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- PDB-4ar3: Near-atomic resolution neutron crystallography on the oxidised fo... -

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Basic information

Entry
Database: PDB / ID: 4ar3
TitleNear-atomic resolution neutron crystallography on the oxidised form perdeuterated Pyrococcus furiosus rubredoxin.
ComponentsRubredoxin
KeywordsELECTRON TRANSPORT / PERDEUTERATED / MONOCHROMATIC NEUTRON CRYSTALLOGRAPHY
Function / homology
Function and homology information


alkane catabolic process / electron transfer activity / iron ion binding
Similarity search - Function
Rubredoxin / Rubredoxin, iron-binding site / Rubredoxin signature. / Rubrerythrin, domain 2 - #10 / Rubredoxin domain / Rubredoxin / Rubredoxin-like domain / Rubredoxin-like domain profile. / Rubrerythrin, domain 2 / Single Sheet / Mainly Beta
Similarity search - Domain/homology
trideuteriooxidanium / : / DEUTERATED WATER / : / Rubredoxin
Similarity search - Component
Biological speciesPyrococcus furiosus (archaea)
MethodNEUTRON DIFFRACTION / NUCLEAR REACTOR / Resolution: 1.05 Å
AuthorsCuypers, M.G. / Mason, S.A. / Blakeley, M.P. / Mitchell, E.P. / Haertlein, M. / Forsyth, V.T.
CitationJournal: Angew.Chem.Int.Ed.Engl. / Year: 2013
Title: Near-Atomic Resolution Neutron Crystallography on Perdeuterated Pyrococcus Furiosus Rubredoxin: Implication of Hydronium Ions and Protonation State Equilibria in Redox Changes.
Authors: Cuypers, M.G. / Mason, S.A. / Blakeley, M.P. / Mitchell, E.P. / Haertlein, M. / Forsyth, V.T.
History
DepositionApr 20, 2012Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 16, 2013Provider: repository / Type: Initial release
Revision 1.1Mar 6, 2013Group: Database references
Revision 1.2Aug 14, 2013Group: Atomic model
Revision 1.3Mar 22, 2017Group: Data collection
Revision 1.4Aug 28, 2019Group: Data collection / Category: reflns
Item: _reflns.pdbx_Rrim_I_all / _reflns.pdbx_Rsym_value / _reflns.pdbx_netI_over_sigmaI
Revision 2.0Jun 9, 2021Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Non-polymer description / Other / Source and taxonomy / Structure summary
Category: chem_comp / citation ...chem_comp / citation / entity / entity_name_com / entity_src_gen / pdbx_database_status / pdbx_struct_assembly_prop / reflns / struct_conn / struct_ref / struct_site
Item: _chem_comp.formula / _citation.journal_id_ASTM ..._chem_comp.formula / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _entity.pdbx_description / _entity_name_com.name / _entity_src_gen.gene_src_strain / _entity_src_gen.pdbx_beg_seq_num / _entity_src_gen.pdbx_end_seq_num / _entity_src_gen.pdbx_gene_src_gene / _entity_src_gen.pdbx_gene_src_ncbi_taxonomy_id / _entity_src_gen.pdbx_gene_src_scientific_name / _entity_src_gen.pdbx_host_org_scientific_name / _entity_src_gen.pdbx_host_org_vector / _entity_src_gen.pdbx_seq_type / _pdbx_database_status.status_code_sf / _reflns.d_resolution_high / _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_ref.pdbx_align_begin / _struct_ref.pdbx_seq_one_letter_code / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 2.1May 8, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Rubredoxin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)6,18410
Polymers6,0321
Non-polymers1529
Water2,684149
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area11000 Å2
ΔGint71 kcal/mol
Surface area8570 Å2
MethodPISA
Unit cell
Length a, b, c (Å)34.360, 35.316, 43.993
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 Rubredoxin / Rd


