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- PDB-1vcx: Neutron Crystal Structure of the Wild Type Rubredoxin from Pyroco... -

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Basic information

Entry
Database: PDB / ID: 1vcx
TitleNeutron Crystal Structure of the Wild Type Rubredoxin from Pyrococcus Furiosus at 1.5A Resolution
ComponentsRubredoxin
KeywordsELECTRON TRANSPORT / Neutron structure / Hydrogen atom position / Hydration water structure / Hydrogen/Deuterium exchange / Iron-sulfur core / N-terminal region
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
DEUTERATED WATER / : / Rubredoxin
Similarity search - Component
Biological speciesPyrococcus furiosus (archaea)
MethodNEUTRON DIFFRACTION / NUCLEAR REACTOR / MOLECULAR REPLACEMENT / Resolution: 1.5 Å
AuthorsKurihara, K. / Tanaka, I. / Chatake, T. / Adams, M.W.W. / Jenney Jr., F.E. / Moiseeva, N. / Bau, R. / Niimura, N.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2004
Title: Neutron crystallographic study on rubredoxin from Pyrococcus furiosus by BIX-3, a single-crystal diffractometer for biomacromolecules
Authors: Kurihara, K. / Tanaka, I. / Chatake, T. / Adams, M.W.W. / Jenney Jr., F.E. / Moiseeva, N. / Bau, R. / Niimura, N.
History
DepositionMar 17, 2004Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Aug 10, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Non-polymer description / Version format compliance
Revision 1.3Mar 7, 2018Group: Data collection / Category: diffrn_detector / diffrn_radiation
Item: _diffrn_detector.detector / _diffrn_detector.type ..._diffrn_detector.detector / _diffrn_detector.type / _diffrn_radiation.pdbx_diffrn_protocol / _diffrn_radiation.pdbx_monochromatic_or_laue_m_l
Revision 1.4Jul 11, 2018Group: Data collection / Category: diffrn_radiation / diffrn_source
Item: _diffrn_radiation.pdbx_scattering_type / _diffrn_source.pdbx_synchrotron_beamline ..._diffrn_radiation.pdbx_scattering_type / _diffrn_source.pdbx_synchrotron_beamline / _diffrn_source.pdbx_synchrotron_site / _diffrn_source.type
Revision 1.5Jul 18, 2018Group: Data collection / Category: diffrn_radiation
Item: _diffrn_radiation.pdbx_diffrn_protocol / _diffrn_radiation.pdbx_monochromatic_or_laue_m_l
Revision 1.6Oct 25, 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 / struct_conn / struct_conn_type / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _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_conn_type.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)5,9562
Polymers5,9011
Non-polymers561
Water66737
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)34.320, 35.310, 44.230
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 / / PF Rd


Mass: 5900.532 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pyrococcus furiosus (archaea) / Plasmid: pT7-7 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21-DE3 / 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-DOD / water / Heavy water


Mass: 18.015 Da / Num. of mol.: 37 / 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: 298 K / Method: macroseeding / pH: 8
Details: sodium dihydrogen phosphate, dipotassium hydrogen phosphate, pH 8.0, Macroseeding, temperature 298K

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Data collection

DiffractionMean temperature: 298 K
Diffraction sourceSource: NUCLEAR REACTOR / Site: JRR-3M / Beamline: 1G-A / Wavelength: 2.33 Å
DetectorType: MACSCIENCE DIP100 / Detector: IMAGE PLATE / Date: Aug 24, 1999
RadiationMonochromator: elastically-bent perfect Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: neutron
Radiation wavelengthWavelength: 2.33 Å / Relative weight: 1
ReflectionResolution: 1.5→30 Å / Num. obs: 7417 / % possible obs: 81.9 % / Redundancy: 3.3 % / Biso Wilson estimate: 6.4 Å2 / Rsym value: 0.096 / Net I/σ(I): 8.5
Reflection shellResolution: 1.5→1.55 Å / Redundancy: 1.7 % / Mean I/σ(I) obs: 3.1 / Num. unique all: 469 / Rsym value: 0.232 / % possible all: 53.1

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Processing

Software
NameVersionClassification
CNS1refinement
DENZOdata reduction
SCALEPACKdata scaling
X-PLORphasing
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1BRF

1brf


Resolution: 1.5→27.6 Å / Rfactor Rfree error: 0.008 / Data cutoff high absF: 103355.67 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 2
Stereochemistry target values: MAXIMUM LIKELIHOOD TARGET USING AMPLITUDES
Details: X-PLOR 3.851 was also used for the refinement. THE STANDARD TOPOLOGY AND PARAMETER FILES WERE CHANGED FOR HYDROGEN AND DEUTERIUM ATOM PARAMETERS TO MEET THE REQUIREMENTS OF THE NEUTRON STRUCTURE REFINEMENT.
RfactorNum. reflection% reflectionSelection details
Rfree0.217 789 10.8 %RANDOM
Rwork0.186 ---
obs-7286 80.5 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 100 Å2 / ksol: 0.05010384 e/Å3
Displacement parametersBiso mean: 11.9 Å2
Baniso -1Baniso -2Baniso -3
1--0.35 Å20 Å20 Å2
2--0.03 Å20 Å2
3---0.32 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.19 Å0.16 Å
Luzzati d res low-5 Å
Luzzati sigma a0.17 Å0.15 Å
Refinement stepCycle: LAST / Resolution: 1.5→27.6 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms413 0 1 37 451
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
NEUTRON DIFFRACTIONc_bond_d0.01
NEUTRON DIFFRACTIONc_angle_deg1.24
NEUTRON DIFFRACTIONc_dihedral_angle_d25.8
NEUTRON DIFFRACTIONc_improper_angle_d1.2
NEUTRON DIFFRACTIONc_mcbond_it1.331.5
NEUTRON DIFFRACTIONc_mcangle_it2.192
NEUTRON DIFFRACTIONc_scbond_it1.892
NEUTRON DIFFRACTIONc_scangle_it2.492.5
LS refinement shellResolution: 1.5→1.55 Å / Rfactor Rfree error: 0.043 / Total num. of bins used: 10
RfactorNum. reflection% reflection
Rfree0.298 48 10.3 %
Rwork0.271 416 -
obs-464 52.5 %
Xplor file
Refine-IDSerial noParam fileTopol file
NEUTRON DIFFRACTION1PROTEIN.PARAMPROTEIN-ALLHDG.TOP
NEUTRON DIFFRACTION2WATER.PARAMWATER.TOP

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