5BNH | pdb_00005bnh

Crystal structure of the HLTF HIRAN domain with a ssDNA fragment

• PDB DOI: https://doi.org/10.2210/pdb5BNH/pdb
• NAKB: 5BNH

• Classification: DNA BINDING PROTEIN/DNA
• Organism(s): synthetic construct, Homo sapiens
• Expression System: Enterobacteria phage L1
• Mutation(s): No 


• Deposited: 2015-05-26 Released: 2016-05-25 
• Deposition Author(s): Neculai, D., Walker, J.R., Weigelt, J., Bountra, C., Edwards, A.M., Arrowsmith, C.H., Dhe-Paganon, S.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.70 Å
• R-Value Free: 
  0.214 (Depositor), 0.220 (DCC) 
• R-Value Work: 
  0.165 (Depositor), 0.180 (DCC) 
• R-Value Observed: 
  0.167 (Depositor) 

Literature

Co-crystal structure of the HLTF HIRAN domain with a ssDNA fragment

Neculai, D., Walker, J.R., Weigelt, J., Bountra, C., Edwards, A.M., Arrowsmith, C.H., Dhe-Paganon, S.

To be published.

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 29.25 kDa 
• Atom Count: 2,170 
• Modeled Residue Count: 252 
• Deposited Residue Count: 252 
• Unique protein chains: 1
• Unique nucleic acid chains: 2

Macromolecules

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
Helicase-like transcription factor	C [auth A], D	123	Homo sapiens	Mutation(s): 0  Gene Names: HLTF EC: 3.6.4 (PDB Primary Data), 6.3.2 (PDB Primary Data), 2.3.2.27 (UniProt)
UniProt & NIH Common Fund Data Resources
Find proteins for Q14527 (Homo sapiens) Explore Q14527  Go to UniProtKB:  Q14527
PHAROS:  Q14527 GTEx:  ENSG00000071794

Entity ID: 1
Molecule	Chains	Length	Organism	Image
DNA (5'-D(*(GD)P*GP*TP*G)-3')	A [auth B]	3	synthetic construct

Entity ID: 2
Molecule	Chains	Length	Organism	Image
DNA (5'-D(*(TD)P*TP*G)-3')	B [auth C]	3	synthetic construct

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
PO4	G [auth A], H [auth A]	PHOSPHATE ION O4 P NBIIXXVUZAFLBC-UHFFFAOYSA-K
ACT	I [auth D], J [auth D], K [auth D], L [auth D]	ACETATE ION C2 H3 O2 QTBSBXVTEAMEQO-UHFFFAOYSA-M
NA	E [auth A], F [auth A]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.70 Å
• R-Value Free:  0.214 (Depositor), 0.220 (DCC) 
• R-Value Work:  0.165 (Depositor), 0.180 (DCC) 
• R-Value Observed: 0.167 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 48.469	α = 90
b = 50.117	β = 90
c = 102.763	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
XDS	data reduction
XDS	data scaling
PHASER	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2016-05-25 
Deposition Author(s): Neculai, D., Walker, J.R., Weigelt, J., Bountra, C., Edwards, A.M., Arrowsmith, C.H., Dhe-Paganon, S.

Revision History  

• Version 1.0: 2016-05-25
  Type: Initial release
  
• Version 1.1: 2016-09-21
  Changes: Source and taxonomy
• Version 1.2: 2024-03-20
  Changes: Data collection, Database references, Derived calculations