[English] 日本語
Yorodumi
- PDB-4e5y: Structure of human FX protein, the key enzyme in the biosynthesis... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 4e5y
TitleStructure of human FX protein, the key enzyme in the biosynthesis of GDP-L-fucose
ComponentsGDP-L-fucose synthase
KeywordsOXIDOREDUCTASE / biosynthesis / GDP-L-fucose
Function / homology
Function and homology information


GDP-4-dehydro-D-rhamnose reductase activity / GDP-mannose 3,5-epimerase activity / GDP-fucose biosynthesis / GDP-L-fucose synthase / GDP-mannose metabolic process / GDP-L-fucose synthase activity / positive regulation of endothelial cell-matrix adhesion via fibronectin / 'de novo' GDP-L-fucose biosynthetic process / leukocyte cell-cell adhesion / positive regulation of endothelial cell migration ...GDP-4-dehydro-D-rhamnose reductase activity / GDP-mannose 3,5-epimerase activity / GDP-fucose biosynthesis / GDP-L-fucose synthase / GDP-mannose metabolic process / GDP-L-fucose synthase activity / positive regulation of endothelial cell-matrix adhesion via fibronectin / 'de novo' GDP-L-fucose biosynthetic process / leukocyte cell-cell adhesion / positive regulation of endothelial cell migration / electron transfer activity / extracellular exosome / identical protein binding / cytosol
Similarity search - Function
GDP-L-fucose synthase/GDP-L-colitose synthase / UDP-galactose 4-epimerase, domain 1 / UDP-galactose 4-epimerase; domain 1 / NAD-dependent epimerase/dehydratase / NAD dependent epimerase/dehydratase family / NAD(P)-binding Rossmann-like Domain / NAD(P)-binding domain superfamily / Alpha-Beta Complex / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Chem-NDP / GDP-L-fucose synthase
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.37 Å
AuthorsZhou, H. / He, J.H.
CitationJournal: To be Published
Title: Structure of human FX protein, the key enzyme in the biosynthesis of GDP-L-fucose
Authors: Zhou, H. / He, J.H.
History
DepositionMar 15, 2012Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Apr 17, 2013Provider: repository / Type: Initial release
Revision 1.1Mar 20, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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: GDP-L-fucose synthase
B: GDP-L-fucose synthase
C: GDP-L-fucose synthase
D: GDP-L-fucose synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)146,7248
Polymers143,7424
Non-polymers2,9824
Water39622
1
A: GDP-L-fucose synthase
B: GDP-L-fucose synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)73,3624
Polymers71,8712
Non-polymers1,4912
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4950 Å2
ΔGint-24 kcal/mol
Surface area24910 Å2
MethodPISA
2
C: GDP-L-fucose synthase
D: GDP-L-fucose synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)73,3624
Polymers71,8712
Non-polymers1,4912
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4910 Å2
ΔGint-24 kcal/mol
Surface area25730 Å2
MethodPISA
Unit cell
Length a, b, c (Å)85.772, 136.440, 139.849
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

-
Components

#1: Protein
GDP-L-fucose synthase / GDP-4-keto-6-deoxy-D-mannose-3 / 5-epimerase-4-reductase / Protein FX / Red cell NADP(H)-binding ...GDP-4-keto-6-deoxy-D-mannose-3 / 5-epimerase-4-reductase / Protein FX / Red cell NADP(H)-binding protein / Short-chain dehydrogenase/reductase family 4E member 1


Mass: 35935.590 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: TSTA3, SDR4E1 / Production host: Escherichia coli (E. coli) / References: UniProt: Q13630, GDP-L-fucose synthase
#2: Chemical
ChemComp-NDP / NADPH DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE


Mass: 745.421 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C21H30N7O17P3
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 22 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION

-
Sample preparation

CrystalDensity Matthews: 2.85 Å3/Da / Density % sol: 56.79 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 8
Details: 100mM Tris pH 8.0, 30% PEG 2000, VAPOR DIFFUSION, SITTING DROP, temperature 277K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 0.97883 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: May 18, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97883 Å / Relative weight: 1
ReflectionResolution: 2.37→50 Å / Num. obs: 67223
Reflection shellResolution: 2.37→2.41 Å

-
Processing

Software
NameVersionClassification
ADSCQuantumdata collection
PHENIXmodel building
PHENIX(phenix.refine: 1.6.2_432)refinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.37→39.267 Å / SU ML: 0.38 / σ(F): 0 / Phase error: 31.41 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2915 1862 2.96 %
Rwork0.2323 --
obs0.2341 63005 93.57 %
Solvent computationShrinkage radii: 0.95 Å / VDW probe radii: 1.2 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 32.495 Å2 / ksol: 0.342 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-15.2606 Å2-0 Å2-0 Å2
2---7.8349 Å20 Å2
3----7.4256 Å2
Refinement stepCycle: LAST / Resolution: 2.37→39.267 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9689 0 192 22 9903
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00910132
X-RAY DIFFRACTIONf_angle_d1.36613771
X-RAY DIFFRACTIONf_dihedral_angle_d24.5393853
X-RAY DIFFRACTIONf_chiral_restr0.1031511
X-RAY DIFFRACTIONf_plane_restr0.0061745
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 10

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.3697-2.45440.38711710.2634536783
2.4544-2.55260.39041620.2686550386
2.5526-2.66880.3461700.259576989
2.6688-2.80950.34231850.2553594592
2.8095-2.98540.31621920.2718610294
2.9854-3.21580.32611820.2596626796
3.2158-3.53930.34011920.249636198
3.5393-4.0510.28411980.2252647299
4.051-5.1020.2361970.1947654999
5.102-39.27210.24162130.2119680899

+
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