5D6A

2.7 Angstrom Crystal Structure of ABC transporter ATPase from Vibrio vulnificus in Complex with Adenylyl-imidodiphosphate (AMP-PNP)

PDB DOI: https://doi.org/10.2210/pdb5D6A/pdb

Classification: HYDROLASE
Organism(s): Vibrio vulnificus YJ016
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2015-08-11 Released: 2015-08-26
Deposition Author(s): Minasov, G., Wawrzak, Z., Shuvalova, L., Dubrovska, I., Flores, K., Grimshaw, S., Kwon, K., Anderson, W.F., Center for Structural Genomics of Infectious Diseases (CSGID)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.70 Å
R-Value Free: 0.256
R-Value Work: 0.194
R-Value Observed: 0.200

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

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

Literature

2.7 Angstrom Crystal Structure of ABC transporter ATPase from Vibrio vulnificus in Complex with Adenylyl-imidodiphosphate (AMP-PNP)

Minasov, G., Wawrzak, Z., Shuvalova, L., Dubrovska, I., Flores, K., Grimshaw, S., Kwon, K., Anderson, W.F., Center for Structural Genomics of Infectious Diseases (CSGID)

To be published.

Macromolecule Content

Total Structure Weight: 65.45 kDa
Atom Count: 4,429
Modelled Residue Count: 548
Deposited Residue Count: 575
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Predicted ATPase of the ABC class	A	575	Vibrio vulnificus YJ016	Mutation(s): 0 Gene Names: VVA0769
UniProt
Find proteins for Q7MEA1 (Vibrio vulnificus (strain YJ016)) Explore Q7MEA1 Go to UniProtKB: Q7MEA1
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q7MEA1
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
ANP Query on ANP Download Ideal Coordinates CCD File SDF format, chain C [auth A] MOL2 format, chain C [auth A]	C [auth A]	PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER C₁₀ H₁₇ N₆ O₁₂ P₃ PVKSNHVPLWYQGJ-KQYNXXCUSA-N		Interactions Focus chain C [auth A] Interactions & Density Focus chain C [auth A]
NA Query on NA Download Ideal Coordinates CCD File SDF format, chain B [auth A] MOL2 format, chain B [auth A]	B [auth A]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N		Interactions Focus chain B [auth A] Interactions & Density Focus chain B [auth A]

Modified Residues 1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
MSE Query on MSE	A	L-PEPTIDE LINKING	C₅ H₁₁ N O₂ Se		MET

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.70 Å
R-Value Free: 0.256
R-Value Work: 0.194
R-Value Observed: 0.200
Space Group: P 3₁ 2 1
Diffraction Data: https://doi.org/10.18430/M35D6A

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 104.957	α = 90
b = 104.957	β = 90
c = 85.354	γ = 120

Software Package:

Software Name	Purpose
REFMAC	refinement
BLU-MAX	data collection
HKL-3000	phasing
HKL-3000	data scaling
PHENIX	phasing

Structure Validation

View Full Validation Report

Ligand Structure Quality Assessment

Entry History

Deposition Data

Released Date: 2015-08-26

Deposition Author(s):

Center for Structural Genomics of Infectious Diseases (CSGID)

Revision History (Full details and data files)

Version 1.0: 2015-08-26
Type: Initial release
Version 1.1: 2017-11-22
Changes: Derived calculations, Refinement description

RCSB PDB Core Operations are funded by the National Science Foundation (DBI-1832184), 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 R01GM133198.