6KCO | pdb_00006kco

Shuguo PWWP in complex with ssDNA

PDB DOI: https://doi.org/10.2210/pdb6KCO/pdb
NAKB: 6KCO

Classification: DNA BINDING PROTEIN/DNA
Organism(s): Drosophila melanogaster, synthetic construct
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2019-06-28 Released: 2020-07-01
Deposition Author(s): Liu, Y.C., Huang, Y.
Funding Organization(s): National Natural Science Foundation of China

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.40 Å
R-Value Free:
0.236 (Depositor), 0.238 (DCC)
R-Value Work:
0.198 (Depositor), 0.200 (DCC)
R-Value Observed:
0.200 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Validation slider image for 6KCO

This is version 1.1 of the entry. See complete history.

Literature

Shuguo PWWP in complex with ssDNA

Liu, Y.C., Huang, Y.

To be published.

Macromolecule Content

Total Structure Weight: 177.42 kDa
Atom Count: 11,761
Modeled Residue Count: 1,355
Deposited Residue Count: 1,440
Unique protein chains: 1
Unique nucleic acid chains: 1

Macromolecules

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Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
LD23804p	A, B, C, D, E A, B, C, D, E, F, G, H, I, J, K, L, M, N, O, P	85	Drosophila melanogaster	Mutation(s): 0 Gene Names: Dmel\CG7946, CG7946, Dmel_CG7946
UniProt
Find proteins for Q9VAA9 (Drosophila melanogaster) Explore Q9VAA9 Go to UniProtKB: Q9VAA9
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q9VAA9
Sequence Annotations Expand
Reference Sequence

Find similar nucleic acids by: Sequence

Molecule	Chains	Length	Organism	Image
Entity ID: 2
DNA (5'-D(TPCPCPCP*T)-3')	AA [auth 3L] BA [auth 9N] CA [auth 6A] DA [auth 3B] EA [auth 7C] AA [auth 3L], BA [auth 9N], CA [auth 6A], DA [auth 3B], EA [auth 7C], FA [auth 8K], Q [auth 1O], R [auth 2M], S [auth 1P], T [auth 1H], U [auth 4D], V [auth 7E], W [auth 6F], X [auth 2G], Y [auth 5I], Z [auth 4J]	5	synthetic construct
Sequence Annotations Expand
Reference Sequence

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.40 Å
R-Value Free: 0.236 (Depositor), 0.238 (DCC)
R-Value Work: 0.198 (Depositor), 0.200 (DCC)
R-Value Observed: 0.200 (Depositor)

Space Group: P 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 70.666	α = 101.753
b = 76.326	β = 106.077
c = 85.256	γ = 113.754

Software Package:

Software Name	Purpose
PHENIX	refinement
HKL-3000	data reduction
HKL-3000	data scaling
PHENIX	phasing

Structure Validation

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Entry History

& Funding Information

Deposition Data

Released Date: 2020-07-01

Deposition Author(s):

Funding Organization	Location	Grant Number
National Natural Science Foundation of China	China	31870741
National Natural Science Foundation of China	China	91640102

Revision History (Full details and data files)

Version 1.0: 2020-07-01
Type: Initial release
Version 1.1: 2023-11-22
Changes: Data collection, Database references, Refinement description

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RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.