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- PDB-1gn9: Hybrid Cluster Protein from Desulfovibrio desulfuricans ATCC 2777... -

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Basic information

Entry
Database: PDB / ID: 1gn9
TitleHybrid Cluster Protein from Desulfovibrio desulfuricans ATCC 27774 X-ray structure at 2.6A resolution using synchrotron radiation at a wavelength of 1.722A
ComponentsHYBRID CLUSTER PROTEIN
KeywordsHYBRID CLUSTER / HYBRID CLUSTER PROTEIN / ANAEROBIC DESULFOVIBRIO DESULFURICANS / IRON ANOMALOUS
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 DESULFURICANS (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / IRON ANOMALOUS, MOLECULAR REPLACEMENT / Resolution: 2.6 Å
AuthorsMacedo, S. / Mitchell, E.P. / Romao, C.V. / Cooper, S.J. / Coelho, R. / Liu, M.Y. / Xavier, A.V. / Legall, J. / Bailey, S. / Garner, D.C. ...Macedo, S. / Mitchell, E.P. / Romao, C.V. / Cooper, S.J. / Coelho, R. / Liu, M.Y. / Xavier, A.V. / Legall, J. / Bailey, S. / Garner, D.C. / Hagen, W.R. / Teixeira, M. / Carrondo, M.A. / Lindley, P.
CitationJournal: J.Biol.Inorg.Chem. / Year: 2002
Title: Hybrid Cluster Proteins (Hcps) from Desulfovibrio Desulfuricans Atcc 27774 and Desulfovibrio Vulgaris (Hildenborough): X-Ray Structures at 1.25 A Resolution Using Synchrotron Radiation.
Authors: Macedo, S. / Mitchell, E.P. / Romao, C.V. / Cooper, S.J. / Coelho, R. / Liu, M.Y. / Xavier, A.V. / Legall, J. / Bailey, S. / Garner, D.C. / Hagen, W.R. / Teixeira, M. / Carrondo, M.A. / Lindley, P.
History
DepositionOct 4, 2001Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 11, 2002Provider: repository / Type: Initial release
Revision 1.1Apr 15, 2015Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Non-polymer description / Other / Structure summary / Version format compliance
Revision 2.0May 8, 2019Group: Atomic model / Data collection ...Atomic model / Data collection / Derived calculations / Experimental preparation / Other
Category: atom_site / exptl_crystal_grow ...atom_site / exptl_crystal_grow / pdbx_database_proc / pdbx_database_status / pdbx_seq_map_depositor_info / struct_conn
Item: _exptl_crystal_grow.temp / _pdbx_database_status.recvd_author_approval ..._exptl_crystal_grow.temp / _pdbx_database_status.recvd_author_approval / _pdbx_seq_map_depositor_info.one_letter_code_mod / _struct_conn.pdbx_leaving_atom_flag
Revision 3.0Dec 23, 2020Group: Atomic model / Data collection ...Atomic model / Data collection / Derived calculations / Non-polymer description / Other / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / entity / pdbx_database_status / pdbx_entity_nonpoly / pdbx_nonpoly_scheme / pdbx_struct_conn_angle / struct_asym / struct_conn / struct_site
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_atom_id / _atom_site.auth_comp_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _atom_site.label_entity_id / _atom_site.type_symbol / _chem_comp.formula / _chem_comp.formula_weight / _chem_comp.id / _chem_comp.mon_nstd_flag / _chem_comp.name / _chem_comp.type / _pdbx_database_status.status_code_sf / _pdbx_nonpoly_scheme.entity_id / _pdbx_nonpoly_scheme.mon_id / _pdbx_nonpoly_scheme.pdb_mon_id / _struct_asym.entity_id / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_asym_id / _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_asym_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.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 3.1Dec 13, 2023Group: Data collection / Database references ...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 / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: HYBRID CLUSTER PROTEIN
B: HYBRID CLUSTER PROTEIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)118,6946
Polymers117,2562
Non-polymers1,4384
Water3,603200
1
A: HYBRID CLUSTER PROTEIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)59,3473
Polymers58,6281
Non-polymers7192
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
2
B: HYBRID CLUSTER PROTEIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)59,3473
Polymers58,6281
Non-polymers7192
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)57.400, 61.800, 72.200
Angle α, β, γ (deg.)82.70, 73.70, 87.30
Int Tables number1
Space group name H-MP1

