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- PDB-1e1d: Hybrid Cluster Protein from Desulfovibrio vulgaris -

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Basic information

Entry
Database: PDB / ID: 1e1d
TitleHybrid Cluster Protein from Desulfovibrio vulgaris
ComponentsHYDROXYLAMINE REDUCTASE
KeywordsOXIDOREDUCTASE / HYBRID CLUSTER / CUBANE / IRON SULFUR / PRISMANE / FUSCOREDOXIN
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
IRON/SULFUR/OXYGEN HYBRID CLUSTER / IRON/SULFUR CLUSTER / Hydroxylamine reductase
Similarity search - Component
Biological speciesDESULFOVIBRIO VULGARIS (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MIR / Resolution: 1.72 Å
AuthorsArendsen, A.F. / Cooper, S.J. / Bailey, S. / Garner, C.D. / Hagen, W.R. / Lindley, P.F.
CitationJournal: Biochemistry / Year: 2000
Title: Hybrid-Cluster Protein (Hcp) from Desulfovibrio Vulgaris (Hildenborough) at 1.6 A Resolution.
Authors: Cooper, S.J. / Garner, C.D. / Hagen, W.R. / Lindley, P.F. / Bailey, S.
History
DepositionMay 2, 2000Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 21, 2000Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Dec 23, 2020Group: Derived calculations / Other
Category: pdbx_database_status / pdbx_struct_conn_angle ...pdbx_database_status / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _pdbx_database_status.status_code_sf / _struct_conn.pdbx_dist_value ..._pdbx_database_status.status_code_sf / _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: HYDROXYLAMINE REDUCTASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)60,9483
Polymers60,2291
Non-polymers7192
Water7,476415
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)64.500, 65.500, 155.200
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 / PRISMANE PROTEIN


Mass: 60228.898 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) DESULFOVIBRIO VULGARIS (bacteria) / Strain: HILDENBOROUGH NCIMB8303 / Plasmid: PJSP104 / Production host: DESULFOVIBRIO VULGARIS (bacteria) / Strain (production host): HILDENBOROUGH NCIMB8303 / References: UniProt: P31101
#2: Chemical ChemComp-FSO / IRON/SULFUR/OXYGEN HYBRID CLUSTER


Mass: 367.573 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Fe4O3S3
#3: Chemical ChemComp-SF4 / IRON/SULFUR CLUSTER / Iron–sulfur cluster


Mass: 351.640 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Fe4S4
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 415 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.7 Å3/Da / Density % sol: 54 %
Crystal growpH: 5.9
Details: PROTEIN WAS CRYSTALLISED FROM 0.1M MES PH5.9,60MM MAGNESIUM ACETATE AND 25-30% PEG 8000, pH 5.90
Crystal grow
*PLUS
Temperature: 277 K / Method: vapor diffusion / Details: Arendsen, A., (1996) Acta Crystallogr. D.52, 1211.
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
124 mg/mlprotein1drop
25 mMTris-HCl1drop
350 mM1dropNaCl
40.1 MMES1drop
566 mMmagnesium acetate1drop
60.1 MMES1reservoir
766 mMmagnesium acetate1reservoir

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Data collection

DiffractionMean temperature: 293 K
Diffraction sourceSource: SYNCHROTRON / Site: SRS / Beamline: PX9.6 / Wavelength: 0.87
DetectorType: MARRESEARCH / Detector: IMAGE PLATE
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.87 Å / Relative weight: 1
ReflectionResolution: 1.72→21.88 Å / Num. obs: 70418 / % possible obs: 97.2 % / Redundancy: 2.8 % / Rsym value: 0.036 / Net I/σ(I): 10.5
Reflection shellResolution: 1.72→1.77 Å / Redundancy: 2.5 % / Mean I/σ(I) obs: 3.7 / Rsym value: 0.162 / % possible all: 81.3
Reflection
*PLUS
Rmerge(I) obs: 0.036
Reflection shell
*PLUS
% possible obs: 81.3 % / Rmerge(I) obs: 0.162

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Processing

Software
NameClassification
RESTRAINrefinement
MOSFLMdata reduction
Agrovatadata scaling
MLPHAREphasing
RefinementMethod to determine structure: MIR / Resolution: 1.72→12 Å / Cross valid method: THROUGHOUT / σ(F): 0 / Details: FS4 AND FSO CLUSTER ATOMS REFINED ANISOTROPICALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.208 -4.9 %RANDOM
Rwork0.171 ---
obs-66619 98.66 %-
Displacement parametersBiso mean: 22.55 Å2
Refinement stepCycle: LAST / Resolution: 1.72→12 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4216 0 18 415 4649
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONp_bond_d0.0110.02
X-RAY DIFFRACTIONp_angle_d0.0110.04
X-RAY DIFFRACTIONp_angle_deg
X-RAY DIFFRACTIONp_planar_d
X-RAY DIFFRACTIONp_hb_or_metal_coord
X-RAY DIFFRACTIONp_mcbond_it
X-RAY DIFFRACTIONp_mcangle_it
X-RAY DIFFRACTIONp_scbond_it
X-RAY DIFFRACTIONp_scangle_it
X-RAY DIFFRACTIONp_plane_restr0.0070.01
X-RAY DIFFRACTIONp_chiral_restr0.010.02
X-RAY DIFFRACTIONp_singtor_nbd
X-RAY DIFFRACTIONp_multtor_nbd
X-RAY DIFFRACTIONp_xhyhbond_nbd
X-RAY DIFFRACTIONp_xyhbond_nbd
X-RAY DIFFRACTIONp_planar_tor
X-RAY DIFFRACTIONp_staggered_tor
X-RAY DIFFRACTIONp_orthonormal_tor
X-RAY DIFFRACTIONp_transverse_tor
X-RAY DIFFRACTIONp_special_tor
Software
*PLUS
Name: RESTRAIN / Classification: refinement
Refine LS restraints
*PLUS
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONx_bond_d0.0110.02
X-RAY DIFFRACTIONx_angle_d0.0110.04
X-RAY DIFFRACTIONx_plane_restr0.0070.01
X-RAY DIFFRACTIONx_chiral_restr0.010.02

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