9GVH | pdb_00009gvh

Crystal structure of Chitin Binding Protein from Iberis umbellata L.

• PDB DOI: https://doi.org/10.2210/pdb9GVH/pdb

• Classification: PLANT PROTEIN
• Organism(s): Iberis umbellata
• Mutation(s): No 


• Deposited: 2024-09-24 Released: 2024-12-11 
• Deposition Author(s): Saeed, A., Betzel, C., Brognaro, H., Alves Franca, B., Mehmood, S., Rajaiah Prabhu, P., Ishaq, U., Akrem, A.
• Funding Organization(s): Other government

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.34 Å
• R-Value Free: 
  0.212 (Depositor), 0.212 (DCC) 
• R-Value Work: 
  0.190 (Depositor), 0.189 (DCC) 
• R-Value Observed: 
  0.191 (Depositor) 

Starting Model: experimental

Literature

Crystal structure of Chitin Binding Protein from Iberis umbellata L.

Saeed, A., Betzel, C., Brognaro, H., Alves Franca, B., Mehmood, S., Rajaiah Prabhu, P., Ishaq, U., Akrem, A.

To be published.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - A1B1 

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: SAXS

Macromolecule Content 

• Total Structure Weight: 12.84 kDa 
• Atom Count: 935 
• Modeled Residue Count: 109 
• Deposited Residue Count: 109 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Chitin Binding Protein	A	35	Iberis umbellata	Mutation(s): 0
UniProt
Find proteins for A0ABF7PQC2 (Iberis umbellata) Explore A0ABF7PQC2  Go to UniProtKB:  A0ABF7PQC2

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Chitin Binding Protein	B	74	Iberis umbellata	Mutation(s): 0
UniProt
Find proteins for A0AC62AEI5 (Iberis umbellata) Explore A0AC62AEI5  Go to UniProtKB:  A0AC62AEI5

Small Molecules

Ligands 5 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
SO4 (Subject of Investigation/LOI)	C [auth A], L [auth B], M [auth B]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L
NO3 (Subject of Investigation/LOI)	I [auth A], J [auth A], K [auth A], Q [auth B], R [auth B]	NITRATE ION N O3 NHNBFGGVMKEFGY-UHFFFAOYSA-N
ACT (Subject of Investigation/LOI)	D [auth A], E [auth A], F [auth A], G [auth A], N [auth B]	ACETATE ION C2 H3 O2 QTBSBXVTEAMEQO-UHFFFAOYSA-M
CL (Subject of Investigation/LOI)	S [auth B]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M
NA (Subject of Investigation/LOI)	H [auth A], O [auth B], P [auth B]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.34 Å
• R-Value Free:  0.212 (Depositor), 0.212 (DCC) 
• R-Value Work:  0.190 (Depositor), 0.189 (DCC) 
• R-Value Observed: 0.191 (Depositor) 

Diffraction Data: https://doi.org/10.51093/xrd-00317

Space Group: P 2₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 45.135	α = 90
b = 73.235	β = 90
c = 31.25	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
autoPROC	data processing
pointless	data scaling
PHENIX	phasing
XDS	data reduction

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2024-12-11 
Deposition Author(s): Saeed, A., Betzel, C., Brognaro, H., Alves Franca, B., Mehmood, S., Rajaiah Prabhu, P., Ishaq, U., Akrem, A.

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Funding Organization	Location	Grant Number
Other government	Pakistan	IRSIP 51 BMS 32

Revision History  

• Version 1.0: 2024-12-11
  Type: Initial release
  
• Version 1.1: 2024-12-25
  Changes: Database references
• Version 2.0: 2025-07-16
  Type: Coordinate replacement
  Reason: Sequence discrepancy
  Changes: Atomic model, Author supporting evidence, Data collection, Database references, Derived calculations, Non-polymer description, Other, Polymer sequence, Refinement description, Source and taxonomy, Structure summary