2YPN

Hydroxymethylbilane synthase

• PDB DOI: https://doi.org/10.2210/pdb2YPN/pdb

• Classification: TRANSFERASE
• Organism(s): Escherichia coli
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 1999-01-11 Released: 1999-02-02 
• Deposition Author(s): Nieh, Y.P., Raftery, J., Weisgerber, S., Habash, J., Schotte, F., Ursby, T., Wulff, M., Haedener, A., Campbell, J.W., Hao, Q., Helliwell, J.R.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.30 Å
• R-Value Free: 0.269 
• R-Value Work: 0.194 

Literature

Accurate and highly complete synchrotron protein crystal Laue diffraction data using the ESRF CCD and the Daresbury Laue software

Nieh, Y.P., Raftery, J., Weisgerber, S., Habash, J., Schotte, F., Ursby, T., Wulff, M., Haedener, A., Campbell, J.W., Hao, Q., Helliwell, J.R.

(1999) J Synchrotron Radiat 6: 995-1006

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 34.31 kDa 
• Atom Count: 2,408 
• Modelled Residue Count: 294 
• Deposited Residue Count: 313 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
PROTEIN (HYDROXYMETHYLBILANE SYNTHASE)	A	313	Escherichia coli	Mutation(s): 0  EC: 2.5.1.61
UniProt
Find proteins for P06983 (Escherichia coli (strain K12)) Explore P06983  Go to UniProtKB:  P06983

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
DPM	B [auth A]	3-[5-{[3-(2-carboxyethyl)-4-(carboxymethyl)-5-methyl-1H-pyrrol-2-yl]methyl}-4-(carboxymethyl)-1H-pyrrol-3-yl]propanoic acid C20 H24 N2 O8 LCAXMKQKEYTFDM-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.30 Å
• R-Value Free: 0.269 
• R-Value Work: 0.194 
• Space Group: P 2₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 88.06	α = 90
b = 75.73	β = 90
c = 50.35	γ = 90

Software Package:

Software Name	Purpose
DARESBURY	data collection
LAUENORM/AGROVATA	data reduction
X-PLOR	model building
O	model building
X-PLOR	refinement
DARESBURY	data reduction
LAUENORM	data scaling
CCP4	data scaling
X-PLOR	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 1999-02-02 
Deposition Author(s): Nieh, Y.P., Raftery, J., Weisgerber, S., Habash, J., Schotte, F., Ursby, T., Wulff, M., Haedener, A., Campbell, J.W., Hao, Q., Helliwell, J.R.

Revision History  

• Version 1.0: 1999-02-02
  Type: Initial release
  
• Version 1.1: 2008-04-26
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance
• Version 1.3: 2013-09-18
  Changes: Non-polymer description
• Version 1.4: 2017-10-04
  Changes: Refinement description
• Version 1.5: 2023-08-30
  Changes: Data collection, Database references, Derived calculations, Refinement description