1ZZM | pdb_00001zzm

Crystal structure of YJJV, TATD Homolog from Escherichia coli k12, at 1.8 A resolution

• PDB DOI: https://doi.org/10.2210/pdb1ZZM/pdb

• Classification: STRUCTURAL GENOMICS, UNKNOWN FUNCTION
• Organism(s): Escherichia coli
• Expression System: Escherichia coli BL21
• Mutation(s): No 


• Deposited: 2005-06-14 Released: 2005-06-28 
• Deposition Author(s): Malashkevich, V.N., Xiang, D.F., Raushel, F.M., Almo, S.C., Burley, S.K., New York SGX Research Center for Structural Genomics (NYSGXRC)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.80 Å
• R-Value Free: 
  0.231 (Depositor), 0.230 (DCC) 
• R-Value Work: 
  0.171 (Depositor), 0.170 (DCC) 
• R-Value Observed: 
  0.171 (Depositor) 

Starting Model: experimental

Literature

Crystal structure of YJJV, TATD homolog from Escherichia coli K12, at 1.8 A resolution

Malashkevich, V.N., Xiang, D.F., Raushel, F.M., Almo, S.C.

To be published.

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 29.53 kDa 
• Atom Count: 2,441 
• Modeled Residue Count: 259 
• Deposited Residue Count: 259 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
putative deoxyribonuclease yjjV	A	259	Escherichia coli	Mutation(s): 0  EC: 3.1.21 (PDB Primary Data), 3.1 (UniProt)
UniProt
Find proteins for P39408 (Escherichia coli (strain K12)) Explore P39408  Go to UniProtKB:  P39408

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
P33	F [auth A]	3,6,9,12,15,18-HEXAOXAICOSANE-1,20-DIOL C14 H30 O8 XPJRQAIZZQMSCM-UHFFFAOYSA-N
ZN	B [auth A], C [auth A], D [auth A], E [auth A]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.80 Å
• R-Value Free:  0.231 (Depositor), 0.230 (DCC) 
• R-Value Work:  0.171 (Depositor), 0.170 (DCC) 
• R-Value Observed: 0.171 (Depositor) 

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 47.186	α = 90
b = 45.007	β = 100.75
c = 57.824	γ = 90

Software Package:

Software Name	Purpose
CNS	refinement
MAR345	data collection
SCALEPACK	data scaling
PHASER	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2005-06-28 
Deposition Author(s): Malashkevich, V.N., Xiang, D.F., Raushel, F.M., Almo, S.C., Burley, S.K., New York SGX Research Center for Structural Genomics (NYSGXRC)

Revision History  

• Version 1.0: 2005-06-28
  Type: Initial release
  
• Version 1.1: 2008-04-30
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance
• Version 1.3: 2017-10-11
  Changes: Refinement description
• Version 1.4: 2021-02-03
  Changes: Derived calculations, Structure summary
• Version 1.5: 2023-08-23
  Changes: Data collection, Database references, Refinement description