Mass: 6031.728 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: OXIDISED, FE (III) STATE, HYDRONIUM IONS, CARBOXYLIC DEUTERONS
Source: (gene. exp.) Pyrococcus furiosus (strain ATCC 43587 / DSM 3638 / JCM 8422 / Vc1) (archaea)
Strain: ATCC 43587 / DSM 3638 / JCM 8422 / Vc1 / Gene: rub, PF1282 / Production host: Escherichia coli (E. coli) / References: UniProt: P24297
#2: Chemical ChemComp-FE / FE (III) ION


Mass: 55.845 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Fe
#3: Chemical
ChemComp-D8U / deuterium(1+)


Mass: 2.014 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: D
#4: Chemical
ChemComp-D3O / trideuteriooxidanium / perdeuterated oxonium


Mass: 22.042 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: D3O
#5: Chemical ChemComp-DOD / water


Mass: 18.015 Da / Num. of mol.: 149 / Source method: isolated from a natural source / Formula: D2O
Sequence detailsM IN POSITION 0

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Experimental details

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Experiment

ExperimentMethod: NEUTRON DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 1.46 Å3/Da / Density % sol: 15.08 % / Description: NONE
Crystal growpH: 6.5 / Details: PH 6.5

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Data collection

Diffraction sourceSource: NUCLEAR REACTOR / Site: ILL / Beamline: D19 / Wavelength: 1.46
DetectorType: INSTITUT LAUE LANGEVIN DETECTOR GROUP / Detector: 5ATM 3HE, CURVED 120X30 DEGREES / Details: BORON CARBIDE BEAM DEFINING APERTURES
RadiationMonochromator: PYROLYTIC GRAPHITE (002) / Scattering type: neutron
Radiation wavelengthWavelength: 1.46 Å / Relative weight: 1
ReflectionResolution: 1.05→18.67 Å / Num. obs: 10521 / % possible obs: 93 % / Observed criterion σ(I): 1.5 / Redundancy: 3.1 % / Biso Wilson estimate: 8.36 Å2 / Rmerge(I) obs: 0.08 / Rrim(I) all: 0.095 / Net I/σ(I): 10.1

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Processing

Software
NameVersionClassification
PHENIX(PHENIX.REFINE)refinement
RETREATdata reduction
RETREATdata scaling
RefinementStarting model: NONE

Resolution: 1.05→15.705 Å / SU ML: 0.2 / σ(F): 1.33 / Phase error: 26.39 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2374 1159 5.1 %
Rwork0.199 --
obs0.201 22729 88.73 %
Solvent computationShrinkage radii: 0.6 Å / VDW probe radii: 0.9 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 80.058 Å2 / ksol: 0.6 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--0.4276 Å20 Å20 Å2
2--0.1858 Å20 Å2
3---0.2418 Å2
Refinement stepCycle: LAST / Resolution: 1.05→15.705 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms421 0 5 149 575
Refine LS restraints
Refine-IDTypeDev idealNumber
NEUTRON DIFFRACTIONf_bond_d0.0231022
NEUTRON DIFFRACTIONf_angle_d1.9761702
NEUTRON DIFFRACTIONf_dihedral_angle_d13.321245
NEUTRON DIFFRACTIONf_chiral_restr0.12263
NEUTRON DIFFRACTIONf_plane_restr0.011143
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.0501-1.09780.39891360.39242331NEUTRON DIFFRACTION79
1.0978-1.15570.37841350.34372551NEUTRON DIFFRACTION85
1.1557-1.22810.34411460.31332603NEUTRON DIFFRACTION87
1.2281-1.32290.31591350.27152619NEUTRON DIFFRACTION87
1.3229-1.45590.25951550.22792677NEUTRON DIFFRACTION89
1.4559-1.66640.23271530.18552735NEUTRON DIFFRACTION91
1.6664-2.09870.1971540.13772897NEUTRON DIFFRACTION94
2.0987-15.70720.17851450.15773157NEUTRON DIFFRACTION98

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