[English] 日本語
Yorodumi
- PDB-6xxk: Crystal Structure of Human Deoxyhypusine Synthase in complex with... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6xxk
TitleCrystal Structure of Human Deoxyhypusine Synthase in complex with spermidine
ComponentsDeoxyhypusine synthase
KeywordsTRANSFERASE / hypusination / deoxyhypusine synthase / EIF5A / translation / hypusine / posttranslational modification / polyamines / deoxyhypusine
Function / homology
Function and homology information


deoxyhypusine synthase / Hypusine synthesis from eIF5A-lysine / peptidyl-lysine modification to peptidyl-hypusine / deoxyhypusine synthase activity / spermidine metabolic process / spermidine catabolic process / positive regulation of T cell proliferation / glucose homeostasis / translation / positive regulation of cell population proliferation ...deoxyhypusine synthase / Hypusine synthesis from eIF5A-lysine / peptidyl-lysine modification to peptidyl-hypusine / deoxyhypusine synthase activity / spermidine metabolic process / spermidine catabolic process / positive regulation of T cell proliferation / glucose homeostasis / translation / positive regulation of cell population proliferation / identical protein binding / cytoplasm / cytosol
Similarity search - Function
Deoxyhypusine synthase / Deoxyhypusine synthase superfamily / Deoxyhypusine synthase / DHS-like NAD/FAD-binding domain superfamily
Similarity search - Domain/homology
ACETATE ION / BETA-MERCAPTOETHANOL / FORMIC ACID / SPERMIDINE / Deoxyhypusine synthase
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.65 Å
AuthorsWator, E. / Wilk, P. / Grudnik, P.
Funding support Poland, 1items
OrganizationGrant numberCountry
Polish National Science CentreUMO-2019/33/B/NZ1/01839 Poland
CitationJournal: Biomolecules / Year: 2020
Title: Half Way to Hypusine-Structural Basis for Substrate Recognition by Human Deoxyhypusine Synthase.
Authors: Wator, E. / Wilk, P. / Grudnik, P.
History
DepositionJan 27, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 15, 2020Provider: repository / Type: Initial release
Revision 1.1Jan 24, 2024Group: 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
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Deoxyhypusine synthase
B: Deoxyhypusine synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)84,71743
Polymers82,0892
Non-polymers2,62841
Water7,296405
1
A: Deoxyhypusine synthase
B: Deoxyhypusine synthase
hetero molecules

A: Deoxyhypusine synthase
B: Deoxyhypusine synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)169,43486
Polymers164,1784
Non-polymers5,25682
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation5_555x-y,-y,-z+1/31
Buried area43840 Å2
ΔGint-65 kcal/mol
Surface area40390 Å2
MethodPISA
Unit cell
Length a, b, c (Å)104.980, 104.980, 160.898
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number154
Space group name H-MP3221

-
Components

-
Protein , 1 types, 2 molecules AB

#1: Protein Deoxyhypusine synthase / DHS


Mass: 41044.500 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: DHPS, DS / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P49366, deoxyhypusine synthase

-
Non-polymers , 7 types, 446 molecules

#2: Chemical ChemComp-SPD / SPERMIDINE / N-(2-AMINO-PROPYL)-1,4-DIAMINOBUTANE / PA(34)


Mass: 145.246 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C7H19N3 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 14 / Source method: obtained synthetically / Formula: C2H6O2
#4: Chemical
ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: C2H3O2
#5: Chemical
ChemComp-BME / BETA-MERCAPTOETHANOL


Mass: 78.133 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C2H6OS
#6: Chemical
ChemComp-FMT / FORMIC ACID


Mass: 46.025 Da / Num. of mol.: 11 / Source method: obtained synthetically / Formula: CH2O2
#7: Chemical ChemComp-MRD / (4R)-2-METHYLPENTANE-2,4-DIOL


Mass: 118.174 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H14O2 / Comment: precipitant*YM
#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 405 / Source method: isolated from a natural source / Formula: H2O

-
Details

Has ligand of interestY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 3.12 Å3/Da / Density % sol: 60.55 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 0.025-0.125 mM carboxylic acid mix, 30-60% precipitant mix, 100 mM Tris-Bicine pH = 8.5

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.1 / Wavelength: 0.9184 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Feb 8, 2019
RadiationMonochromator: 0 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9184 Å / Relative weight: 1
ReflectionResolution: 1.649→46.194 Å / Num. obs: 123691 / % possible obs: 99.9 % / Redundancy: 11.092 % / Biso Wilson estimate: 34.126 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.11 / Rrim(I) all: 0.116 / Χ2: 1.307 / Net I/σ(I): 12.8
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. possibleNum. unique obsCC1/2Rrim(I) all% possible all
1.65-1.7511.1642.3520.9422030419894197340.6722.46599.2
1.75-1.8711.1991.2991.7620831618603186020.861.361100
1.87-2.0210.9110.6573.418982517401173980.950.689100
2.02-2.2111.5690.356.5218539816026160260.9850.366100
2.21-2.4710.9250.19111.3115888714544145440.9940.2100
2.47-2.8511.5420.1218.714879312891128910.9970.125100
2.85-3.4910.9180.07530.2711989610981109810.9980.079100
3.49-4.9210.4750.05244.8889615855685550.9990.055100
4.92-46.19410.2640.04449.7450899496849590.9990.04699.8

