2P0I | pdb_00002p0i

Crystal structure of L-rhamnonate dehydratase from Gibberella zeae

• PDB DOI: https://doi.org/10.2210/pdb2P0I/pdb

• Classification: LYASE
• Organism(s): Fusarium graminearum
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): Yes 


• Deposited: 2007-02-28 Released: 2007-03-13 
• Deposition Author(s): Patskovsky, Y., Toro, R., Sauder, J.M., Dickey, M., Logan, C., Gheyi, T., Wasserman, S.R., Smith, D., Gerlt, J., Burley, S.K., Almo, S.C., New York SGX Research Center for Structural Genomics (NYSGXRC)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.10 Å
• R-Value Free: 
  0.256 (Depositor), 0.254 (DCC) 
• R-Value Work: 
  0.190 (Depositor), 0.192 (DCC) 
• R-Value Observed: 
  0.192 (Depositor) 

Literature

Crystal Structure of L-Rhamnonate Dehydratase from Gibberella Zeae

Patskovsky, Y., Toro, R., Sauder, J.M., Dickey, M., Logan, C., Gheyi, T., Wasserman, S.R., Smith, D., Gerlt, J., Burley, S.K., Almo, S.C.

To be published.

Biological Assembly 1  

Global Symmetry: Dihedral - D4  (Explore in 3D)
Global Stoichiometry: Homo 8-mer - A8 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 409.1 kDa 
• Atom Count: 26,261 
• Modeled Residue Count: 3,142 
• Deposited Residue Count: 3,648 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
L-rhamnonate dehydratase	A, B, C, D, E, F, G, H	456	Fusarium graminearum	Mutation(s): 6  Gene Names: FG09883.1 EC: 4.2.1.90
UniProt
Find proteins for D0VX14 (Gibberella zeae (strain ATCC MYA-4620 / CBS 123657 / FGSC 9075 / NRRL 31084 / PH-1)) Explore D0VX14  Go to UniProtKB:  D0VX14

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
SO4	AA [auth F], I [auth A], KA [auth H], LA [auth H], N [auth B], O [auth B], Q [auth C], R [auth D], S [auth D], V [auth E], W [auth E], X [auth E]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L
GOL	BA [auth F], CA [auth F], DA [auth F], EA [auth F], FA [auth G], GA [auth G], HA [auth G], IA [auth G], J [auth A], JA [auth G], K [auth A], L [auth A], M [auth A], MA [auth H], NA [auth H], P [auth B], T [auth D], U [auth D], Y [auth E], Z [auth E]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N

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

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.10 Å
• R-Value Free:  0.256 (Depositor), 0.254 (DCC) 
• R-Value Work:  0.190 (Depositor), 0.192 (DCC) 
• R-Value Observed: 0.192 (Depositor) 

Space Group: P 2₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 201.404	α = 90
b = 201.135	β = 90
c = 82.402	γ = 90

Software Package:

Software Name	Purpose
SHELX	model building
REFMAC	refinement
MAR345	data collection
HKL-2000	data reduction
HKL-2000	data scaling
SHELX	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2007-03-13 
Deposition Author(s): Patskovsky, Y., Toro, R., Sauder, J.M., Dickey, M., Logan, C., Gheyi, T., Wasserman, S.R., Smith, D., Gerlt, J., Burley, S.K., Almo, S.C., New York SGX Research Center for Structural Genomics (NYSGXRC)

Revision History  

• Version 1.0: 2007-03-13
  Type: Initial release
  
• Version 1.1: 2008-05-01
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Non-polymer description, Version format compliance
• Version 1.3: 2017-10-18
  Changes: Refinement description
• Version 1.4: 2018-11-14
  Changes: Data collection, Structure summary
• Version 1.5: 2021-02-03
  Changes: Database references, Derived calculations, Structure summary
• Version 1.6: 2024-10-30
  Changes: Data collection, Database references, Refinement description, Structure summary