4QFQ | pdb_00004qfq

Crystal structure of natvie Npu DnaE split intein

PDB DOI: https://doi.org/10.2210/pdb4QFQ/pdb

Classification: SPLICING
Organism(s): Nostoc punctiforme PCC 73102
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2014-05-21 Released: 2015-05-27
Deposition Author(s): Lee, Y.Z., Kuo, J.H., Sue, S.C.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.04 Å
R-Value Free:
0.287 (Depositor), 0.289 (DCC)
R-Value Work:
0.230 (Depositor), 0.231 (DCC)
R-Value Observed:
0.236 (Depositor)

Starting Model: experimental
View more details

wwPDB Validation 3D Report Full Report

Validation slider image for 4QFQ

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

Literature

Crystal structure of natvie Npu DnaE split intein

Lee, Y.Z., Kuo, J.H., Sue, S.C.

To be published.

Macromolecule Content

Total Structure Weight: 17.19 kDa
Atom Count: 1,118
Modeled Residue Count: 136
Deposited Residue Count: 148
Unique protein chains: 2

Macromolecules

Find similar proteins by:

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
DNA polymerase III, alpha subunit	A	111	Nostoc punctiforme PCC 73102	Mutation(s): 0 Gene Names: Npun_F4872 EC: 2.7.7.7
UniProt
Find proteins for B2J066 (Nostoc punctiforme (strain ATCC 29133 / PCC 73102)) Explore B2J066 Go to UniProtKB: B2J066
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	B2J066
Sequence Annotations Expand
Reference Sequence

Find similar proteins by:

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Nucleic acid binding, OB-fold, tRNA/helicase-type	B	37	Nostoc punctiforme PCC 73102	Mutation(s): 0 Gene Names: Npun_F5684 EC: 2.7.7.7
UniProt
Find proteins for B2J821 (Nostoc punctiforme (strain ATCC 29133 / PCC 73102)) Explore B2J821 Go to UniProtKB: B2J821
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	B2J821
Sequence Annotations Expand
Reference Sequence

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.04 Å
R-Value Free: 0.287 (Depositor), 0.289 (DCC)
R-Value Work: 0.230 (Depositor), 0.231 (DCC)
R-Value Observed: 0.236 (Depositor)

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 34.798	α = 90
b = 48.694	β = 90
c = 75.686	γ = 90

Software Package:

Software Name	Purpose
HKL-2000	data collection
MOLREP	phasing
PHENIX	refinement
HKL-2000	data reduction
HKL-2000	data scaling

Structure Validation

View Full Validation Report

View more in-depth experimental data

Entry History

Deposition Data

Released Date: 2015-05-27

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2015-05-27
Type: Initial release
Version 1.1: 2023-11-08
Changes: Data collection, Database references, Refinement description

RCSB PDB is hosted by

RCSB PDB is a member of

RCSB Partners
Nucleic Acid Knowledgebase

CoreTrustSeal

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.