4J5U | pdb_00004j5u

X-ray crystal structure of a serine hydroxymethyltransferase with covalently bound PLP from Rickettsia rickettsii str. Sheila Smith

• PDB DOI: https://doi.org/10.2210/pdb4J5U/pdb

• Classification: TRANSFERASE
• Organism(s): Rickettsia rickettsii str. 'Sheila Smith
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2013-02-10 Released: 2013-03-13 
• Deposition Author(s): Seattle Structural Genomics Center for Infectious Disease (SSGCID)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.70 Å
• R-Value Free: 
  0.214 (Depositor), 0.210 (DCC) 
• R-Value Work: 
  0.176 (Depositor), 0.180 (DCC) 
• R-Value Observed: 
  0.178 (Depositor) 

Starting Model: experimental

Literature

X-ray crystal structure of a serine hydroxymethyltransferase with covalently bound PLP from Rickettsia rickettsii str. Sheila Smith

Fairman, J.W., Abendroth, J.A., Edwards, T.E., Lorimer, D.

To be published.

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 92.59 kDa 
• Atom Count: 7,319 
• Modeled Residue Count: 840 
• Deposited Residue Count: 840 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Serine hydroxymethyltransferase	A, B	420	Rickettsia rickettsii str. 'Sheila Smith	Mutation(s): 0  Gene Names: glyA, A1G_06305 EC: 2.1.2.1
UniProt
Find proteins for A8GTI9 (Rickettsia rickettsii (strain Sheila Smith)) Explore A8GTI9  Go to UniProtKB:  A8GTI9

Small Molecules

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
LLP	A, B	L-PEPTIDE LINKING	C14 H22 N3 O7 P		LYS

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.70 Å
• R-Value Free:  0.214 (Depositor), 0.210 (DCC) 
• R-Value Work:  0.176 (Depositor), 0.180 (DCC) 
• R-Value Observed: 0.178 (Depositor) 

Diffraction Data: https://doi.org/10.18430/M34J5U

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 56.27	α = 90
b = 113.28	β = 114.91
c = 65.91	γ = 90

Software Package:

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

Structure Validation

Entry History 

Deposition Data

• Released Date: 2013-03-13 
Deposition Author(s): Seattle Structural Genomics Center for Infectious Disease (SSGCID)

Revision History  

• Version 1.0: 2013-03-13
  Type: Initial release
  
• Version 1.1: 2023-09-20
  Changes: Data collection, Database references, Derived calculations, Refinement description
• Version 1.2: 2023-12-06
  Changes: Data collection