[English] 日本語
Yorodumi
- PDB-4k9f: Neutron structure of Perdeuterated Rubredoxin refined against 1.7... -

+
Open data


ID or keywords:

Loading...

-
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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
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

-
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

-
Experimental details

-
Experiment

ExperimentMethod: NEUTRON DIFFRACTION / Number of used crystals: 1

-
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

-
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

-
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

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbjlc1.pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more