2JGY | pdb_00002jgy

The crystal structure of human orotidine-5'-decarboxylase domain of human uridine monophosphate synthetase (UMPS)

• PDB DOI: https://doi.org/10.2210/pdb2JGY/pdb

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


• Deposited: 2007-02-16 Released: 2007-03-06 
• Deposition Author(s): Moche, M., Ogg, D., Arrowsmith, C., Berglund, H., Busam, R., Collins, R., Dahlgren, L.G., Edwards, A., Ericsson, U.B., Flodin, S., Flores, A., Graslund, S., Hammarstrom, M., Hallberg, B.M., Holmberg-Schiavone, L., Johansson, I., Karlberg, T., Kosinska, U., Kotenyova, T., Lehtio, L., Nilsson, M.E., Nyman, T., Persson, C., Sagemark, J., Stenmark, P., Sundstrom, M., Uppenberg, J., Upsten, M., Thorsell, A.G., van den Berg, S., Weigelt, J., Nordlund, P., Structural Genomics Consortium (SGC)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.95 Å
• R-Value Free: 
  0.197 (Depositor), 0.198 (DCC) 
• R-Value Work: 
  0.158 (Depositor), 0.166 (DCC) 
• R-Value Observed: 
  0.160 (Depositor) 

Starting Model: experimental

Literature

The Crystal Structure of Human Orotidine-5'-Decarboxylase Domain of Human Uridine Monophosphate Synthetase (Umps)

Moche, M., Flodin, S., Nyman, T., Stenmark, P., Nordlund, P.

To be published.

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

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

Macromolecule Content 

• Total Structure Weight: 61.26 kDa 
• Atom Count: 4,575 
• Modeled Residue Count: 494 
• Deposited Residue Count: 558 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
UMP SYNTHASE	A, B	279	Homo sapiens	Mutation(s): 0  EC: 4.1.1.23 (PDB Primary Data), 2.4.2.10 (UniProt)
UniProt & NIH Common Fund Data Resources
Find proteins for P11172 (Homo sapiens) Explore P11172  Go to UniProtKB:  P11172
PHAROS:  P11172 GTEx:  ENSG00000114491

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.95 Å
• R-Value Free:  0.197 (Depositor), 0.198 (DCC) 
• R-Value Work:  0.158 (Depositor), 0.166 (DCC) 
• R-Value Observed: 0.160 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 59.83	α = 90
b = 77.83	β = 90
c = 152.57	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
XDS	data reduction
XSCALE	data scaling
MOLREP	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2007-03-06 
Deposition Author(s): Moche, M., Ogg, D., Arrowsmith, C., Berglund, H., Busam, R., Collins, R., Dahlgren, L.G., Edwards, A., Ericsson, U.B., Flodin, S., Flores, A., Graslund, S., Hammarstrom, M., Hallberg, B.M., Holmberg-Schiavone, L., Johansson, I., Karlberg, T., Kosinska, U., Kotenyova, T., Lehtio, L., Nilsson, M.E., Nyman, T., Persson, C., Sagemark, J., Stenmark, P., Sundstrom, M., Uppenberg, J., Upsten, M., Thorsell, A.G., van den Berg, S., Weigelt, J., Nordlund, P., Structural Genomics Consortium (SGC)

Revision History  

• Version 1.0: 2007-03-06
  Type: Initial release
  
• Version 1.1: 2018-01-17
  Changes: Data collection
• Version 1.2: 2023-12-13
  Changes: Data collection, Database references, Other, Refinement description