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- PDB-1e2u: Low Temperature Structure of Hybrid Cluster Protein from Desulfov... -

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Basic information

Entry
Database: PDB / ID: 1e2u
TitleLow Temperature Structure of Hybrid Cluster Protein from Desulfovibrio vulgaris to 1.6A
ComponentsHYDROXYLAMINE REDUCTASE
KeywordsOXIDOREDUCTASE / CUBANE / IRON SULFUR / FUSCOREDOXIN
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
IRON/SULFUR/OXYGEN HYBRID CLUSTER / IRON/SULFUR CLUSTER / Hydroxylamine reductase
Similarity search - Component
Biological speciesDESULFOVIBRIO VULGARIS (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.6 Å
AuthorsCooper, S.J. / Bailey, S. / 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 26, 2000Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 11, 2000Provider: repository / Type: Initial release
Revision 1.1Nov 28, 2012Group: Database references / Derived calculations ...Database references / Derived calculations / Non-polymer description / Other / Source and taxonomy / Structure summary / Version format compliance
Revision 1.2Apr 24, 2013Group: Structure summary
Revision 1.3Dec 23, 2020Group: Advisory / Derived calculations / Other
Category: pdbx_database_status / pdbx_struct_conn_angle ...pdbx_database_status / pdbx_struct_conn_angle / pdbx_unobs_or_zero_occ_atoms / 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.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 / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Dec 6, 2023Group: Advisory / Data collection ...Advisory / Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_unobs_or_zero_occ_atoms / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag
Revision 1.5Nov 13, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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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)60,7943
Polymers60,0751
Non-polymers7192
Water11,349630
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)63.630, 64.680, 152.290
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: 60074.703 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-SF4 / IRON/SULFUR CLUSTER


Mass: 351.640 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Fe4S4
#3: Chemical ChemComp-FSO / IRON/SULFUR/OXYGEN HYBRID CLUSTER


Mass: 367.573 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Fe4O3S3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 630 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY
Nonpolymer detailsHET GROUP: CSS CSS-S-MERCAPTOCYSTEINE LIGAND TO HYBRID CLUSTER HET GROUP: FS4 FS4-CUBANE IRON ...HET GROUP: CSS CSS-S-MERCAPTOCYSTEINE LIGAND TO HYBRID CLUSTER HET GROUP: FS4 FS4-CUBANE IRON SULFUR CLUSTER HET GROUP: FSO FSO-IRON HYBRID CLUSTER ATOM O10 IS TENTATIVELY ASSIGNED AS AN OXYGEN SR [S7] O | O / \ | / \ TRIS-(MU-2-OXO)-(MU-2-SULFIDO)- / \|/ \ (MU-3-SULPHIDO)-TETRA-IRON FE FE----FE \ /\ \ / \ \ / \ S \ O \ / \ FE----- S THE HETEROGEN FSO IS ESSENTIALLY THE SAME AS THE FSO CLUSTER IN PDB ENTRY 1E1D. IN 1E1D ATOM S7 IS A SULFIDO LIGAND WHILE IN PDB ENTRY 1E2U THIS S ATOM IS CONTRIBUTED BY A THIOCYSTEINE LIGAND.
Sequence detailsMODRES: 1E2U CSS A 406() THIOCYSTEINE-ADDITIONAL SULFUR BOUND TO SG OF CYSTEINE

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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: 2.6 Å3/Da / Density % sol: 52.5 %
Crystal growpH: 5.9
Details: PROTEIN WAS CRYSTALLISED FROM 0.1M MES PH5.9, 60MM MAGNESIUM ACETATE AND 25-30% PEG 8000
Crystal grow
*PLUS
Temperature: 277 K / Method: vapor diffusion, hanging drop
Details: drop consists of equal amounts of protein and precipitant solutions
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
112 mg/mlprotein1drop
25 mMTris-HCl1drop
30.1 MMES1reservoirprecipitant
40.2 Mmagnesium acetate1reservoirprecipitant
525-30 %PEG80001reservoirprecipitant

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SRS / Beamline: PX7.2 / Wavelength: 1.488
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Jun 15, 1998
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.488 Å / Relative weight: 1
ReflectionResolution: 1.59→20 Å / Num. obs: 77446 / % possible obs: 91.3 % / Redundancy: 2.5 % / Biso Wilson estimate: 11.436 Å2 / Rsym value: 0.069 / Net I/σ(I): 5.6
Reflection shellResolution: 1.59→1.68 Å / Redundancy: 2.4 % / Mean I/σ(I) obs: 6.5 / Rsym value: 0.1 / % possible all: 87.7
Reflection
*PLUS
Rmerge(I) obs: 0.07
Reflection shell
*PLUS
% possible obs: 87.7 % / Rmerge(I) obs: 0.1

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Processing

Software
NameClassification
REFMACrefinement
MOSFLMdata reduction
SCALAdata scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1E1D

1e1d


Resolution: 1.6→20 Å / SU B: 1.26981 / SU ML: 0.04585 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.08154 / ESU R Free: 0.08003 / Details: METAL CLUSTERS REFINED WITH ANISOTROPIC B
RfactorNum. reflection% reflectionSelection details
Rfree0.184 3818 5 %RANDOM
Rwork0.16 ---
obs-72244 90.8 %-
Displacement parametersBiso mean: 13.443 Å2
Refinement stepCycle: LAST / Resolution: 1.6→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4218 0 17 630 4865
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONp_bond_d0.0070.02
X-RAY DIFFRACTIONp_angle_d0.0210.04
X-RAY DIFFRACTIONp_angle_deg
X-RAY DIFFRACTIONp_planar_d0.0230.05
X-RAY DIFFRACTIONp_hb_or_metal_coord
X-RAY DIFFRACTIONp_mcbond_it1.3232
X-RAY DIFFRACTIONp_mcangle_it1.793
X-RAY DIFFRACTIONp_scbond_it2.122
X-RAY DIFFRACTIONp_scangle_it2.9643
X-RAY DIFFRACTIONp_plane_restr0.01820.03
X-RAY DIFFRACTIONp_chiral_restr0.0940.15
X-RAY DIFFRACTIONp_singtor_nbd
X-RAY DIFFRACTIONp_multtor_nbd
X-RAY DIFFRACTIONp_xhyhbond_nbd
X-RAY DIFFRACTIONp_xyhbond_nbd
X-RAY DIFFRACTIONp_planar_tor3.37
X-RAY DIFFRACTIONp_staggered_tor11.515
X-RAY DIFFRACTIONp_orthonormal_tor
X-RAY DIFFRACTIONp_transverse_tor32.320
X-RAY DIFFRACTIONp_special_tor15
Software
*PLUS
Name: REFMAC / Classification: refinement
Refinement
*PLUS
Rfactor Rfree: 0.183
Solvent computation
*PLUS
Displacement parameters
*PLUS

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