3LZZ

Crystal structures of Cupin superfamily BbDUF985 from Branchiostoma belcheri tsingtauense in apo and GDP-bound forms

• PDB DOI: https://doi.org/10.2210/pdb3LZZ/pdb

• Classification: UNKNOWN FUNCTION
• Organism(s): Branchiostoma belcheri tsingtauense
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2010-03-02 Released: 2010-06-02 
• Deposition Author(s): Du, Y., He, Y.-X., Saren, G., Zhang, X., Zhang, S.-C., Chen, Y., Zhou, C.-Z.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.50 Å
• R-Value Free: 0.241 
• R-Value Work: 0.198 
• R-Value Observed: 0.201 

Starting Model: experimental

Literature

Crystal structures of the apo and GDP-bound forms of a cupin-like protein BbDUF985 from Branchiostoma belcheri tsingtauense

Zou, C.Z., Du, Y., He, Y.-X., Saren, G., Zhang, X., Chen, Y., Zhang, S.-C.

(2010) Proteins 

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)

Macromolecule Content

• Total Structure Weight: 40.12 kDa 
• Atom Count: 2,820 
• Modelled Residue Count: 322 
• Deposited Residue Count: 344 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Putative uncharacterized protein	A, B	172	Branchiostoma belcheri tsingtauense	Mutation(s): 0
UniProt
Find proteins for Q6WRH7 (Branchiostoma belcheri tsingtauense) Explore Q6WRH7  Go to UniProtKB:  Q6WRH7

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
GDP	C [auth A], E [auth B]	GUANOSINE-5'-DIPHOSPHATE C10 H15 N5 O11 P2 QGWNDRXFNXRZMB-UUOKFMHZSA-N
ACT	D [auth A], F [auth B]	ACETATE ION C2 H3 O2 QTBSBXVTEAMEQO-UHFFFAOYSA-M

Binding Affinity Annotations
ID	Source	Binding Affinity
GDP	PDBBind:  3LZZ	Kd: 1.46e+5 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.50 Å
• R-Value Free: 0.241 
• R-Value Work: 0.198 
• R-Value Observed: 0.201 
• Space Group: I 4₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 88.86	α = 90
b = 88.86	β = 90
c = 168.17	γ = 90

Software Package:

Software Name	Purpose
MAR345dtb	data collection
MOLREP	phasing
REFMAC	refinement
MOSFLM	data reduction
SCALA	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2010-06-02 
Deposition Author(s): Du, Y., He, Y.-X., Saren, G., Zhang, X., Zhang, S.-C., Chen, Y., Zhou, C.-Z.

Revision History  

• Version 1.0: 2010-06-02
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Version format compliance
• Version 1.2: 2023-11-01
  Changes: Data collection, Database references, Derived calculations, Refinement description