRID CLUSTER / DESULFOVIBRIO DESULFURICANS / REDUCED FORMS / HIGH-RESOLUTION
Function / homology
Function and homology information


hydroxylamine reductase / hydroxylamine reductase activity / 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 DESULFURICANS (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / DIRECT METHODS / Resolution: 1.25 Å
AuthorsMacedo, S. / Aragao, D. / 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. ...Macedo, S. / Aragao, D. / 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.
History
DepositionDec 23, 2002Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 8, 2003Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 27, 2019Group: Data collection / Database references ...Data collection / Database references / Experimental preparation / Other
Category: citation / citation_author ...citation / citation_author / exptl_crystal_grow / pdbx_database_proc / pdbx_database_status / struct_biol
Item: _citation.journal_abbrev / _citation.page_last ..._citation.journal_abbrev / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.title / _citation_author.name / _exptl_crystal_grow.method / _exptl_crystal_grow.temp / _pdbx_database_status.recvd_author_approval
Revision 1.4Mar 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 1.5Feb 7, 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

Downloads & links

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Assembly

Deposited unit
A: PRISMANE PROTEIN
B: PRISMANE PROTEIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)118,7297
Polymers117,1922
Non-polymers1,5385
Water40,7862264
1
A: PRISMANE PROTEIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)59,4624
Polymers58,5961
Non-polymers8663
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
2
B: PRISMANE PROTEIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)59,2673
Polymers58,5961
Non-polymers6712
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)57.750, 61.990, 72.800
Angle α, β, γ (deg.)82.72, 73.74, 87.44
Int Tables number1
Space group name H-MP1
Noncrystallographic symmetry (NCS)NCS oper: (Code: given
Matrix: (0.98077, -0.19502, -0.00761), (-0.19513, -0.97903, -0.05856), (0.00397, 0.05892, -0.99825)
Vector: -43.88155, 46.56174, 30.71064)

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Components

#1: Protein PRISMANE PROTEIN / / HYBRID CLUSTER PROTEIN


Mass: 58595.879 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Details: CUBANE CLUSTER [4FE-4S] HYBRID CLUSTER [4FE-3S] / Source: (natural) DESULFOVIBRIO DESULFURICANS (bacteria) / References: UniProt: Q01770
#2: Chemical ChemComp-SF4 / IRON/SULFUR CLUSTER / Iron–sulfur cluster


Mass: 351.640 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Fe4S4
#3: Chemical ChemComp-SF3 / FE4-S3 CLUSTER


Mass: 319.575 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Fe4S3
#4: Chemical ChemComp-MES / 2-(N-MORPHOLINO)-ETHANESULFONIC ACID / MES (buffer)


Mass: 195.237 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H13NO4S / Comment: pH buffer*YM
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 2264 / 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: 2.03 Å3/Da / Density % sol: 39 %
Crystal growTemperature: 277 K / Method: vapor diffusion / pH: 6
Details: 35% PEG 4000, 0.1M MES PH6.5, TEMPERATURE 277 KELVIN, pH 6.00
Crystal grow
*PLUS
Temperature: 279 K / pH: 7.6 / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetailsChemical formula
135 %PEG40001reservoir
20.1 MMES1reservoirpH6.5
312.6 mg/mlprotein1drop
420 mMTris-HCl1droppH7.6
50.2 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: Aug 8, 2001 / Details: TOROIDAL 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: 1.25→28.63 Å / Num. obs: 246621 / % possible obs: 92.7 % / Redundancy: 1.8 % / Rmerge(I) obs: 0.04 / Net I/σ(I): 7.8
Reflection shellResolution: 1.25→1.28 Å / Redundancy: 1.8 % / Rmerge(I) obs: 0.098 / Mean I/σ(I) obs: 3.6 / % possible all: 78.7
Reflection
*PLUS
Num. measured all: 448850 / Rmerge(I) obs: 0.04
Reflection shell
*PLUS
% possible obs: 78.7 %

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Processing

Software
NameClassification
REFMACrefinement
DENZOdata reduction
SCALAdata scaling
ACORNphasing
RefinementMethod to determine structure: DIRECT METHODS
Starting model: [4FE-4S] CUBANE CLUSTER FROM PDB ENTRY 1GNL

1gnl


Resolution: 1.25→29.49 Å / SU B: 0.498 / SU ML: 0.023 / Cross valid method: THROUGHOUT / ESU R: 0.04 / ESU R Free: 0.041 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.15036 6123 2.5 %RANDOM
Rwork0.13315 ---
obs0.13358 240495 92.67 %-
Displacement parametersBiso mean: 8.172 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refinement stepCycle: LAST / Resolution: 1.25→29.49 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8210 0 42 2264 10516
Refinement
*PLUS
Rfactor Rfree: 0.148 / Rfactor Rwork: 0.131
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONp_bond_d0.008
X-RAY DIFFRACTIONp_angle_d
X-RAY DIFFRACTIONp_angle_deg1.245
X-RAY DIFFRACTIONp_plane_restr0.006
X-RAY DIFFRACTIONp_chiral_restr0.138
LS refinement shell
*PLUS
Highest resolution: 1.25 Å / Rfactor Rfree: 0.166 / Num. reflection Rfree: 365 / % reflection Rfree: 365 % / Rfactor Rwork: 0.15 / Num. reflection Rwork: 14346

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