6JOH | pdb_00006joh

The crystal of nucleoside diphosphate kinase from Aspergillus flavus

PDB DOI: https://doi.org/10.2210/pdb6JOH/pdb

Classification: TRANSFERASE
Organism(s): Aspergillus flavus NRRL3357
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2019-03-21 Released: 2020-01-29
Deposition Author(s): Wang, Y., Wang, S., Wang, S.H.
Funding Organization(s): National Natural Science Foundation of China

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.40 Å
R-Value Free:
0.268 (Depositor), 0.270 (DCC)
R-Value Work:
0.222 (Depositor), 0.220 (DCC)
R-Value Observed:
0.224 (Depositor)

Starting Model: experimental
View more details

wwPDB Validation 3D Report Full Report

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

Literature

Molecular and structural basis of Nucleoside Diphosphate Kinase regulating the spores and sclerotia development in Aspergillus flavus

Wang, Y., Wang, S.H.

To be published.

Macromolecule Content

Total Structure Weight: 412.48 kDa
Atom Count: 28,040
Modeled Residue Count: 3,570
Deposited Residue Count: 3,720
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Nucleoside diphosphate kinase	A B C D E A, B, C, D, E, F, G, H, I, J, K, L, M, N, O [auth Q], P [auth R], Q [auth U], R [auth V], S [auth W], T [auth X], U [auth O], V [auth P], W [auth S], X [auth T]	155	Aspergillus flavus NRRL3357	Mutation(s): 0 Gene Names: AFLA_006300 EC: 2.7.4.6
UniProt
Find proteins for B8NQF0 (Aspergillus flavus (strain ATCC 200026 / FGSC A1120 / IAM 13836 / NRRL 3357 / JCM 12722 / SRRC 167)) Explore B8NQF0 Go to UniProtKB: B8NQF0
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	B8NQF0
Sequence Annotations Expand
Reference Sequence

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.40 Å
R-Value Free: 0.268 (Depositor), 0.270 (DCC)
R-Value Work: 0.222 (Depositor), 0.220 (DCC)
R-Value Observed: 0.224 (Depositor)

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 190.836	α = 90
b = 169.47	β = 92.92
c = 146.937	γ = 90

Software Package:

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

Structure Validation

View Full Validation Report

Entry History & Funding Information

Deposition Data

Released Date: 2020-01-29

Deposition Author(s):

Funding Organization	Location	Grant Number
National Natural Science Foundation of China	China	31772105

Revision History (Full details and data files)

Version 1.0: 2020-01-29
Type: Initial release
Version 1.1: 2023-11-22
Changes: Data collection, Database references, Refinement description

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.