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- PDB-5ome: The cryofrozen atomic resolution X-ray crystal structure of the r... -

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Entry
Database: PDB / ID: 5ome
TitleThe cryofrozen atomic resolution X-ray crystal structure of the reduced form (Fe2+) perdeuterated Pyrococcus furiosus Rubredoxin in D2O (100K, 0.75 Angstrom resolution)
ComponentsRubredoxin
KeywordsELECTRON TRANSPORT / Perdeuterated rubredoxin / pyrococcus furiosus / atomic resolution / cryofrozen / reduced / iron
Function / homology
Function and homology information


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
: / PHOSPHATE ION / Rubredoxin
Similarity search - Component
Biological speciesPyrococcus furiosus (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / AB INITIO PHASING / Resolution: 0.747 Å
AuthorsCuypers, M.G. / Mason, S.A. / Mossou, E. / Haertlein, M. / Mitchell, E.P. / Forsyth, V.T.
Funding support United Kingdom, France, 4items
OrganizationGrant numberCountry
Engineering and Physical Sciences Research CouncilEP/C015452/1 United Kingdom
European UnionRII3-CT-2003-505925 France
ESRF France
Institut Laue-Langevin France
CitationJournal: To Be Published
Title: The cryofrozen atomic resolution X-ray crystal structure of the reduced form (Fe2+) perdeuterated Pyrococcus furiosus Rubredoxin in D2O (100K, 0.75 Angstrom resolution)
Authors: Cuypers, M.G. / Mason, S.A. / Mossou, E. / Haertlein, M. / Mitchell, E.P. / Forsyth, V.T.
History
DepositionJul 31, 2017Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 5, 2018Provider: repository / Type: Initial release
Revision 1.1Feb 15, 2023Group: Author supporting evidence / Database references / Derived calculations
Category: database_2 / pdbx_audit_support ...database_2 / pdbx_audit_support / pdbx_struct_conn_angle / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_audit_support.funding_organization / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_alt_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_alt_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_ptnr1_label_alt_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_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_symmetry
Revision 1.2Feb 22, 2023Group: Advisory / Category: pdbx_database_PDB_obs_spr

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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)6,3015
Polymers6,0321
Non-polymers2694
Water3,765209
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area450 Å2
ΔGint-18 kcal/mol
Surface area3490 Å2
MethodPISA
Unit cell
Length a, b, c (Å)33.993, 34.803, 43.233
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: perdeuterated form
Source: (gene. exp.) Pyrococcus furiosus (strain ATCC 43587 / DSM 3638 / JCM 8422 / Vc1) (archaea)
Gene: rub, PF1282 / Plasmid: PET28
Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
References: UniProt: P24297
#2: Chemical ChemComp-FE / FE (III) ION / Iron


Mass: 55.845 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Fe
#3: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#4: Chemical ChemComp-PO4 / PHOSPHATE ION / Phosphate


Mass: 94.971 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: PO4
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 209 / 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: 2.12 Å3/Da / Density % sol: 41.98 %
Description: bipyramid bright red (Fe3+), Subsequently reduced with Na2S2O3 to get transparent (Fe2+) crystal. X-ray data collection performed with helicoidal strategy over 180 degrees rotation.
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.5 / Details: SEEDED 3.4M EQUIMOLAR NA/K PHOSPHATE BUFFER / Temp details: controlled room

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Data collection

DiffractionMean temperature: 100 K
Ambient temp details: Cryostream frozen (never flash frozen in liquid N2)
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.77 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jul 7, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.77 Å / Relative weight: 1
ReflectionResolution: 0.747→34.8 Å / Num. obs: 57618 / % possible obs: 85.7 % / Redundancy: 4.3 % / Biso Wilson estimate: 4.1 Å2 / CC1/2: 0.997 / Rmerge(I) obs: 0.054 / Rpim(I) all: 0.027 / Rrim(I) all: 0.06 / Net I/σ(I): 15.8
Reflection shellResolution: 0.75→0.79 Å / Redundancy: 1.7 % / Rmerge(I) obs: 0.202 / Mean I/σ(I) obs: 3.4 / Num. unique obs: 2727 / CC1/2: 0.786 / Rpim(I) all: 0.17 / Rrim(I) all: 0.266 / % possible all: 28.3

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Processing

Software
NameVersionClassification
PHENIX(1.12_2829: ???)refinement
XDSdata reduction
SCALAdata scaling
ACORNphasing
RefinementMethod to determine structure: AB INITIO PHASING / Resolution: 0.747→18.363 Å / SU ML: 0.02 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 10.12
Details: Deuterium atoms are isotropic, protein atoms, Fe atom and solvent O atoms are anisotropic
RfactorNum. reflection% reflectionSelection details
Rfree0.1214 2892 5.03 %random
Rwork0.111 ---
obs0.1115 57545 85.72 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 0.747→18.363 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms421 0 12 209 642
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.008498
X-RAY DIFFRACTIONf_angle_d1.01687
X-RAY DIFFRACTIONf_dihedral_angle_d17.92191
X-RAY DIFFRACTIONf_chiral_restr0.08464
X-RAY DIFFRACTIONf_plane_restr0.00996
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
0.747-0.75930.2897150.1935261X-RAY DIFFRACTION9
0.7593-0.77230.14500.1481865X-RAY DIFFRACTION29
0.7723-0.78640.143590.13611360X-RAY DIFFRACTION45
0.7864-0.80150.1257830.1251848X-RAY DIFFRACTION61
0.8015-0.81790.12521420.11242226X-RAY DIFFRACTION75
0.8179-0.83570.10461300.1112640X-RAY DIFFRACTION87
0.8357-0.85510.11091660.10582831X-RAY DIFFRACTION95
0.8551-0.87650.10751350.10083003X-RAY DIFFRACTION100
0.8765-0.90020.11361530.09363025X-RAY DIFFRACTION100
0.9002-0.92670.1021620.09142991X-RAY DIFFRACTION100
0.9267-0.95660.1021530.08993027X-RAY DIFFRACTION100
0.9566-0.99080.11121710.08563013X-RAY DIFFRACTION100
0.9908-1.03040.09691510.0873034X-RAY DIFFRACTION100
1.0304-1.07730.09421760.08532994X-RAY DIFFRACTION100
1.0773-1.13410.09261490.08753048X-RAY DIFFRACTION100
1.1341-1.20520.10191760.09363017X-RAY DIFFRACTION100
1.2052-1.29820.10481840.10413022X-RAY DIFFRACTION100
1.2982-1.42880.11481610.11643053X-RAY DIFFRACTION100
1.4288-1.63540.13241460.12083097X-RAY DIFFRACTION100
1.6354-2.060.12911680.133096X-RAY DIFFRACTION99
2.06-18.36830.15431620.1263202X-RAY DIFFRACTION98

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