[English] 日本語
Yorodumi
- PDB-1oni: Crystal structure of a human p14.5, a translational inhibitor rev... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1oni
TitleCrystal structure of a human p14.5, a translational inhibitor reveals different mode of ligand binding near the invariant residues of the Yjgf/UK114 protein family
Components14.5 kDa translational inhibitor protein
KeywordsTRANSLATION / YjgF/YER057c/UK114 family / Trichloroacetic acid soluble protein / Translational inhibitor
Function / homology
Function and homology information


Threonine catabolism / : / 2-iminobutanoate/2-iminopropanoate deaminase / 2-iminobutanoate deaminase activity / 2-iminopropanoate deaminase activity / L-threonine catabolic process to glycine / deaminase activity / mRNA destabilization / mRNA catabolic process / lipid metabolic process ...Threonine catabolism / : / 2-iminobutanoate/2-iminopropanoate deaminase / 2-iminobutanoate deaminase activity / 2-iminopropanoate deaminase activity / L-threonine catabolic process to glycine / deaminase activity / mRNA destabilization / mRNA catabolic process / lipid metabolic process / RNA endonuclease activity, producing 3'-phosphomonoesters / peroxisome / negative regulation of translation / mitochondrial matrix / mRNA binding / mitochondrion / RNA binding / extracellular exosome / nucleus / cytosol / cytoplasm
Similarity search - Function
RidA, conserved site / Uncharacterized protein family UPF0076 signature. / RidA family / RutC-like / YjgF/YER057c/UK114 family / Endoribonuclease L-PSP / RutC-like superfamily / 60s Ribosomal Protein L30; Chain: A; / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
BENZOIC ACID / 2-iminobutanoate/2-iminopropanoate deaminase
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.9 Å
AuthorsManjasetty, B.A. / Delbrueck, H. / Mueller, U. / Erdmann, M.F. / Heinemann, U.
CitationJournal: Proteins / Year: 2004
Title: Crystal structure of Homo sapiens protein hp14.5.
Authors: Manjasetty, B.A. / Delbruck, H. / Pham, D.T. / Mueller, U. / Fieber-Erdmann, M. / Scheich, C. / Sievert, V. / Bussow, K. / Niesen, F.H. / Weihofen, W. / Loll, B. / Saenger, W. / Heinemann, U. / Neisen, F.H.
History
DepositionFeb 28, 2003Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 8, 2003Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.3Oct 11, 2017Group: Advisory / Refinement description / Category: pdbx_unobs_or_zero_occ_atoms / software / Item: _software.classification / _software.name
Revision 1.4Feb 14, 2024Group: Advisory / Data collection ...Advisory / Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_unobs_or_zero_occ_atoms / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _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: 14.5 kDa translational inhibitor protein
B: 14.5 kDa translational inhibitor protein
C: 14.5 kDa translational inhibitor protein
D: 14.5 kDa translational inhibitor protein
E: 14.5 kDa translational inhibitor protein
F: 14.5 kDa translational inhibitor protein
G: 14.5 kDa translational inhibitor protein
H: 14.5 kDa translational inhibitor protein
I: 14.5 kDa translational inhibitor protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)132,26422
Polymers130,6769
Non-polymers1,58813
Water7,981443
1
A: 14.5 kDa translational inhibitor protein
B: 14.5 kDa translational inhibitor protein
C: 14.5 kDa translational inhibitor protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)44,1698
Polymers43,5593
Non-polymers6115
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8640 Å2
ΔGint-15 kcal/mol
Surface area15690 Å2
MethodPISA
2
D: 14.5 kDa translational inhibitor protein
E: 14.5 kDa translational inhibitor protein
F: 14.5 kDa translational inhibitor protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)44,0477
Polymers43,5593
Non-polymers4884
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8650 Å2
ΔGint-14 kcal/mol
Surface area14950 Å2
MethodPISA
3
G: 14.5 kDa translational inhibitor protein
H: 14.5 kDa translational inhibitor protein
I: 14.5 kDa translational inhibitor protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)44,0477
Polymers43,5593
Non-polymers4884
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8670 Å2
ΔGint-14 kcal/mol
Surface area15380 Å2
MethodPISA
Unit cell
Length a, b, c (Å)154.158, 154.158, 104.559
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number152
Space group name H-MP3121

