3VNQ | pdb_00003vnq

Co-crystal structure of NRPS adenylation protein CytC1 with ATP from streptomyces

PDB DOI: https://doi.org/10.2210/pdb3VNQ/pdb

Classification: LIGASE
Organism(s): Streptomyces sp.
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2012-01-17 Released: 2013-01-23
Deposition Author(s): Okumura, H., Ueki, M., Shiro, Y., Osada, H.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.10 Å
R-Value Free:
0.221 (Depositor), 0.220 (DCC)
R-Value Work:
0.184 (Depositor), 0.180 (DCC)
R-Value Observed:
0.186 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

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

Literature

Substrate recognition mechanism of NRPS adenylation protein from Streptomyces

Ueki, M., Okumura, H., Osada, H.

To be published.

Macromolecule Content

Total Structure Weight: 59.5 kDa
Atom Count: 4,117
Modelled Residue Count: 497
Deposited Residue Count: 544
Unique protein chains: 1

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
NRPS adenylation protein CytC1	A	544	Streptomyces sp.	Mutation(s): 0
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations Expand
Reference Sequence LOADING

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
ATP Query on ATP Download Ideal Coordinates CCD File SDF format, chain B [auth A] MOL2 format, chain B [auth A] mmCIF format, chain B [auth A]	B [auth A]	ADENOSINE-5'-TRIPHOSPHATE C₁₀ H₁₆ N₅ O₁₃ P₃ ZKHQWZAMYRWXGA-KQYNXXCUSA-N		Interactions Focus chain B [auth A] Interactions & Density Focus chain B [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.10 Å
R-Value Free: 0.221 (Depositor), 0.220 (DCC)
R-Value Work: 0.184 (Depositor), 0.180 (DCC)
R-Value Observed: 0.186 (Depositor)

Space Group: I 2 3

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 156.146	α = 90
b = 156.146	β = 90
c = 156.146	γ = 90

Software Package:

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

Structure Validation

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Ligand Structure Quality Assessment

Entry History

Deposition Data

Released Date: 2013-01-23

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2013-01-23
Type: Initial release
Version 1.1: 2023-11-08
Changes: Data collection, Database references, Derived calculations, 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.