4IHA | pdb_00004iha

Crystal structure of rice DWARF14 (D14) in complex with a GR24 hydrolysis intermediate

• PDB DOI: https://doi.org/10.2210/pdb4IHA/pdb

• Classification: HYDROLASE
• Organism(s): Oryza sativa Japonica Group
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2012-12-18 Released: 2013-01-23 
• Deposition Author(s): Zhou, X.E., Zhao, L.-H., Wu, Z.-S., Yi, W., Li, S., Li, Y., Xu, Y., Xu, T.-H., Liu, Y., Chen, R.-Z., Kovach, A., Kang, Y., Hou, L., He, Y., Zhang, C., Melcher, K., Xu, H.E.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.55 Å
• R-Value Free: 
  0.201 (Depositor), 0.209 (DCC) 
• R-Value Work: 
  0.181 (Depositor), 0.189 (DCC) 
• R-Value Observed: 
  0.183 (Depositor) 

Starting Model: experimental

Literature

Crystal structures of two phytohormone signal-transducing alpha / beta hydrolases: karrikin-signaling KAI2 and strigolactone-signaling DWARF14.

Zhao, L.H., Zhou, X.E., Wu, Z.S., Yi, W., Xu, Y., Li, S., Xu, T.H., Liu, Y., Chen, R.Z., Kovach, A., Kang, Y., Hou, L., He, Y., Xie, C., Song, W., Zhong, D., Xu, Y., Wang, Y., Li, J., Zhang, C., Melcher, K., Xu, H.E.

(2013) Cell Res 23: 436-439

• PubMed: 23381136 
• DOI: https://doi.org/10.1038/cr.2013.19
• Primary Citation Related Structures: 
  4IH1, 4IH4, 4IH9, 4IHA

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)

Macromolecule Content 

• Total Structure Weight: 58.97 kDa 
• Atom Count: 4,578 
• Modeled Residue Count: 536 
• Deposited Residue Count: 536 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Dwarf 88 esterase	A, B	268	Oryza sativa Japonica Group	Mutation(s): 0  Gene Names: D14, D88, LOC_Os03g10620, Os03g0203200 EC: 3.1
UniProt
Find proteins for Q10QA5 (Oryza sativa subsp. japonica) Explore Q10QA5  Go to UniProtKB:  Q10QA5

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
OPL	C [auth A], D [auth B]	(2R,3R)-2,4,4-trihydroxy-3-methylbutanal C5 H10 O4 NTSABUYTFOFFJR-DMTCNVIQSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.55 Å
• R-Value Free:  0.201 (Depositor), 0.209 (DCC) 
• R-Value Work:  0.181 (Depositor), 0.189 (DCC) 
• R-Value Observed: 0.183 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 48.188	α = 90
b = 88.729	β = 90
c = 118.315	γ = 90

Software Package:

Software Name	Purpose
SCALEPACK	data scaling
REFMAC	refinement
PDB_EXTRACT	data extraction
HKL-2000	data reduction

Structure Validation

Entry History 

Deposition Data

• Released Date: 2013-01-23 
Deposition Author(s): Zhou, X.E., Zhao, L.-H., Wu, Z.-S., Yi, W., Li, S., Li, Y., Xu, Y., Xu, T.-H., Liu, Y., Chen, R.-Z., Kovach, A., Kang, Y., Hou, L., He, Y., Zhang, C., Melcher, K., Xu, H.E.

Revision History  

• Version 1.0: 2013-01-23
  Type: Initial release
  
• Version 1.1: 2013-10-23
  Changes: Database references
• Version 1.2: 2023-09-20
  Changes: Data collection, Database references, Derived calculations, Refinement description
• Version 1.3: 2024-10-30
  Changes: Structure summary