3VNR | pdb_00003vnr

Co-crystal structure of NRPS adenylation protein CytC1 with aminobutyric acid and AMP from streptomyces

PDB DOI: https://doi.org/10.2210/pdb3VNR/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: 1.75 Å
R-Value Free:
0.211 (Depositor), 0.206 (DCC)
R-Value Work:
0.189 (Depositor), 0.184 (DCC)
R-Value Observed:
0.190 (Depositor)

Starting Model: experimental
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Ligand Structure Quality Assessment

This is version 1.3 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: 59.44 kDa
Atom Count: 4,135
Modeled Residue Count: 493
Deposited Residue Count: 544
Unique protein chains: 1

Macromolecules

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Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
NRPS adenylation protein CytC1	A	544	Streptomyces sp.	Mutation(s): 0

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
AMP Query on AMP 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 MONOPHOSPHATE C₁₀ H₁₄ N₅ O₇ P UDMBCSSLTHHNCD-KQYNXXCUSA-N		Interactions Focus chain B [auth A] Interactions & Density Focus chain B [auth A]
ABA Query on ABA Download:Ideal Coordinates CCD File SDF format, chain C [auth A] MOL2 format, chain C [auth A] mmCIF format, chain C [auth A]	C [auth A]	ALPHA-AMINOBUTYRIC ACID C₄ H₉ N O₂ QWCKQJZIFLGMSD-VKHMYHEASA-N		Interactions Focus chain C [auth A] Interactions & Density Focus chain C [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.75 Å
R-Value Free: 0.211 (Depositor), 0.206 (DCC)
R-Value Work: 0.189 (Depositor), 0.184 (DCC)
R-Value Observed: 0.190 (Depositor)

Space Group: I 2 3

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 157.016	α = 90
b = 157.016	β = 90
c = 157.016	γ = 90

Software Package:

Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
MOLREP	phasing
PHENIX	refinement
PDB_EXTRACT	data extraction
BSS	data collection
HKL-2000	data reduction
HKL-2000	data scaling

Structure Validation

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Ligand Structure Quality Assessment

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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: 2017-11-22
Changes: Refinement description
Version 1.2: 2023-11-08
Changes: Data collection, Database references, Derived calculations, Refinement description
Version 1.3: 2023-12-06
Changes: Data collection

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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.