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- PDB-1gnl: Hybrid Cluster Protein from Desulfovibrio desulfuricans X-ray str... -

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Basic information

Entry
Database: PDB / ID: 1gnl
TitleHybrid Cluster Protein from Desulfovibrio desulfuricans X-ray structure at 1.25A resolution using synchrotron radiation at a wavelength of 0.933A
ComponentsHYBRID CLUSTER PROTEIN
KeywordsHYBRID CLUSTER PROTEIN / ANAEROBIC DESULFOVIBRIO DESULFURICANS / IRON ANOMALOUS
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
ACETATE ION / IRON/SULFUR/OXYGEN HYBRID CLUSTER / IRON/SULFUR CLUSTER / Hydroxylamine reductase
Similarity search - Component
Biological speciesDESULFOVIBRIO DESULFURICANS (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.25 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 5, 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 2.0Mar 6, 2019Group: Atomic model / Data collection ...Atomic model / Data collection / Derived calculations / Experimental preparation / Other
Category: atom_site / atom_site_anisotrop ...atom_site / atom_site_anisotrop / exptl_crystal_grow / pdbx_database_proc / pdbx_database_status / struct_conn
Item: _atom_site_anisotrop.id / _exptl_crystal_grow.temp ..._atom_site_anisotrop.id / _exptl_crystal_grow.temp / _pdbx_database_status.recvd_author_approval / _struct_conn.pdbx_leaving_atom_flag
Revision 2.1Dec 23, 2020Group: Derived calculations
Category: pdbx_struct_conn_angle / struct_conn / struct_site
Item: _struct_conn.conn_type_id / _struct_conn.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.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 2.2Dec 13, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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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)118,6897
Polymers117,1922
Non-polymers1,4975
Water28,1391562
1
A: HYBRID CLUSTER PROTEIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)59,3744
Polymers58,5961
Non-polymers7783
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
2
B: HYBRID CLUSTER PROTEIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)59,3153
Polymers58,5961
Non-polymers7192
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)57.330, 61.650, 72.250
Angle α, β, γ (deg.)82.77, 73.67, 87.31
Int Tables number1
Space group name H-MP1

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Components

#1: Protein HYBRID CLUSTER PROTEIN / HCP


Mass: 58595.879 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-SF4 / IRON/SULFUR CLUSTER / Iron–sulfur cluster


Mass: 351.640 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Fe4S4
#3: Chemical ChemComp-FSO / IRON/SULFUR/OXYGEN HYBRID CLUSTER


Mass: 367.573 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Fe4O3S3
#4: Chemical ChemComp-ACT / ACETATE ION / Acetate


Mass: 59.044 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H3O2
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 1562 / 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 / pH: 6 / Details: 25% PEG 4000, 0.1M MES PH6.0, T=277K, 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: ID14-2 / Wavelength: 0.933
DetectorType: ADSC CCD / Detector: CCD / Date: May 15, 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: 247243 / % possible obs: 94.9 % / Redundancy: 3.7 % / Rsym value: 0.054 / Net I/σ(I): 8
Reflection shellResolution: 1.25→1.29 Å / Redundancy: 3.7 % / Mean I/σ(I) obs: 3.1 / Rsym value: 0.215 / % possible all: 85.3
Reflection
*PLUS
Num. measured all: 915955 / Rmerge(I) obs: 0.054
Reflection shell
*PLUS
% possible obs: 85.3 % / Rmerge(I) obs: 0.215

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Processing

Software
NameVersionClassification
REFMAC5.0.36refinement
DENZOdata reduction
SCALAdata scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB FROM ENTRY 1GN9

1gn9


Resolution: 1.25→28.63 Å / Cor.coef. Fo:Fc: 0.973 / Cor.coef. Fo:Fc free: 0.969 / SU B: 0.672 / SU ML: 0.031 / Cross valid method: THROUGHOUT / ESU R: 0.038 / ESU R Free: 0.038 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.145 12427 5 %RANDOM
Rwork0.129 ---
obs0.13 234815 94.9 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL PLUS MASK
Refinement stepCycle: LAST / Resolution: 1.25→28.63 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8222 0 40 1562 9824
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0218423
X-RAY DIFFRACTIONr_bond_other_d0.0010.027741
X-RAY DIFFRACTIONr_angle_refined_deg
X-RAY DIFFRACTIONr_angle_other_deg1.5361.96211422
X-RAY DIFFRACTIONr_dihedral_angle_1_deg
X-RAY DIFFRACTIONr_dihedral_angle_2_deg
X-RAY DIFFRACTIONr_dihedral_angle_3_deg1.475318058
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.1050.21323
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.029401
X-RAY DIFFRACTIONr_gen_planes_other0.0020.021609
X-RAY DIFFRACTIONr_nbd_refined0.2370.31912
X-RAY DIFFRACTIONr_nbd_other0.1910.37541
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other0.6190.57
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2080.51109
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.3280.331
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2060.381
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.340.5165
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.6151.55386
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.10228634
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it1.73133037
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it2.7314.52787
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.25→1.28 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.18 780
Rwork0.154 15152
Software
*PLUS
Name: REFMAC / Version: '5.0.36 18/01/2001' / Classification: refinement
Refinement
*PLUS
Num. reflection obs: 235815 / Rfactor obs: 0.13 / Rfactor Rwork: 0.13
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONp_bond_d0.01
X-RAY DIFFRACTIONp_angle_d
X-RAY DIFFRACTIONp_angle_deg1.564
X-RAY DIFFRACTIONp_plane_restr0.006
X-RAY DIFFRACTIONp_chiral_restr0.108
LS refinement shell
*PLUS
Rfactor Rfree: 0.179 / Num. reflection Rfree: 780 / % reflection Rfree: 780 % / Rfactor Rwork: 0.154 / Num. reflection obs: 15152 / Rfactor obs: 0.154

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