-
Processing

Software
NameVersionClassification
XSCALEdata scaling
PHENIXv.1.17.1refinement
PDB_EXTRACT3.25data extraction
XDSdata reduction
PHASERv.1.17.1phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1DHS

1dhs


Resolution: 1.65→46.194 Å / SU ML: 0.21 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 20.4
RfactorNum. reflection% reflection
Rfree0.1622 2099 1.7 %
Rwork0.1553 --
obs0.1554 123541 99.74 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 169.49 Å2 / Biso mean: 40.2291 Å2 / Biso min: 17.88 Å2
Refinement stepCycle: final / Resolution: 1.65→46.194 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5362 0 383 405 6150
Biso mean--62.37 44.94 -
Num. residues----691
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
1.649-1.68710.40331370.3785789498
1.6871-1.72930.32721390.32027990100
1.7293-1.77610.32041380.29078023100
1.7761-1.82830.29461380.25718037100
1.8283-1.88730.25661390.23428008100
1.8873-1.95480.22661390.20028061100
1.9548-2.03310.1851390.17198042100
2.0331-2.12560.15041400.15558064100
2.1256-2.23760.16211390.1438089100
2.2376-2.37780.1451390.13588076100
2.3778-2.56140.1311410.13068125100
2.5614-2.81910.13521400.1318119100
2.8191-3.2270.15851410.13358166100
3.227-4.06530.11691430.13048243100
4.0653-46.1940.15961470.14918505100
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)
10.83380.3574-1.41430.7816-1.85897.38240.02740.10130.3319-0.0858-0.0469-0.0943-0.13010.32590.0330.636-0.0976-0.02160.9436-0.05280.7863-14.744515.689642.1045
23.6147-1.95741.33973.1744-0.81231.3064-0.00070.18870.0161-0.07120.0034-0.1485-0.25980.3312-0.00330.3062-0.1190.02440.31310.01980.2604-33.108725.320820.02
30.82760.0288-0.19871.00920.2261.449-0.13860.2061-0.0178-0.42490.1361-0.2354-0.03440.459-0.01980.3653-0.120.08130.4347-0.01620.3197-25.30188.48341.9105
40.44530.08380.00310.5951-0.02240.8902-0.06360.0891-0.0256-0.22440.075-0.00920.04880.0744-0.00890.3201-0.06410.00650.27060.00180.2245-44.5526-2.8942-0.4086
50.6846-0.59440.38531.37850.03990.7335-0.0855-0.04030.02040.00650.1031-0.160.02650.2124-0.00970.2671-0.01560.02070.3692-0.01590.2996-28.1867-1.416117.1586
63.36550.1995-1.44612.8884-0.02014.5460.06270.09890.3461-0.35870.0561-0.2344-0.40750.1746-0.10830.3235-0.09240.02840.26580.01340.2705-35.835916.04924.3981
71.431-1.05360.89071.8283-0.84411.65870.0004-0.0778-0.15380.15750.07190.08110.2532-0.0127-0.04210.32460.05410.01780.23670.02410.2452-48.5286-17.995246.0971
82.00280.56740.52541.1623-0.17290.7953-0.01350.278-0.2608-0.16680.14660.10390.3325-0.1679-0.13390.3472-0.0351-0.03130.25320.00630.2575-53.7578-25.830420.9618
90.5288-0.00160.03860.6461-0.10010.9407-0.04060.0425-0.0601-0.1520.0673-0.07880.24020.135-0.0260.3140.0160.01720.2536-0.0150.2388-39.0836-20.790313.637
104.16932.52181.81726.0312-0.73124.1789-1.48911.41-0.1002-2.50282.21131.02360.4039-2.4328-0.72791.34680.0917-0.08951.35040.0271.1337-46.8493-42.555720.9984
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 9 through 27 )A9 - 27
2X-RAY DIFFRACTION2chain 'A' and (resid 28 through 53 )A28 - 53
3X-RAY DIFFRACTION3chain 'A' and (resid 54 through 88 )A54 - 88
4X-RAY DIFFRACTION4chain 'A' and (resid 89 through 307 )A89 - 307
5X-RAY DIFFRACTION5chain 'A' and (resid 308 through 342 )A308 - 342
6X-RAY DIFFRACTION6chain 'A' and (resid 343 through 363 )A343 - 363
7X-RAY DIFFRACTION7chain 'B' and (resid 28 through 53 )B28 - 53
8X-RAY DIFFRACTION8chain 'B' and (resid 54 through 110 )B54 - 110
9X-RAY DIFFRACTION9chain 'B' and (resid 111 through 363 )B111 - 363
10X-RAY DIFFRACTION10chain 'B' and (resid 364 through 364 )B364

+
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://pdbjlvh1.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