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- PDB-4ar4: Neutron crystallographic structure of the reduced form perdeutera... -

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Basic information

Entry
Database: PDB / ID: 4ar4
TitleNeutron crystallographic structure of the reduced form perdeuterated Pyrococcus furiosus rubredoxin to 1.38 Angstrom resolution.
ComponentsRubredoxin
KeywordsELECTRON TRANSPORT / PERDEUTERATED / MONOCHROMATIC NEUTRON CRYSTALLOGRAPHY / HYDRONIUM / PROTONATION STATE
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: 1.381 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: Atomic model / Data collection / Structure summary
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: Database references / Derived calculations ...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 / pdbx_struct_conn_angle / 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 / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _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_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 3, 2023Group: Database references / Category: database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 2.2Jun 19, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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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)6,1808
Polymers6,0321
Non-polymers1487
Water1,874104
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9090 Å2
ΔGint40 kcal/mol
Surface area6170 Å2
MethodPISA
Unit cell
Length a, b, c (Å)34.375, 35.183, 43.994
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: REDUCED STATE (FE II), 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.: 2 / 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.: 104 / 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: 6.2 / Details: pH 6.2

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Data collection

Diffraction sourceSource: NUCLEAR REACTOR / Site: ILL / Beamline: D19 / Wavelength: 2.42
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: 2.42 Å / Relative weight: 1
ReflectionResolution: 1.38→27.42 Å / Num. obs: 10521 / % possible obs: 93.1 % / Observed criterion σ(I): 1.3 / Redundancy: 3.7 % / Biso Wilson estimate: 11.4 Å2 / Rmerge(I) obs: 0.07 / Rrim(I) all: 0.084 / Net I/σ(I): 12.1

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Processing

Software
NameClassification
PHENIXrefinement
RETREATdata reduction
RETREATdata scaling
RefinementResolution: 1.381→27.465 Å / SU ML: 0.27 / σ(F): 0 / Phase error: 22.14 / Stereochemistry target values: ML
Details: THE HIGH HYGROSCOPICITY OF SODIUM DITHIONITE ADDED TO THE CRYSTAL FOR FE REDUCTION LEADS TO THE INTRODUCTION OF EXCHANGEABLE H AND D ATOM POSITIONS DESPITE EFFORTS TO AVOID THE PRESENCE OF HYDROGEN ATOMS.
RfactorNum. reflection% reflection
Rfree0.2264 505 4.8 %
Rwork0.1861 --
obs0.1881 10500 91.97 %
Solvent computationShrinkage radii: 0.6 Å / VDW probe radii: 0.9 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 40.158 Å2 / ksol: 0.6 e/Å3
Displacement parametersBiso mean: 11.52 Å2
Baniso -1Baniso -2Baniso -3
1--0.5527 Å20 Å20 Å2
2--0.12 Å20 Å2
3---0.4326 Å2
Refinement stepCycle: LAST / Resolution: 1.381→27.465 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms421 0 5 104 530
Refine LS restraints
Refine-IDTypeDev idealNumber
NEUTRON DIFFRACTIONf_bond_d0.0051120
NEUTRON DIFFRACTIONf_angle_d0.8651873
NEUTRON DIFFRACTIONf_dihedral_angle_d13.09257
NEUTRON DIFFRACTIONf_chiral_restr0.06564
NEUTRON DIFFRACTIONf_plane_restr0.006186
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.3812-1.52020.41661230.35962306NEUTRON DIFFRACTION87
1.5202-1.74010.25681140.22032486NEUTRON DIFFRACTION92
1.7401-2.19220.20711390.14852538NEUTRON DIFFRACTION94
2.1922-27.47020.19351290.16562665NEUTRON DIFFRACTION94

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