-
Components

#1: Protein
14.5 kDa translational inhibitor protein / p14.5 / UK114 antigen homolog


Mass: 14519.549 Da / Num. of mol.: 9 / Fragment: Translational inhibitor
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Description: PROTEIN STRUCTURE FACTORY CLONE ID 104124 / Gene: PSP / Plasmid: PSFEP758H0822 / Cellular location (production host): cytoplasm / Production host: Escherichia coli (E. coli) / Strain (production host): SCS1 / References: UniProt: P52758
#2: Chemical
ChemComp-BEZ / BENZOIC ACID


Mass: 122.121 Da / Num. of mol.: 13 / Source method: obtained synthetically / Formula: C7H6O2
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 443 / 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: 2.67 Å3/Da / Density % sol: 53.65 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7
Details: Sodium malonate, sodium benzoate, pH 7.00, VAPOR DIFFUSION, SITTING DROP, temperature 293.0K
Crystal grow
*PLUS
Temperature: 293 K / pH: 7
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
112.8 mg/mlprotein1drop
22 Msodium malonate1reservoir
30.3 Msodium benzoate1reservoirpH7.0

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.2 / Wavelength: 0.98004
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Dec 6, 2002 / Details: MIRRORS
RadiationMonochromator: MIRRORS / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98004 Å / Relative weight: 1
ReflectionResolution: 1.9→20 Å / Num. obs: 110385 / % possible obs: 98.4 % / Observed criterion σ(I): 0 / Redundancy: 6.8 % / Biso Wilson estimate: 29.8 Å2 / Rmerge(I) obs: 0.081 / Rsym value: 0.081 / Net I/σ(I): 22.9
Reflection shellResolution: 1.9→1.92 Å / Rmerge(I) obs: 0.55 / Mean I/σ(I) obs: 2.3 / Rsym value: 0.55 / % possible all: 94.4
Reflection
*PLUS
Highest resolution: 1.9 Å / Lowest resolution: 20 Å / Num. measured all: 754078
Reflection shell
*PLUS
% possible obs: 94.4 % / Rmerge(I) obs: 0.55 / Mean I/σ(I) obs: 2.3