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Components

#1: Protein HYBRID CLUSTER PROTEIN / HCP


Mass: 58627.949 Da / Num. of mol.: 2 / Source method: isolated from a natural source
Details: CUBANE CLUSTER [4FE-4S] HYBRID CLUSTER [4FE-3S-3O] PERSULPHIDE BOND BETWEEN S7 (HYBRID CLUSTER) AND S OF CYS399
Source: (natural) DESULFOVIBRIO DESULFURICANS (bacteria) / References: UniProt: Q01770
#2: Chemical ChemComp-FSO / IRON/SULFUR/OXYGEN HYBRID CLUSTER


Mass: 367.573 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Fe4O3S3
#3: Chemical ChemComp-SF4 / IRON/SULFUR CLUSTER


Mass: 351.640 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Fe4S4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 200 / 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: 293 K / pH: 6 / Details: 25% PEG 4000, 0.1M MES PH6.0, T=293K, pH 6.00
Crystal grow
*PLUS
Temperature: 293 K / pH: 7.6 / Method: vapor diffusion, sitting drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetailsChemical formula
125 %PEG40001reservoir
20.1 MMES1reservoirpH6.0
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: BM14 / Wavelength: 1.722
DetectorType: MARRESEARCH / Detector: CCD / Date: Nov 15, 2000 / Details: COLLIMATING AND FOCUSING MIRROR
RadiationMonochromator: SI (111) CHANNEL-CUT / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.722 Å / Relative weight: 1
ReflectionResolution: 2.6→30 Å / Num. obs: 27761 / % possible obs: 95.9 % / Redundancy: 4.1 % / Biso Wilson estimate: 18.7 Å2 / Rsym value: 0.08 / Net I/σ(I): 4.2
Reflection shellResolution: 2.6→2.69 Å / Redundancy: 4.1 % / Mean I/σ(I) obs: 2.6 / Rsym value: 0.13 / % possible all: 94.5
Reflection
*PLUS
Lowest resolution: 30 Å / Num. measured all: 114637 / Rmerge(I) obs: 0.08
Reflection shell
*PLUS
Highest resolution: 2.6 Å / % possible obs: 94.5 % / Rmerge(I) obs: 0.13

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Processing

Software
NameVersionClassification
CNS1refinement
DENZOdata reduction
SCALAdata scaling
AMoREphasing
RefinementMethod to determine structure: IRON ANOMALOUS, MOLECULAR REPLACEMENT
Starting model: PDB FROM ENTRY 1E2U, EXCLUDING ALL CLUSTER ATOMS AND SOLVENT MOLECULES

1e2u


Resolution: 2.6→25.01 Å / Rfactor Rfree error: 0.01 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: THE STRUCTURE FACTOR FILE THAT ACCOMPANIES THIS ENTRY INCLUDES ANOMALOUS PAIRS BUT THE ANOMALOUS DATA WERE NOT USED IN THE REFINEMENT OF THE STRUCTURE.
RfactorNum. reflection% reflectionSelection details
Rfree0.26 732 2.6 %RANDOM
Rwork0.193 ---
obs0.193 27982 96.3 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 23.0504 Å2 / ksol: 0.338115 e/Å3
Displacement parametersBiso mean: 10.9 Å2
Baniso -1Baniso -2Baniso -3
1-0.73 Å20.12 Å2-2.94 Å2
2---0.38 Å20.4 Å2
3----0.35 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.37 Å0.26 Å
Luzzati d res low-5 Å
Luzzati sigma a0.36 Å0.23 Å
Refinement stepCycle: LAST / Resolution: 2.6→25.01 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8173 0 31 200 8404
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.013
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.3
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d22.3
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d2.38
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it2.991.5
X-RAY DIFFRACTIONc_mcangle_it4.642
X-RAY DIFFRACTIONc_scbond_it3.792
X-RAY DIFFRACTIONc_scangle_it5.382.5
LS refinement shellResolution: 2.6→2.76 Å / Rfactor Rfree error: 0.026 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.293 129 2.8 %
Rwork0.225 4427 -
obs--94.6 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2WATER_REP.PARAMALL_R6.TOP
X-RAY DIFFRACTION3ALL_R6.PARCSS.TOP
X-RAY DIFFRACTION4CIS_PEPTIDE.PAR
Refinement
*PLUS
Rfactor Rfree: 0.26
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg22.3
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg2.38
LS refinement shell
*PLUS
Rfactor obs: 0.225

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