3VNS

Co-crystal structure of NRPS adenylation protein CytC1 with D-valine and AMP from streptomyces

PDB DOI: https://doi.org/10.2210/pdb3VNS/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: 2.00 ?
R-Value Free: 0.216
R-Value Work: 0.191
R-Value Observed: 0.193

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.2 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: 59.46 kDa
Atom Count: 4,114
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

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]
DVA Query on DVA 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]	D-VALINE C₅ H₁₁ N O₂ KZSNJWFQEVHDMF-SCSAIBSYSA-N		Interactions Focus chain C [auth A] Interactions & Density Focus chain C [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.00 ?
R-Value Free: 0.216
R-Value Work: 0.191
R-Value Observed: 0.193
Space Group: I 2 3

Unit Cell:

Length ( ? )	Angle ( ? )
a = 156.544	α = 90
b = 156.544	β = 90
c = 156.544	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

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

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Help and Resources

3VNS

Co-crystal structure of NRPS adenylation protein CytC1 with D-valine and AMP from streptomyces

Substrate recognition mechanism of NRPS adenylation protein from Streptomyces

Entity ID: 1

Entity Groups

Sequence Annotations

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Experimental Data

Structure Validation

Ligand Structure Quality Assessment

Deposition Data

Revision History (Full details and data files)