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- PDB-4k9f: Neutron structure of Perdeuterated Rubredoxin refined against 1.7... -

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Basic information

Entry
Database: PDB / ID: 4k9f
TitleNeutron structure of Perdeuterated Rubredoxin refined against 1.75 resolution data collected on the new IMAGINE instrument at HFIR, ORNL
ComponentsRubredoxin
KeywordsELECTRON TRANSPORT / IRON / METAL-BINDING / TRANSPORT
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 ...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
DEUTERATED WATER / : / Rubredoxin
Similarity search - Component
Biological speciesPyrococcus furiosus (archaea)
MethodNEUTRON DIFFRACTION / NUCLEAR REACTOR / MOLECULAR REPLACEMENT / Resolution: 1.75 Å
AuthorsMunshi, P. / Meilleur, F. / Myles, D.
CitationJournal: Acta Crystallogr.,Sect.D / Year: 2013
Title: The IMAGINE instrument: first neutron protein structure and new capabilities for neutron macromolecular crystallography.
Authors: Meilleur, F. / Munshi, P. / Robertson, L. / Stoica, A.D. / Crow, L. / Kovalevsky, A. / Koritsanszky, T. / Chakoumakos, B.C. / Blessing, R. / Myles, D.A.
History
DepositionApr 19, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 4, 2013Provider: repository / Type: Initial release
Revision 1.1Jun 13, 2018Group: Data collection / Category: diffrn_radiation
Item: _diffrn_radiation.pdbx_diffrn_protocol / _diffrn_radiation.pdbx_monochromatic_or_laue_m_l
Revision 1.2Sep 20, 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 / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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_seq_id / _struct_conn.ptnr1_label_seq_id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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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)6,0882
Polymers6,0321
Non-polymers561
Water1,04558
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)33.822, 34.803, 43.351
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
Source: (gene. exp.) Pyrococcus furiosus (archaea) / Strain: ATCC 43587 / DSM 3638 / JCM 8422 / Vc1 / Gene: PF1282, rub / Plasmid: PET24D / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / 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-DOD / water


Mass: 18.015 Da / Num. of mol.: 58 / Source method: isolated from a natural source / Formula: D2O

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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

Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 20 mg/ml rubredoxin in 1.9 M SODIUM/POTASSIUM PHOSPHATE sitting drop equilibrated against 3.8 M SODIUM/POTASSIUM PHOSPHATE reservoir, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 293 K
Diffraction sourceSource: NUCLEAR REACTOR / Type: OTHER / Wavelength: 2.78 - 4.0
DetectorType: QLD: IMAGINE CG4D HFIR / Detector: IMAGE PLATE / Date: Jan 1, 2013
RadiationMonochromator: HFIR Source / Protocol: LAUE / Monochromatic (M) / Laue (L): L / Scattering type: neutron
Radiation wavelength
IDWavelength (Å)Relative weight
12.781
241
ReflectionResolution: 1.75→27.14 Å / Num. all: 4095 / Num. obs: 4095 / % possible obs: 76.4 % / Observed criterion σ(I): 2 / Redundancy: 3.5 % / Rmerge(I) obs: 0.127 / Net I/σ(I): 7
Reflection shellResolution: 1.75→1.84 Å / Redundancy: 2.2 % / Rmerge(I) obs: 0.185 / Mean I/σ(I) obs: 3.7 / Num. unique all: 410 / % possible all: 54.1

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Processing

Software
NameVersionClassification
Quasi-LaueDiffractometer v4.06data collection
PHENIX(phenix.refine: 1.8_1069)refinement
LAUEGENdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3KYW

3kyw


Resolution: 1.75→27.139 Å / SU ML: 0.22 / σ(F): 1.63 / σ(I): 2 / Phase error: 21.05 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2412 424 10.35 %random
Rwork0.1985 ---
obs0.2029 4095 74.37 %-
all-4095 --
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.75→27.139 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms412 0 1 58 471
Refine LS restraints
Refine-IDTypeDev idealNumber
NEUTRON DIFFRACTIONf_bond_d0.013888
NEUTRON DIFFRACTIONf_angle_d0.9941497
NEUTRON DIFFRACTIONf_dihedral_angle_d9.98217
NEUTRON DIFFRACTIONf_chiral_restr0.07957
NEUTRON DIFFRACTIONf_plane_restr0.005133
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.7501-2.00330.27561150.2335950NEUTRON DIFFRACTION59
2.0033-2.52360.25271340.19731215NEUTRON DIFFRACTION74
2.5236-27.14250.22011750.18551506NEUTRON DIFFRACTION88

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