4QUP | pdb_00004qup

Crystal structure of stachydrine demethylase with N-methyl proline from low X-ray dose composite datasets

• PDB DOI: https://doi.org/10.2210/pdb4QUP/pdb

• Classification: OXIDOREDUCTASE
• Organism(s): Sinorhizobium meliloti 1021
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2014-07-11 Released: 2015-07-15 
• Deposition Author(s): Agarwal, R., Andi, B., Gizzi, A., Bonanno, J.B., Almo, S.C., Orville, A.M.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.70 Å
• R-Value Free: 
  0.217 (Depositor), 0.220 (DCC) 
• R-Value Work: 
  0.182 (Depositor), 0.190 (DCC) 
• R-Value Observed: 
  0.184 (Depositor) 

Starting Model: experimental

Literature

Tracking photoelectron induced in-crystallo enzyme catalysis

Agarwal, R., Andi, B., Gizzi, A., Bonanno, J.B., Almo, S.C., Orville, A.M.

To be published.

Biological Assembly 1  

Global Symmetry: Cyclic - C3  (Explore in 3D)
Global Stoichiometry: Homo 3-mer - A3 

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

Macromolecule Content 

• Total Structure Weight: 49.85 kDa 
• Atom Count: 3,560 
• Modeled Residue Count: 414 
• Deposited Residue Count: 435 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Monoxygenase; demethylase	A	435	Sinorhizobium meliloti 1021	Mutation(s): 0  Gene Names: SMa0751 EC: 1 (PDB Primary Data), 1.14.13.247 (UniProt)
UniProt
Find proteins for Q92ZP9 (Rhizobium meliloti (strain 1021)) Explore Q92ZP9  Go to UniProtKB:  Q92ZP9

Small Molecules

Ligands 6 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
FES	B [auth A]	FE2/S2 (INORGANIC) CLUSTER Fe2 S2 NIXDOXVAJZFRNF-UHFFFAOYSA-N
NCO	G [auth A]	COBALT HEXAMMINE(III) Co H18 N6 DYLMFCCYOUSRTK-UHFFFAOYSA-N
3BY	D [auth A]	1-methyl-L-proline C6 H11 N O2 CWLQUGTUXBXTLF-YFKPBYRVSA-N
TRS	E [auth A]	2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL C4 H12 N O3 LENZDBCJOHFCAS-UHFFFAOYSA-O
GOL	F [auth A]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N
FE	C [auth A]	FE (III) ION Fe VTLYFUHAOXGGBS-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.70 Å
• R-Value Free:  0.217 (Depositor), 0.220 (DCC) 
• R-Value Work:  0.182 (Depositor), 0.190 (DCC) 
• R-Value Observed: 0.184 (Depositor) 

Space Group: P 6₃ 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 97.746	α = 90
b = 97.746	β = 90
c = 177.984	γ = 120

Software Package:

Software Name	Purpose
CBASS	data collection
MOLREP	phasing
REFMAC	refinement
HKL-2000	data reduction
HKL-2000	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2015-07-15 
Deposition Author(s): Agarwal, R., Andi, B., Gizzi, A., Bonanno, J.B., Almo, S.C., Orville, A.M.

Revision History  

• Version 1.0: 2015-07-15
  Type: Initial release
  
• Version 1.1: 2015-10-14
  Changes: Non-polymer description
• Version 1.2: 2016-03-09
  Changes: Structure summary
• Version 1.3: 2023-09-20
  Changes: Data collection, Database references, Derived calculations, Refinement description