[English] 日本語
Yorodumi
- PDB-1jal: YCHF PROTEIN (HI0393) -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1jal
TitleYCHF PROTEIN (HI0393)
ComponentsYchF protein
KeywordsSTRUCTURAL GENOMICS / UNKNOWN FUNCTION / nucleotide-binding fold / Structure 2 Function Project / S2F
Function / homology
Function and homology information


ribosomal large subunit binding / ribosome binding / GTP binding / ATP hydrolysis activity / ATP binding / metal ion binding / cytoplasm
Similarity search - Function
Obg-related GTPase Ych/YyaF, coiled-coil domain / Ribosome-binding ATPase YchF/Obg-like ATPase 1 / YchF, C-terminal domain / TGS-like domain superfamily / YchF, N-terminal / Protein of unknown function (DUF933) / TGS domain profile. / TGS-like / OBG-type guanine nucleotide-binding (G) domain / OBG-type guanine nucleotide-binding (G) domain profile. ...Obg-related GTPase Ych/YyaF, coiled-coil domain / Ribosome-binding ATPase YchF/Obg-like ATPase 1 / YchF, C-terminal domain / TGS-like domain superfamily / YchF, N-terminal / Protein of unknown function (DUF933) / TGS domain profile. / TGS-like / OBG-type guanine nucleotide-binding (G) domain / OBG-type guanine nucleotide-binding (G) domain profile. / Beta-grasp domain / 50S ribosome-binding GTPase / GTP binding domain / Beta-grasp domain superfamily / Ubiquitin-like (UB roll) / DNA polymerase; domain 1 / P-loop containing nucleotide triphosphate hydrolases / Roll / P-loop containing nucleoside triphosphate hydrolase / Rossmann fold / Orthogonal Bundle / 3-Layer(aba) Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
Ribosome-binding ATPase YchF
Similarity search - Component
Biological speciesHaemophilus influenzae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MIR / Resolution: 2.4 Å
AuthorsTeplyakov, A. / Gilliland, G.L. / Structure 2 Function Project (S2F)
CitationJournal: J.BACTERIOL. / Year: 2003
Title: Crystal structure of the YchF protein reveals binding sites for GTP and nucleic acid
Authors: Teplyakov, A. / Gilliland, G.L.
History
DepositionMay 30, 2001Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 25, 2003Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 7, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: YchF protein
B: YchF protein


Theoretical massNumber of molelcules
Total (without water)79,5892
Polymers79,5892
Non-polymers00
Water8,719484
1
A: YchF protein


Theoretical massNumber of molelcules
Total (without water)39,7941
Polymers39,7941
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: YchF protein


Theoretical massNumber of molelcules
Total (without water)39,7941
Polymers39,7941
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)61.000, 93.600, 85.200
Angle α, β, γ (deg.)90.00, 100.10, 90.00
Int Tables number4
Space group name H-MP1211

-
Components

#1: Protein YchF protein / HI0393 / PROBABLE GTP-BINDING PROTEIN HI0393


Mass: 39794.270 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Haemophilus influenzae (bacteria) / Gene: YchF / Production host: Escherichia coli (E. coli) / References: UniProt: P44681
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 484 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
Sample preparation

CrystalDensity Matthews: 3 Å3/Da / Density % sol: 59 %
Crystal growTemperature: 290 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: PEG8000, Magnesium acetate, Bicine buffer, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 290K
Crystal grow
*PLUS
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
10.1 MBicine1reservoirpH7.5
20.3 Mmagnesium acetate1reservoir
313 %PEG80001reservoir

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 17-ID / Wavelength: 1.0597 Å
DetectorType: MARRESEARCH / Detector: CCD / Date: Sep 20, 2000
RadiationMonochromator: graphite / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0597 Å / Relative weight: 1
ReflectionResolution: 2.4→11 Å / Num. all: 36364 / Num. obs: 36364 / % possible obs: 99.2 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 5.3 % / Biso Wilson estimate: 55 Å2 / Rmerge(I) obs: 0.045 / Net I/σ(I): 38
Reflection shellResolution: 2.4→2.45 Å / Redundancy: 5.3 % / Rmerge(I) obs: 0.26 / % possible all: 98.9
Reflection
*PLUS
Lowest resolution: 10 Å / Num. obs: 36325 / % possible obs: 99.4 % / Redundancy: 5.4 % / Rmerge(I) obs: 0.044
Reflection shell
*PLUS
Highest resolution: 2.4 Å / Lowest resolution: 2.46 Å / % possible obs: 98.8 % / Redundancy: 5.2 % / Num. unique obs: 2379 / Rmerge(I) obs: 0.242 / Mean I/σ(I) obs: 4.4

-
Processing

Software
NameVersionClassification
DENZOdata reduction
SCALEPACKdata scaling
SHARPphasing
REFMAC5refinement
RefinementMethod to determine structure: MIR / Resolution: 2.4→10 Å / Cor.coef. Fo:Fc: 0.939 / SU B: 2.764 / SU ML: 0.071 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.328 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.247 1836 5.1 %RANDOM
Rwork0.204 ---
obs0.208 34399 99.4 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 59.75 Å2
Baniso -1Baniso -2Baniso -3
1--2.73 Å20 Å2-0.03 Å2
2--1.85 Å20 Å2
3---0.87 Å2
Refinement stepCycle: LAST / Resolution: 2.4→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5243 0 0 484 5727
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.0225322
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.5531.9687190
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg10.645677
X-RAY DIFFRACTIONr_dihedral_angle_2_deg
X-RAY DIFFRACTIONr_chiral_restr0.0990.2821
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.024004
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.3010.22760
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2010.2395
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.3460.291
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2610.223
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_mcbond_it7.25943377
X-RAY DIFFRACTIONr_mcangle_it9.66485405
X-RAY DIFFRACTIONr_scbond_it12.20881945
X-RAY DIFFRACTIONr_scangle_it12.6581785
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.4→2.48 Å / Total num. of bins used: 15 /
RfactorNum. reflection
Rfree0.264 168
Rwork0.222 3221
Refinement
*PLUS
Highest resolution: 2.4 Å / Lowest resolution: 10 Å / % reflection Rfree: 5 % / Rfactor Rwork: 0.208
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONr_bond_d0.016
X-RAY DIFFRACTIONr_angle_d
X-RAY DIFFRACTIONr_angle_deg1.5
LS refinement shell
*PLUS
Lowest resolution: 2.46 Å

+
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://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