2V30 | pdb_00002v30

Human orotidine 5'-phosphate decarboxylase domain of uridine monophospate synthetase (UMPS) in complex with its product UMP.

• PDB DOI: https://doi.org/10.2210/pdb2V30/pdb

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


• Deposited: 2007-06-10 Released: 2007-07-24 
• Deposition Author(s): Moche, M., Ogg, D., Arrowsmith, C., Berglund, H., Busam, R., Collins, R., Dahlgren, L.G., Edwards, A., Flodin, S., Flores, A., Graslund, S., Hammarstrom, M., Hallberg, B.M., Holmberg-Schiavone, L., Johansson, I., Kallas, A., Karlberg, T., Kotenyova, T., Lehtio, L., Nyman, T., Persson, C., Sagemark, J., Stenmark, P., Sundstrom, M., Thorsell, A.G., van den Berg, S., Weigelt, J., Welin, M., Nordlund, P., Structural Genomics Consortium (SGC)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free: 
  0.188 (Depositor), 0.195 (DCC) 
• R-Value Work: 
  0.153 (Depositor), 0.160 (DCC) 
• R-Value Observed: 
  0.155 (Depositor) 

Starting Model: experimental

Literature

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

Moche, M., Ogg, D., Arrowsmith, C., Berglund, H., Busam, R., Collins, R., Dahlgren, L.G., Edwards, A., Flodin, S., Flores, A., Graslund, S., Hammarstrom, M., Hallberg, B.M., Holmberg-Schiavone, L., Johansson, I., Kallas, A., Karlberg, T., Kotenyova, T., Lehtio, L., Nyman, T., Persson, C., Sagemark, J., Stenmark, P., Sundstrom, M., Thorsell, A.G., van den Berg, S., Weigelt, J., Welin, M., 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: 61.91 kDa 
• Atom Count: 4,824 
• Modeled Residue Count: 518 
• Deposited Residue Count: 558 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
OROTIDINE 5'-PHOSPHATE DECARBOXYLASE	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

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
U5P	C [auth A], D [auth B]	URIDINE-5'-MONOPHOSPHATE C9 H13 N2 O9 P DJJCXFVJDGTHFX-XVFCMESISA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free:  0.188 (Depositor), 0.195 (DCC) 
• R-Value Work:  0.153 (Depositor), 0.160 (DCC) 
• R-Value Observed: 0.155 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 60.103	α = 90
b = 77.853	β = 90
c = 153.209	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
MOSFLM	data reduction
SCALA	data scaling
MOLREP	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2007-07-24 
Deposition Author(s): Moche, M., Ogg, D., Arrowsmith, C., Berglund, H., Busam, R., Collins, R., Dahlgren, L.G., Edwards, A., Flodin, S., Flores, A., Graslund, S., Hammarstrom, M., Hallberg, B.M., Holmberg-Schiavone, L., Johansson, I., Kallas, A., Karlberg, T., Kotenyova, T., Lehtio, L., Nyman, T., Persson, C., Sagemark, J., Stenmark, P., Sundstrom, M., Thorsell, A.G., van den Berg, S., Weigelt, J., Welin, M., Nordlund, P., Structural Genomics Consortium (SGC)

Revision History  

• Version 1.0: 2007-07-24
  Type: Initial release
  
• Version 1.1: 2017-12-13
  Changes: Database references, Structure summary
• Version 1.2: 2023-12-13
  Changes: Data collection, Database references, Other, Refinement description