5UNC | pdb_00005unc

The crystal structure of PHOSPHOENOLPYRUVATE PHOSPHOMUTASE from Streptomyces platensis subsp. rosaceus

• PDB DOI: https://doi.org/10.2210/pdb5UNC/pdb

• Classification: ISOMERASE
• Organism(s): Streptomyces platensis
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2017-01-30 Released: 2017-02-22 
• Deposition Author(s): Tan, K., Hatzos-Skintges, C., Endres, M., Phillips Jr., G.N., Joachimiak, A., Midwest Center for Structural Genomics (MCSG), Enzyme Discovery for Natural Product Biosynthesis (NatPro)
• Funding Organization(s): National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.71 Å
• R-Value Free: 
  0.177 (Depositor), 0.179 (DCC) 
• R-Value Work: 
  0.155 (Depositor), 0.158 (DCC) 
• R-Value Observed: 
  0.156 (Depositor) 

Literature

The crystal structure of PHOSPHOENOLPYRUVATE PHOSPHOMUTASE from Streptomyces platensis subsp. rosaceus

Tan, K., Hatzos-Skintges, C., Endres, M., Phillips Jr., G.N., Joachimiak, A.

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 and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 145.96 kDa 
• Atom Count: 9,992 
• Modeled Residue Count: 1,151 
• Deposited Residue Count: 1,348 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
PHOSPHOENOLPYRUVATE PHOSPHOMUTASE	A, B, C, D	337	Streptomyces platensis	Mutation(s): 0
UniProt
Find proteins for A0A0A0V023 (Streptomyces platensis) Explore A0A0A0V023  Go to UniProtKB:  A0A0A0V023

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
XYS	F [auth A], G [auth A], M [auth C], O [auth D]	alpha-D-xylopyranose C5 H10 O5 SRBFZHDQGSBBOR-LECHCGJUSA-N
TLA	E [auth A], H [auth B], J [auth C], K [auth C], N [auth D]	L(+)-TARTARIC ACID C4 H6 O6 FEWJPZIEWOKRBE-JCYAYHJZSA-N
FMT	I [auth B], L [auth C]	FORMIC ACID C H2 O2 BDAGIHXWWSANSR-UHFFFAOYSA-N

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

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.71 Å
• R-Value Free:  0.177 (Depositor), 0.179 (DCC) 
• R-Value Work:  0.155 (Depositor), 0.158 (DCC) 
• R-Value Observed: 0.156 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 89.326	α = 90
b = 122.036	β = 90
c = 136.681	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
HKL-3000	data reduction
HKL-3000	data scaling
HKL-3000	phasing

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2017-02-22 
Deposition Author(s): Tan, K., Hatzos-Skintges, C., Endres, M., Phillips Jr., G.N., Joachimiak, A., Midwest Center for Structural Genomics (MCSG), Enzyme Discovery for Natural Product Biosynthesis (NatPro)

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Funding Organization	Location	Grant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	United States	GM115586

Revision History  

• Version 1.0: 2017-02-22
  Type: Initial release
  
• Version 1.1: 2017-09-20
  Changes: Author supporting evidence
• Version 1.2: 2020-01-01
  Changes: Author supporting evidence, Data collection
• Version 1.3: 2020-07-29
  Type: Remediation
  Reason: Carbohydrate remediation
  Changes: Data collection, Derived calculations, Structure summary
• Version 1.4: 2024-10-23
  Changes: Data collection, Database references, Structure summary