3VER | pdb_00003ver

Crystal structure of the O-carbamoyltransferase TobZ in complex with carbamoyl adenylate intermediate

• PDB DOI: https://doi.org/10.2210/pdb3VER/pdb

• Classification: TRANSFERASE
• Organism(s): Streptoalloteichus tenebrarius
• Expression System: Streptomyces lividans TK24
• Mutation(s): No 


• Deposited: 2012-01-09 Released: 2012-01-25 
• Deposition Author(s): Parthier, C., Stubbs, M.T., Goerlich, S., Jaenecke, F.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.34 Å
• R-Value Free: 
  0.224 (Depositor), 0.223 (DCC) 
• R-Value Work: 
  0.169 (Depositor), 0.168 (DCC) 
• R-Value Observed: 
  0.172 (Depositor) 

Starting Model: experimental

Literature

The O-Carbamoyltransferase TobZ Catalyzes an Ancient Enzymatic Reaction.

Parthier, C., Gorlich, S., Jaenecke, F., Breithaupt, C., Brauer, U., Fandrich, U., Clausnitzer, D., Wehmeier, U.F., Bottcher, C., Scheel, D., Stubbs, M.T.

(2012) Angew Chem Int Ed Engl 51: 4046-4052

• PubMed: 22383337 
• DOI: https://doi.org/10.1002/anie.201108896
• Primary Citation Related Structures: 
  3VEN, 3VEO, 3VER, 3VES, 3VET, 3VEW, 3VEX, 3VEZ, 3VF2, 3VF4, 4E1B

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Organizational Affiliation: 
• Institut für Biochemie und Biotechnologie, Martin-Luther-Universität Halle-Wittenberg, Kurt-Mothes-Strasse 3, 06120 Halle (Saale), Germany.

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 64.31 kDa 
• Atom Count: 4,745 
• Modeled Residue Count: 566 
• Deposited Residue Count: 576 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
O-carbamoyltransferase TobZ	A	576	Streptoalloteichus tenebrarius	Mutation(s): 0  Gene Names: tacA, tobZ EC: 2.1.3 (PDB Primary Data), 6.1.2.2 (UniProt)
UniProt
Find proteins for Q70IY1 (Streptoalloteichus tenebrarius (strain ATCC 17920 / DSM 40477 / JCM 4838 / CBS 697.72 / NBRC 16177 / NCIMB 11028 / NRRL B-12390 / A12253. 1 / ISP 5477)) Explore Q70IY1  Go to UniProtKB:  Q70IY1

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
CA0	D [auth A], E [auth A]	5'-O-[(S)-(carbamoyloxy)(hydroxy)phosphoryl]adenosine C11 H15 N6 O8 P CHSNPOFVFYPELH-KQYNXXCUSA-N
FE2	B [auth A]	FE (II) ION Fe CWYNVVGOOAEACU-UHFFFAOYSA-N
NA	C [auth A]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.34 Å
• R-Value Free:  0.224 (Depositor), 0.223 (DCC) 
• R-Value Work:  0.169 (Depositor), 0.168 (DCC) 
• R-Value Observed: 0.172 (Depositor) 

Space Group: P 6₁ 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 99.262	α = 90
b = 99.262	β = 90
c = 281.323	γ = 120

Software Package:

Software Name	Purpose
XSCALE	data scaling
PHENIX	refinement
PDB_EXTRACT	data extraction
MAR345	data collection
XDS	data reduction
PHASER	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2012-01-25 
Deposition Author(s): Parthier, C., Stubbs, M.T., Goerlich, S., Jaenecke, F.

Revision History  

• Version 1.0: 2012-01-25
  Type: Initial release
  
• Version 1.1: 2012-03-14
  Changes: Database references
• Version 1.2: 2012-05-02
  Changes: Database references
• Version 1.3: 2017-11-15
  Changes: Refinement description
• Version 1.4: 2023-09-13
  Changes: Data collection, Database references, Derived calculations, Refinement description