9KKV | pdb_00009kkv

Structure-guided interface engineering for modifying substrate binding and catalytic activity of 2-keto-3-deoxy-D-xylonate dehydratase

• PDB DOI: https://doi.org/10.2210/pdb9KKV/pdb

• Classification: CARBOHYDRATE
• Organism(s): Caulobacter vibrioides NA1000
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2024-11-14 Released: 2025-11-19 
• Deposition Author(s): Liang, B.
• Funding Organization(s): National Science Foundation (NSF, China)

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.77 Å
• R-Value Free: 
  0.202 (Depositor), 0.202 (DCC) 
• R-Value Work: 
  0.174 (Depositor), 0.176 (DCC) 
• R-Value Observed: 
  0.175 (Depositor) 

Starting Model: in silico

Literature

Structural directed engineering of 2-keto-3-deoxy-D-xylonate dehydratase for improving catalytic activity

Liang, B.

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 PISA (software)

Biological Assembly Evidence: gel filtration

Macromolecule Content 

• Total Structure Weight: 82.78 kDa 
• Atom Count: 6,730 
• Modeled Residue Count: 761 
• Deposited Residue Count: 766 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Fumarylacetoacetate hydrolase family protein	A [auth B], B [auth A]	383	Caulobacter vibrioides NA1000	Mutation(s): 0  Gene Names: xylX, CCNA_00866 EC: 5.3.3
UniProt
Find proteins for A0A0H3C4T2 (Caulobacter vibrioides (strain NA1000 / CB15N)) Explore A0A0H3C4T2  Go to UniProtKB:  A0A0H3C4T2

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
2HP (Subject of Investigation/LOI)	C [auth B], E [auth A], G [auth A], H [auth A]	DIHYDROGENPHOSPHATE ION H2 O4 P NBIIXXVUZAFLBC-UHFFFAOYSA-M
NH4 (Subject of Investigation/LOI)	D [auth B], F [auth A], I [auth A]	AMMONIUM ION H4 N QGZKDVFQNNGYKY-UHFFFAOYSA-O

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.77 Å
• R-Value Free:  0.202 (Depositor), 0.202 (DCC) 
• R-Value Work:  0.174 (Depositor), 0.176 (DCC) 
• R-Value Observed: 0.175 (Depositor) 

Space Group: P 4₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 101.808	α = 90
b = 101.808	β = 90
c = 211.239	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
PDB_EXTRACT	data extraction
HKL-3000	data scaling
PHASER	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2025-11-19 
Deposition Author(s): Liang, B.

---

Funding Organization	Location	Grant Number
National Science Foundation (NSF, China)	China	--

Revision History  

• Version 1.0: 2025-11-19
  Type: Initial release