-
Processing

Software
NameVersionClassification
REFMAC5refinement
MAR345data collection
SCALEPACKdata scaling
SnBphasing
SOLVEphasing
RefinementMethod to determine structure: SAD / Resolution: 1.9→20 Å / Cor.coef. Fo:Fc: 0.964 / Cor.coef. Fo:Fc free: 0.951 / SU B: 4.239 / SU ML: 0.127 / TLS residual ADP flag: LIKELY RESIDUAL / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / ESU R: 0.136 / ESU R Free: 0.127 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS REFINEMENT WITH TLS PARAMETERS.
RfactorNum. reflection% reflectionSelection details
Rfree0.216 5511 5 %RANDOM
Rwork0.185 ---
all-110333 --
obs-104822 98.2 %-
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: 20.6 Å2
Baniso -1Baniso -2Baniso -3
1--1.24 Å2-0.62 Å20 Å2
2---1.24 Å20 Å2
3---1.86 Å2
Refinement stepCycle: LAST / Resolution: 1.9→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8981 0 117 443 9541
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0229224
X-RAY DIFFRACTIONr_bond_other_d0.0020.028589
X-RAY DIFFRACTIONr_angle_refined_deg1.5421.97712493
X-RAY DIFFRACTIONr_angle_other_deg1.467319982
X-RAY DIFFRACTIONr_dihedral_angle_1_deg15.09731201
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.46151627
X-RAY DIFFRACTIONr_chiral_restr0.0940.21472
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0210316
X-RAY DIFFRACTIONr_gen_planes_other0.0050.021683
X-RAY DIFFRACTIONr_nbd_refined0.2980.31880
X-RAY DIFFRACTIONr_nbd_other0.2180.38235
X-RAY DIFFRACTIONr_nbtor_other0.3160.57
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1590.5702
X-RAY DIFFRACTIONr_xyhbond_nbd_other0.1210.514
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1810.327
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2420.340
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.210.59
X-RAY DIFFRACTIONr_mcbond_it0.9151.56022
X-RAY DIFFRACTIONr_mcangle_it1.62729677
X-RAY DIFFRACTIONr_scbond_it2.2433189
X-RAY DIFFRACTIONr_scangle_it3.6924.52829
LS refinement shellResolution: 1.9→1.95 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.292 369
Rwork0.242 7101
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
11.25830.12450.30791.32510.44441.2979-0.00020.06710.0421-0.1365-0.0394-0.0872-0.13960.06110.03960.2355-0.0149-0.02370.17750.05960.083835.12829.95715.401
21.5152-0.25430.55461.66550.05851.4506-0.0926-0.1645-0.08330.26020.02290.06610.0181-0.09450.06960.2626-0.00360.00140.1920.05530.073427.84217.42633.741
31.67660.2980.53941.60950.44141.2539-0.0305-0.011-0.1795-0.0645-0.0068-0.20590.13690.1550.03730.25440.01860.00940.19770.06350.144341.5257.64417.552
41.20030.7033-0.16552.1195-1.07752.3256-0.05260.07010.1632-0.11590.16280.3188-0.0427-0.0211-0.11020.256-0.0124-0.02630.17920.03040.046456.22452.23228.026
51.7906-0.1550.78751.8062-0.33111.84290.21030.1036-0.1834-0.14770.02980.08140.3070.1508-0.24010.30430.0302-0.05680.1977-0.01040.023462.64831.41136.066
61.24660.07360.74162.082-1.24183.0711-0.0010.11280.13080.359-0.1625-0.2258-0.32340.53390.16360.3228-0.0683-0.03290.27890.0150.003672.3150.73144.726
72.72740.2291-0.37971.4850.01741.425-0.12620.0478-0.28190.0292-0.10070.17120.0593-0.16680.2270.2398-0.02330.01470.3039-0.07220.1189-4.9229.86730.044
82.83350.842-0.29812.1937-0.4451.76710.25630.07790.28820.2286-0.07180.4828-0.2914-0.1033-0.18450.34720.0270.07530.2854-0.07850.2177-12.94151.39633.263
91.7339-0.1027-0.3522.59490.38682.41170.14460.26880.1224-0.3317-0.1789-0.0256-0.2667-0.1480.03440.31510.0529-0.01140.34320.00510.07332.69347.37516.631
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA25 - 12526 - 126
2X-RAY DIFFRACTION2BB25 - 12526 - 126
3X-RAY DIFFRACTION3CC25 - 12526 - 126
4X-RAY DIFFRACTION4DD25 - 12526 - 126
5X-RAY DIFFRACTION5EE25 - 12526 - 126
6X-RAY DIFFRACTION6FF25 - 12526 - 126
7X-RAY DIFFRACTION7GG25 - 12526 - 126
8X-RAY DIFFRACTION8HH25 - 12526 - 126
9X-RAY DIFFRACTION9II25 - 12526 - 126
Refinement
*PLUS
Highest resolution: 1.9 Å / Lowest resolution: 20 Å / % reflection Rfree: 5 %
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONr_bond_d0.013
X-RAY DIFFRACTIONr_angle_d
X-RAY DIFFRACTIONr_angle_deg1.542

+
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