5HM8 | pdb_00005hm8

2.85 Angstrom Crystal Structure of S-adenosylhomocysteinase from Cryptosporidium parvum in Complex with Adenosine and NAD.

• PDB DOI: https://doi.org/10.2210/pdb5HM8/pdb

• Classification: HYDROLASE
• Organism(s): Cryptosporidium parvum Iowa II
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2016-01-15 Released: 2016-01-27 
• Deposition Author(s): Minasov, G., Shuvalova, L., Halavaty, A., Kiryukhina, O., Dubrovska, I., Bishop, B., Kwon, K., Anderson, W.F., Center for Structural Genomics of Infectious Diseases (CSGID)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.85 Å
• R-Value Free: 
  0.200 (Depositor), 0.200 (DCC) 
• R-Value Work: 
  0.173 (Depositor), 0.174 (DCC) 
• R-Value Observed: 
  0.174 (Depositor) 

Starting Model: experimental

Literature

2.85 Angstrom Crystal Structure of S-adenosylhomocysteinase from Cryptosporidium parvum in Complex with Adenosine and NAD.

Minasov, G., Shuvalova, L., Halavaty, A., Kiryukhina, O., Dubrovska, I., Bishop, B., Kwon, K., Anderson, W.F., Center for Structural Genomics of Infectious Diseases (CSGID)

To be published.

Biological Assembly 1  

Global Symmetry: Dihedral - D2  (Explore in 3D)
Global Stoichiometry: Homo 4-mer - A4 

Biological assembly 1 assigned by authors.

Biological Assembly 2  

Global Symmetry: Dihedral - D2  (Explore in 3D)
Global Stoichiometry: Homo 4-mer - A4 

Biological assembly 2 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 458.2 kDa 
• Atom Count: 32,193 
• Modeled Residue Count: 3,932 
• Deposited Residue Count: 3,984 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Adenosylhomocysteinase	A, B, C, D, E, F, G, H	498	Cryptosporidium parvum Iowa II	Mutation(s): 0  Gene Names: cgd3_80 EC: 3.3.1.1 (PDB Primary Data), 3.13.2.1 (UniProt)
UniProt
Find proteins for Q5CPH1 (Cryptosporidium parvum (strain Iowa II)) Explore Q5CPH1  Go to UniProtKB:  Q5CPH1

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
NAD	AA [auth D], GA [auth E], J [auth A], KA [auth F], OA [auth G], P [auth B], UA [auth H], V [auth C]	NICOTINAMIDE-ADENINE-DINUCLEOTIDE C21 H27 N7 O14 P2 BAWFJGJZGIEFAR-NNYOXOHSSA-N
ADN	FA [auth E], I [auth A], JA [auth F], NA [auth G], O [auth B], TA [auth H], U [auth C], Z [auth D]	ADENOSINE C10 H13 N5 O4 OIRDTQYFTABQOQ-KQYNXXCUSA-N
SO4	IA [auth E], N [auth A], SA [auth G], T [auth B], Y [auth C]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L
CL	BA [auth D], CA [auth D], DA [auth D], EA [auth D], HA [auth E], K [auth A], L [auth A], LA [auth F], M [auth A], MA [auth F], PA [auth G], Q [auth B], QA [auth G], R [auth B], RA [auth G], S [auth B], VA [auth H], W [auth C], X [auth C]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.85 Å
• R-Value Free:  0.200 (Depositor), 0.200 (DCC) 
• R-Value Work:  0.173 (Depositor), 0.174 (DCC) 
• R-Value Observed: 0.174 (Depositor) 

Diffraction Data: https://doi.org/10.18430/m35hm8

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 107.837	α = 90
b = 185.31	β = 97.85
c = 122.439	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
HKL-3000	data reduction
HKL-3000	data scaling
BALBES	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2016-01-27 
Deposition Author(s): Minasov, G., Shuvalova, L., Halavaty, A., Kiryukhina, O., Dubrovska, I., Bishop, B., Kwon, K., Anderson, W.F., Center for Structural Genomics of Infectious Diseases (CSGID)

Revision History  

• Version 1.0: 2016-01-27
  Type: Initial release
  
• Version 1.1: 2023-09-27
  Changes: Data collection, Database references, Derived calculations, Refinement description