2NUH | pdb_00002nuh

Crystal structure of CutA from the phytopathgen bacterium Xylella fastidiosa

PDB DOI: https://doi.org/10.2210/pdb2NUH/pdb

Classification: UNKNOWN FUNCTION
Organism(s): Xylella fastidiosa 9a5c
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2006-11-09 Released: 2007-01-03
Deposition Author(s): Medrano, F.J., Benedetti, C.E.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.39 Å
R-Value Free:
0.205 (Depositor), 0.209 (DCC)
R-Value Work:
0.196 (Depositor), 0.195 (DCC)
R-Value Observed:
0.197 (Depositor)

Starting Model: experimental
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This is version 1.3 of the entry. See complete history.

Literature

Crystal structure of CutA from the phytopathgen bacterium Xylella fastidiosa

Medrano, F.J., Benedetti, C.E.

To be published.

Macromolecule Content

Total Structure Weight: 13.45 kDa
Atom Count: 931
Modeled Residue Count: 104
Deposited Residue Count: 118
Unique protein chains: 1

Macromolecules

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Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Periplasmic divalent cation tolerance protein	A	118	Xylella fastidiosa 9a5c	Mutation(s): 0 Gene Names: cutA
UniProt
Find proteins for Q9PFN8 (Xylella fastidiosa (strain 9a5c)) Explore Q9PFN8 Go to UniProtKB: Q9PFN8
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q9PFN8
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
IMD Query on IMD Download:Ideal Coordinates CCD File SDF format, chain B [auth A] SDF format, chain C [auth A] MOL2 format, chain B [auth A] MOL2 format, chain C [auth A] mmCIF format, chain B [auth A] mmCIF format, chain C [auth A]	B [auth A], C [auth A]	IMIDAZOLE C₃ H₅ N₂ RAXXELZNTBOGNW-UHFFFAOYSA-O		Interactions Focus chain B [auth A] Focus chain C [auth A] Interactions & Density Focus chain B [auth A] Focus chain C [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.39 Å
R-Value Free: 0.205 (Depositor), 0.209 (DCC)
R-Value Work: 0.196 (Depositor), 0.195 (DCC)
R-Value Observed: 0.197 (Depositor)

Space Group: P 6₃

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 70.59	α = 90
b = 70.59	β = 90
c = 35.502	γ = 120

Software Package:

Software Name	Purpose
REFMAC	refinement
PDB_EXTRACT	data extraction

Structure Validation

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Entry History

Deposition Data

Released Date: 2007-01-03

Deposition Author(s):

Benedetti, C.E.

Revision History (Full details and data files)

Version 1.0: 2007-01-03
Type: Initial release
Version 1.1: 2008-05-01
Changes: Version format compliance
Version 1.2: 2011-07-13
Changes: Derived calculations, Source and taxonomy, Version format compliance
Version 1.3: 2023-10-25
Changes: Data collection, Database references, Derived calculations, Refinement description

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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.