4B8Z | pdb_00004b8z

Crystal structure of human GDP-L-fucose synthase with bound NADP and GDP, rhombohedral crystal form

• PDB DOI: https://doi.org/10.2210/pdb4B8Z/pdb

• Classification: OXIDOREDUCTASE
• Organism(s): Homo sapiens
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2012-08-31 Released: 2013-02-06 
• Deposition Author(s): Vollmar, M., Krojer, T., Shafqat, N., Rojkova, A., Bunkoczi, G., Yue, W.W., Kavanagh, K., von Delft, F., Weigelt, J., Arrowsmith, C.H., Bountra, C., Edwards, A., Oppermann, U.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.75 Å
• R-Value Free: 
  0.261 (Depositor), 0.277 (DCC) 
• R-Value Work: 
  0.233 (Depositor), 0.249 (DCC) 
• R-Value Observed: 
  0.235 (Depositor) 

Starting Model: experimental

Literature

Crystal Structure of Human Gdp-L-Fucose Synthase with Bound Nadp and Gdp, Rhombohedral Crystal Form

Vollmar, M., Krojer, T., Shafqat, N., Rojkova, A., Bunkoczi, G., Yue, W.W., Kavanagh, K., von Delft, F., Weigelt, J., Arrowsmith, C.H., Bountra, C., Edwards, A., Oppermann, U.

To be published.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors and generated by PISA (software)

Biological Assembly 2  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 2 assigned by authors and generated by PISA (software)

Biological Assembly 3  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 3 assigned by authors and generated by PISA (software)

Biological Assembly 4  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 4 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 148.75 kDa 
• Atom Count: 9,492 
• Modeled Residue Count: 1,254 
• Deposited Residue Count: 1,280 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
GDP-L-FUCOSE SYNTHASE	A, B, C, D	320	Homo sapiens	Mutation(s): 0  EC: 1.1.1.271
UniProt & NIH Common Fund Data Resources
Find proteins for Q13630 (Homo sapiens) Explore Q13630  Go to UniProtKB:  Q13630
PHAROS:  Q13630 GTEx:  ENSG00000104522

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
NAP	E [auth A], G [auth B], I [auth C], K [auth D]	NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE C21 H28 N7 O17 P3 XJLXINKUBYWONI-NNYOXOHSSA-N
GDP	F [auth A], H [auth B], J [auth C], L [auth D]	GUANOSINE-5'-DIPHOSPHATE C10 H15 N5 O11 P2 QGWNDRXFNXRZMB-UUOKFMHZSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.75 Å
• R-Value Free:  0.261 (Depositor), 0.277 (DCC) 
• R-Value Work:  0.233 (Depositor), 0.249 (DCC) 
• R-Value Observed: 0.235 (Depositor) 

Space Group: H 3

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 91.447	α = 90
b = 91.447	β = 90
c = 429.13	γ = 120

Software Package:

Software Name	Purpose
BUSTER	refinement
XDS	data reduction
SCALA	data scaling
PHASER	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2013-02-06 
Deposition Author(s): Vollmar, M., Krojer, T., Shafqat, N., Rojkova, A., Bunkoczi, G., Yue, W.W., Kavanagh, K., von Delft, F., Weigelt, J., Arrowsmith, C.H., Bountra, C., Edwards, A., Oppermann, U.

Revision History  

• Version 1.0: 2013-02-06
  Type: Initial release
  
• Version 1.1: 2018-01-24
  Changes: Database references
• Version 1.2: 2018-06-20
  Changes: Data collection, Derived calculations
• Version 1.3: 2023-12-20
  Changes: Data collection, Database references, Derived calculations, Other, Refinement description