1TLQ | pdb_00001tlq

Crystal structure of protein ypjQ from Bacillus subtilis, Pfam DUF64

• PDB DOI: https://doi.org/10.2210/pdb1TLQ/pdb

• Classification: STRUCTURAL GENOMICS, UNKNOWN FUNCTION
• Organism(s): Bacillus subtilis
• Expression System: Escherichia coli
• Mutation(s): Yes 


• Deposited: 2004-06-09 Released: 2004-06-22 
• Deposition Author(s): Kniewel, R., Rajashankar, K.R., Solorzano, V., Lima, C.D., Burley, S.K., New York SGX Research Center for Structural Genomics (NYSGXRC)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.40 Å
• R-Value Free: 
  0.295 (Depositor), 0.290 (DCC) 
• R-Value Work: 
  0.232 (Depositor), 0.240 (DCC) 
• R-Value Observed: 
  0.235 (Depositor) 

Starting Model: experimental

Literature

Crystal Structure of a Hypothetical Protein from Bacillus subtilis

KNIEWEL, R., RAJASHANKAR, K.R., SOLORZANO, V., LIMA, C.D.

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,PQS (software)

Macromolecule Content 

• Total Structure Weight: 21.61 kDa 
• Atom Count: 1,287 
• Modeled Residue Count: 161 
• Deposited Residue Count: 189 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Hypothetical protein ypjQ	A	189	Bacillus subtilis	Mutation(s): 5  Gene Names: YPJQ, BSU21830
UniProt
Find proteins for P54173 (Bacillus subtilis (strain 168)) Explore P54173  Go to UniProtKB:  P54173

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
CA	B [auth A]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N

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

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.40 Å
• R-Value Free:  0.295 (Depositor), 0.290 (DCC) 
• R-Value Work:  0.232 (Depositor), 0.240 (DCC) 
• R-Value Observed: 0.235 (Depositor) 

Space Group: P 6₄ 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 118.112	α = 90
b = 118.112	β = 90
c = 65.792	γ = 120

Software Package:

Software Name	Purpose
REFMAC	refinement
DENZO	data reduction
SCALEPACK	data scaling
SOLVE	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2004-06-22 
Deposition Author(s): Kniewel, R., Rajashankar, K.R., Solorzano, V., Lima, C.D., Burley, S.K., New York SGX Research Center for Structural Genomics (NYSGXRC)

Revision History  

• Version 1.0: 2004-06-22
  Type: Initial release
  
• Version 1.1: 2008-04-30
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Derived calculations, Version format compliance
• Version 1.3: 2021-02-03
  Changes: Database references, Derived calculations, Structure summary
• Version 1.4: 2024-04-03
  Changes: Data collection, Database references, Refinement description
• Version 1.5: 2024-10-30
  Changes: Structure summary