1VKH | pdb_00001vkh

CRYSTAL STRUCTURE OF A PUTATIVE SERINE HYDROLASE (YDR428C) FROM SACCHAROMYCES CEREVISIAE AT 1.85 A RESOLUTION

• PDB DOI: https://doi.org/10.2210/pdb1VKH/pdb

• Classification: HYDROLASE
• Organism(s): Saccharomyces cerevisiae
• Expression System: Escherichia coli
• Mutation(s): Yes 


• Deposited: 2004-05-20 Released: 2004-06-08 
• Deposition Author(s): Joint Center for Structural Genomics (JCSG)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.85 Å
• R-Value Free: 
  0.189 (Depositor), 0.152 (DCC) 
• R-Value Work: 
  0.143 (Depositor), 0.154 (DCC) 
• R-Value Observed: 
  0.145 (Depositor) 

Literature

Crystal structure of an alpha/beta serine hydrolase (YDR428C) from Saccharomyces cerevisiae at 1.85 A resolution

Arndt, J.W., Schwarzenbacher, R., Page, R., Abdubek, P., Ambing, E., Biorac, T., Canaves, J.M., Chiu, H.J., Dai, X., Deacon, A.M., DiDonato, M., Elsliger, M.A., Godzik, A., Grittini, C., Grzechnik, S.K., Hale, J., Hampton, E., Han, G.W., Haugen, J., Hornsby, M., Klock, H.E., Koesema, E., Kreusch, A., Kuhn, P., Jaroszewski, L., Lesley, S.A., Levin, I., McMullan, D., McPhillips, T.M., Miller, M.D., Morse, A., Moy, K., Nigoghossian, E., Ouyang, J., Peti, W.S., Quijano, K., Reyes, R., Sims, E., Spraggon, G., Stevens, R.C., van den Bedem, H., Velasquez, J., Vincent, J., von Delft, F., Wang, X., West, B., White, A., Wolf, G., Xu, Q., Zagnitko, O., Hodgson, K.O., Wooley, J., Wilson, I.A.

(2005) Proteins 58: 755-758

• PubMed: 15624212 
• DOI: https://doi.org/10.1002/prot.20336
• Primary Citation Related Structures: 
  1VKH

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Organizational Affiliation: 
• The Scripps Research Institute, La Jolla, California 92037, USA.

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 PISA (software)

Biological Assembly 2  

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

Biological assembly 2 generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 63.96 kDa 
• Atom Count: 4,659 
• Modeled Residue Count: 513 
• Deposited Residue Count: 546 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
putative serine hydrolase	A, B	273	Saccharomyces cerevisiae	Mutation(s): 8  Gene Names: ydr428c EC: 3.5.1.9
UniProt
Find proteins for Q04066 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore Q04066  Go to UniProtKB:  Q04066

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
GOL	C [auth A], D [auth A]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N
CL	E [auth B]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
MSE	A, B	L-PEPTIDE LINKING	C5 H11 N O2 Se		MET

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.85 Å
• R-Value Free:  0.189 (Depositor), 0.152 (DCC) 
• R-Value Work:  0.143 (Depositor), 0.154 (DCC) 
• R-Value Observed: 0.145 (Depositor) 

Diffraction Data: https://doi.org/10.18430/M31VKH

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 41.967	α = 90
b = 85.959	β = 97.71
c = 70.479	γ = 90

Software Package:

Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
SOLVE	phasing
RESOLVE	model building
REFMAC	refinement
RESOLVE	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2004-06-08 
Deposition Author(s): Joint Center for Structural Genomics (JCSG)

Revision History  

• Version 1.0: 2004-06-08
  Type: Initial release
  
• Version 1.1: 2008-04-26
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Advisory, Version format compliance
• Version 1.3: 2023-01-25
  Changes: Database references, Derived calculations
• Version 1.4: 2024-10-09
  Changes: Data collection, Structure summary