5IHP | pdb_00005ihp

Crystal Structure of Cobyrinic Acid a,c-diamide synthase from Mycobacterium smegmatis with bound ADP and Magnesium

• PDB DOI: https://doi.org/10.2210/pdb5IHP/pdb

• Classification: LIGASE
• Organism(s): Mycolicibacterium smegmatis MC2 155
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2016-02-29 Released: 2016-03-30 
• Deposition Author(s): Seattle Structural Genomics Center for Infectious Disease (SSGCID)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.85 Å
• R-Value Free: 
  0.203 (Depositor), 0.200 (DCC) 
• R-Value Work: 
  0.172 (Depositor), 0.170 (DCC) 

Starting Model: experimental

Literature

Crystal Structure of Cobyrinic Acid a,c-diamide synthase from Mycobacterium smegmatis with bound ATP analog and Magnesium

Davies, D.R., Horanyi, P.S., Abendroth, J.A., SSGCID

To be published.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

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

Biological Assembly 2  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 2 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 59.72 kDa 
• Atom Count: 3,960 
• Modeled Residue Count: 491 
• Deposited Residue Count: 546 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Cobyrinic Acid a,c-diamide synthase	A, B	273	Mycolicibacterium smegmatis MC2 155	Mutation(s): 0  Gene Names: MSMEG_1927
UniProt
Find proteins for A0QTQ5 (Mycolicibacterium smegmatis (strain ATCC 700084 / mc(2)155)) Explore A0QTQ5  Go to UniProtKB:  A0QTQ5

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
ADP	C [auth A], E [auth B]	ADENOSINE-5'-DIPHOSPHATE C10 H15 N5 O10 P2 XTWYTFMLZFPYCI-KQYNXXCUSA-N
MG	D [auth A], F [auth B]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.85 Å
• R-Value Free:  0.203 (Depositor), 0.200 (DCC) 
• R-Value Work:  0.172 (Depositor), 0.170 (DCC) 

Diffraction Data: https://doi.org/10.18430/M35IHP

Space Group: P 4₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 88.75	α = 90
b = 88.75	β = 90
c = 120.31	γ = 90

Software Package:

Software Name	Purpose
XDS	data reduction
XSCALE	data scaling
PHENIX	refinement
PHASER	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2016-03-30 
Deposition Author(s): Seattle Structural Genomics Center for Infectious Disease (SSGCID)

Revision History  

• Version 1.0: 2016-03-30
  Type: Initial release
  
• Version 1.1: 2016-06-15
  Changes: Database references, Structure summary
• Version 1.2: 2016-07-06
  Changes: Structure summary
• Version 1.3: 2023-09-27
  Changes: Data collection, Database references, Derived calculations, Refinement description