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- PDB-3rzt: Neutron structure of perdeuterated rubredoxin using rapid (14 hou... -

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Basic information

Entry
Database: PDB / ID: 3rzt
TitleNeutron structure of perdeuterated rubredoxin using rapid (14 hours) data
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 / Single Sheet / Mainly Beta
Similarity search - Domain/homology
DEUTERATED WATER / : / Rubredoxin
Similarity search - Component
Biological speciesPyrococcus furiosus (archaea)
MethodNEUTRON DIFFRACTION / NUCLEAR REACTOR / FOURIER SYNTHESIS / Resolution: 1.7504 Å
AuthorsMunshi, P. / Chung, C.-L. / Weiss, K.L. / Blakeley, M.P. / Myles, D.A.A. / Meilleur, F.
CitationJournal: Acta Crystallogr.,Sect.D / Year: 2012
Title: Rapid visualization of hydrogen positions in protein neutron crystallographic structures.
Authors: Munshi, P. / Chung, S.L. / Blakeley, M.P. / Weiss, K.L. / Myles, D.A. / Meilleur, F.
History
DepositionMay 12, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 28, 2011Provider: repository / Type: Initial release
Revision 1.1Jan 4, 2012Group: Database references
Revision 1.2Jan 24, 2018Group: Data collection / Structure summary / Category: audit_author / diffrn_radiation / diffrn_source
Item: _audit_author.name / _diffrn_radiation.pdbx_monochromatic_or_laue_m_l ..._audit_author.name / _diffrn_radiation.pdbx_monochromatic_or_laue_m_l / _diffrn_source.source / _diffrn_source.type
Revision 1.3Sep 13, 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 / diffrn_source / 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 / _diffrn_source.pdbx_synchrotron_beamline / _diffrn_source.pdbx_synchrotron_site / _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
Water63135
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)33.920, 34.870, 43.500
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.: 35 / 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 / Site: ILL / Beamline: LADI III / Wavelength: 3.2 - 4.2
DetectorType: MAATEL QLD: LADI-III / Detector: IMAGE PLATE / Date: Jun 8, 2007
RadiationProtocol: LAUE / Monochromatic (M) / Laue (L): L / Scattering type: neutron
Radiation wavelength
IDWavelength (Å)Relative weight
13.21
24.21
ReflectionResolution: 1.75→27.21 Å / Num. all: 4188 / Num. obs: 4187 / % possible obs: 77.5 % / Observed criterion σ(I): 2 / Redundancy: 4.6 % / Rmerge(I) obs: 0.153 / Net I/σ(I): 8.4
Reflection shellResolution: 1.75→1.84 Å / Redundancy: 2.6 % / Rmerge(I) obs: 0.189 / Mean I/σ(I) obs: 3.6 / % possible all: 56.2

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Processing

Software
NameVersionClassification
LAUEGENdata collection
PHENIX(phenix.refine: 2010_05_02_2130)refinement
LAUEGENdata reduction
SCALAdata scaling
RefinementMethod to determine structure: FOURIER SYNTHESIS
Starting model: PDB ENTRY 3KYW

3kyw


Resolution: 1.7504→27.208 Å / SU ML: 0.44 / σ(F): 1.53 / Phase error: 21.95 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.249 197 4.71 %
Rwork0.2022 --
obs0.2043 4187 75.6 %
all-4188 -
Solvent computationShrinkage radii: 1.2 Å / VDW probe radii: 1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 49.505 Å2 / ksol: 0.6 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--1.2296 Å20 Å20 Å2
2---2.3348 Å20 Å2
3----0.5381 Å2
Refinement stepCycle: LAST / Resolution: 1.7504→27.208 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms392 0 1 35 428
Refine LS restraints
Refine-IDTypeDev idealNumber
NEUTRON DIFFRACTIONf_bond_d0.013795
NEUTRON DIFFRACTIONf_angle_d1.2571388
NEUTRON DIFFRACTIONf_dihedral_angle_d13.083204
NEUTRON DIFFRACTIONf_chiral_restr0.06955
NEUTRON DIFFRACTIONf_plane_restr0.006125
LS refinement shellResolution: 1.7504→27.2108 Å
RfactorNum. reflection% reflection
Rfree0.249 197 -
Rwork0.2022 3990 -
obs--76 %

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