6OOV | pdb_00006oov

Crystal structure of HMCES SRAP domain in complex with palindromic 3' overhang DNA

• PDB DOI: https://doi.org/10.2210/pdb6OOV/pdb
• NAKB: 6OOV

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


• Deposited: 2019-04-23 Released: 2019-05-15 
• Deposition Author(s): Halabelian, L., Zeng, H., Li, Y., Bountra, C., Edwards, A.M., Arrowsmith, C.H., Structural Genomics Consortium (SGC)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.20 Å
• R-Value Free: 
  0.219 (Depositor), 0.207 (DCC) 
• R-Value Work: 
  0.194 (Depositor) 
• R-Value Observed: 
  0.195 (Depositor) 

Starting Model: experimental

Literature

Crystal structure of HMCES SRAP domain in complex with palindromic 3' overhang DNA

Halabelian, L., Zeng, H., Li, Y., Bountra, C., Edwards, A.M., Arrowsmith, C.H., Structural Genomics Consortium (SGC)

To be published.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Homo 2-mer - A2 

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

Biological Assembly Evidence: native gel electrophoresis

Macromolecule Content 

• Total Structure Weight: 71.24 kDa 
• Atom Count: 4,531 
• Modeled Residue Count: 524 
• Deposited Residue Count: 578 
• Unique protein chains: 1
• Unique nucleic acid chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Embryonic stem cell-specific 5-hydroxymethylcytosine-binding protein	A, B	276	Homo sapiens	Mutation(s): 0  Gene Names: HMCES, C3orf37, DC12, SRAPD1 EC: 3.4 (PDB Primary Data), 4 (UniProt)
UniProt & NIH Common Fund Data Resources
Find proteins for Q96FZ2 (Homo sapiens) Explore Q96FZ2  Go to UniProtKB:  Q96FZ2
PHAROS:  Q96FZ2 GTEx:  ENSG00000183624

Entity ID: 2
Molecule	Chains	Length	Organism	Image
DNA (5'-D(*CP*AP*AP*CP*GP*TP*TP*GP*TP*TP*TP*TP*T)-3')	C, D	13	synthetic construct

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
UNX	AA [auth A], BA [auth A], CA [auth A], DA [auth A], E [auth A], EA [auth A], F [auth A], FA [auth B], G [auth A], GA [auth B], H [auth A], HA [auth B], I [auth A], IA [auth B], J [auth A], JA [auth B], K [auth A], KA [auth B], L [auth A], LA [auth B], M [auth A], MA [auth B], N [auth A], NA [auth B], O [auth A], OA [auth B], P [auth A], PA [auth B], Q [auth A], QA [auth B], R [auth A], RA [auth B], S [auth A], SA [auth B], T [auth A], TA [auth B], U [auth A], UA [auth B], V [auth A], VA [auth B], W [auth A], WA [auth B], X [auth A], XA [auth B], Y [auth A], YA [auth B], Z [auth A]	UNKNOWN ATOM OR ION X

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.20 Å
• R-Value Free:  0.219 (Depositor), 0.207 (DCC) 
• R-Value Work:  0.194 (Depositor) 
• R-Value Observed: 0.195 (Depositor) 

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 45.729	α = 90
b = 139.828	β = 99.99
c = 66.613	γ = 90

Software Package:

Software Name	Purpose
XDS	data reduction
Aimless	data scaling
REFMAC	refinement
PDB_EXTRACT	data extraction
REFMAC	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2019-05-15 
Deposition Author(s): Halabelian, L., Zeng, H., Li, Y., Bountra, C., Edwards, A.M., Arrowsmith, C.H., Structural Genomics Consortium (SGC)

Revision History  

• Version 1.0: 2019-05-15
  Type: Initial release
  
• Version 1.1: 2023-10-11
  Changes: Data collection, Database references, Refinement description
• Version 1.2: 2024-11-13
  Changes: Structure summary