3RCY | pdb_00003rcy

CRYSTAL STRUCTURE OF Mandelate racemase/muconate lactonizing enzyme-like protein from Roseovarius sp. TM1035

• PDB DOI: https://doi.org/10.2210/pdb3RCY/pdb

• Classification: ISOMERASE
• Organism(s): Roseovarius sp. TM1035
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2011-03-31 Released: 2011-05-18 
• Deposition Author(s): Malashkevich, V.N., Toro, R., Seidel, R., Garrett, S., Foti, R., Almo, S.C., New York Structural Genomics Research Consortium (NYSGRC)

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.99 Å
• R-Value Free: 
  0.181 (Depositor), 0.190 (DCC) 
• R-Value Work: 
  0.147 (Depositor), 0.150 (DCC) 
• R-Value Observed: 
  0.149 (Depositor) 

Starting Model: experimental

Literature

CRYSTAL STRUCTURE OF Mandelate racemase/muconate lactonizing enzyme-like protein from Roseovarius sp. TM1035

Malashkevich, V.N., Toro, R., Seidel, R., Garrett, S., Foti, R., Almo, S.C.

To be published.

Biological Assembly 1  

Global Symmetry: Dihedral - D4  (Explore in 3D)
Global Stoichiometry: Homo 8-mer - A8 

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

Macromolecule Content 

• Total Structure Weight: 380.56 kDa 
• Atom Count: 26,806 
• Modeled Residue Count: 3,166 
• Deposited Residue Count: 3,464 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Mandelate racemase/muconate lactonizing enzyme-like protein	A, B, C, D, E, F, G, H	433	Roseovarius sp. TM1035	Mutation(s): 0  Gene Names: 149202287, RTM1035_13208

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
RIB	CA [auth E], L [auth A], LA [auth G], M [auth A], NA [auth H], P [auth B], PA [auth H], Z [auth D]	alpha-D-ribofuranose C5 H10 O5 HMFHBZSHGGEWLO-AIHAYLRMSA-N
GOL	AA [auth E], DA [auth E], FA [auth F], GA [auth G], HA [auth G], J [auth A], JA [auth G], K [auth A], KA [auth G], MA [auth H], O [auth B], Q [auth B], R [auth B], T [auth C], U [auth C], W [auth D], X [auth D], Y [auth D]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N
MG	BA [auth E], EA [auth F], I [auth A], IA [auth G], N [auth B], OA [auth H], S [auth C], V [auth D]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.99 Å
• R-Value Free:  0.181 (Depositor), 0.190 (DCC) 
• R-Value Work:  0.147 (Depositor), 0.150 (DCC) 
• R-Value Observed: 0.149 (Depositor) 

Space Group: P 2₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 144.978	α = 90
b = 162.143	β = 90
c = 141.954	γ = 90

Software Package:

Software Name	Purpose
SCALEPACK	data scaling
PHASER	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction
CBASS	data collection
HKL-3000	data reduction

Structure Validation

Entry History 

Deposition Data

• Released Date: 2011-05-18 
Deposition Author(s): Malashkevich, V.N., Toro, R., Seidel, R., Garrett, S., Foti, R., Almo, S.C., New York Structural Genomics Research Consortium (NYSGRC)

Revision History  

• Version 1.0: 2011-05-18
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Version format compliance
• Version 2.0: 2020-07-29
  Type: Remediation
  Reason: Carbohydrate remediation
  Changes: Advisory, Atomic model, Data collection, Database references, Derived calculations, Structure summary
• Version 2.1: 2023-09-13
  Changes: Data collection, Database references, Refinement description, Structure summary