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- PDB-1w9m: AS-isolated hybrid cluster protein from Desulfovibrio vulgaris X-... -

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Basic information

Entry
Database: PDB / ID: 1w9m
TitleAS-isolated hybrid cluster protein from Desulfovibrio vulgaris X-ray structure at 1.35A resolution using iron anomalous signal
ComponentsHYDROXYLAMINE REDUCTASE
KeywordsOXIDOREDUCTASE / HYBRID CLUSTER PROTEIN / ANAEROBIC / OXIDISED / AS-ISOLATED / DESULFOVIBRIO VULGARIS
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
FE-S-O HYBRID CLUSTER / IRON/SULFUR CLUSTER / Hydroxylamine reductase
Similarity search - Component
Biological speciesDESULFOVIBRIO VULGARIS (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.35 Å
AuthorsAragao, D. / Macedo, S. / Mitchell, E.P. / Coelho, D. / Romao, C.V. / Teixeira, M. / Lindley, P.F.
Citation
Journal: Acta Crystallogr.,Sect.D / Year: 2008
Title: Structural and Functional Relationships in the Hybrid Cluster Protein Family:Structure of the Anaerobically Purified Hybrid Cluster Protein from Desulfovibrio Vulgaris at 1.35 A Resolution
Authors: Aragao, D. / Mitchell, E.P. / Frazao, C.F. / Carrondo, M.A. / Lindley, P.F.
#1: Journal: J.Biol.Inorg.Chem. / Year: 2003
Title: Reduced Hybrid Cluster Proteins from Desulfovibrio Desulfuricans Atcc 27774 and Desulfovibrio Vulgaris (Hidenborough). 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, E.M.A.M. / Hagen, W.R. / Teixeira, M. / Carrondo, M.A. / Lindley, P.F.
History
DepositionOct 14, 2004Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 4, 2005Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Mar 6, 2019Group: Data collection / Derived calculations ...Data collection / Derived calculations / Experimental preparation / Other
Category: exptl_crystal_grow / pdbx_database_proc ...exptl_crystal_grow / pdbx_database_proc / pdbx_database_status / struct_conn
Item: _exptl_crystal_grow.temp / _pdbx_database_status.recvd_author_approval / _struct_conn.pdbx_leaving_atom_flag
Revision 1.4May 22, 2019Group: Data collection / Refinement description / Category: refine / Item: _refine.pdbx_ls_cross_valid_method
Revision 1.5Mar 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
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.pdbx_leaving_atom_flag / _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

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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)60,7623
Polymers60,0751
Non-polymers6872
Water14,214789
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)64.270, 66.843, 134.764
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 / / HYBRID CLUSTER PROTEIN


Mass: 60074.703 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: CUBANE CLUSTER [4FE-4S] HYBRID CLUSTER [4FE-3S-3O] PERSULPHIDE BOND BETWEEN S7 (HYBRID CLUSTER) AND S OF CYS406
Source: (gene. exp.) DESULFOVIBRIO VULGARIS (bacteria) / Strain: HILDENBOROUGH / Plasmid: PJSP104 / Production host: DESULFOVIBRIO VULGARIS (bacteria) / Strain (production host): HILDENBOROUGH
References: UniProt: P31101, Oxidoreductases; Acting on other nitrogenous compounds as donors
#2: Chemical ChemComp-SF4 / IRON/SULFUR CLUSTER / Iron–sulfur cluster


Mass: 351.640 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Fe4S4
#3: Chemical ChemComp-FS2 / FE-S-O HYBRID CLUSTER


Mass: 335.508 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Fe4O3S2
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 789 / 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: 2.07 Å3/Da / Density % sol: 40.6 % / Description: ARP/WARP PROGRAM USED TO BUILD MODEL
Crystal growTemperature: 277 K / pH: 6.5 / Details: 25% PEG 4000, 0.1M MES, PH 6.5, T=277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.933
DetectorType: ADSC CCD / Detector: CCD / Date: Nov 15, 2001 / Details: TOROIDAL MIRROR
RadiationMonochromator: DIAMOND (111) CRYSTAL / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.933 Å / Relative weight: 1
ReflectionResolution: 1.35→67.42 Å / Num. obs: 127993 / % possible obs: 100 % / Redundancy: 2.4 % / Rmerge(I) obs: 0.059 / Net I/σ(I): 10.4
Reflection shellResolution: 1.35→1.36 Å / Redundancy: 1.7 % / Rmerge(I) obs: 0.35 / Mean I/σ(I) obs: 3.45 / % possible all: 100

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Processing

Software
NameClassification
SHELXL-97refinement
DENZOdata reduction
SCALEPACKdata scaling
SOLVEphasing
RefinementMethod to determine structure: MAD / Resolution: 1.35→100 Å / Num. parameters: 45607 / Num. restraintsaints: 54284 / Cross valid method: FREE R-VALUE / σ(F): 0 / Stereochemistry target values: ENGH AND HUBER
Details: ANISOTROPIC REFINEMENT REDUCED FREE R (NO CUTOFF) BY 1.6 %
RfactorNum. reflection% reflectionSelection details
Rfree0.1774 6422 5.3 %RANDOM
all0.125 121439 --
obs0.1282 -95 %-
Solvent computationSolvent model: MOEWS & KRETSINGER, J.MOL.BIOL.91(1973)201-2
Refine analyzeNum. disordered residues: 11 / Occupancy sum hydrogen: 0 / Occupancy sum non hydrogen: 5022.9
Refinement stepCycle: LAST / Resolution: 1.35→100 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4218 0 17 789 5024
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONs_bond_d0.012
X-RAY DIFFRACTIONs_angle_d0.027
X-RAY DIFFRACTIONs_similar_dist0
X-RAY DIFFRACTIONs_from_restr_planes0.0262
X-RAY DIFFRACTIONs_zero_chiral_vol0.058
X-RAY DIFFRACTIONs_non_zero_chiral_vol0.069
X-RAY DIFFRACTIONs_anti_bump_dis_restr0.027
X-RAY DIFFRACTIONs_rigid_bond_adp_cmpnt0.004
X-RAY DIFFRACTIONs_similar_adp_cmpnt0.04
X-RAY DIFFRACTIONs_approx_iso_adps0.085

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