1XQ6 | pdb_00001xq6

X-ray Structure of Gene Product from Arabidopsis Thaliana At5g02240

PDB DOI: https://doi.org/10.2210/pdb1XQ6/pdb

Classification: STRUCTURAL GENOMICS, UNKNOWN FUNCTION
Organism(s): Arabidopsis thaliana
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2004-10-11 Released: 2004-10-19
Deposition Author(s): Wesenberg, G.E., Smith, D.W., Phillips Jr., G.N., Bitto, E., Bingman, C.A., Allard, S.T.M., Center for Eukaryotic Structural Genomics (CESG)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.80 Å
R-Value Free:
0.278 (Depositor), 0.278 (DCC)
R-Value Work:
0.218 (Depositor), 0.221 (DCC)
R-Value Observed:
0.221 (Depositor)

wwPDB Validation 3D Report Full Report

Validation slider image for 1XQ6

Ligand Structure Quality Assessment

This is version 1.4 of the entry. See complete history.

Re-refinement Note

A newer entry is available that reflects an alternative modeling of the original data: 2Q46

Literature

X-ray Structure of Gene Product from Arabidopsis Thaliana At5g02240

Center for Eukaryotic Structural Genomics

To be published.

Macromolecule Content

Total Structure Weight: 55.67 kDa
Atom Count: 4,310
Modeled Residue Count: 506
Deposited Residue Count: 506
Unique protein chains: 1

Macromolecules

Find similar proteins by:

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
unknown protein	A, B	253	Arabidopsis thaliana	Mutation(s): 0 Gene Names: At5g02240
UniProt
Find proteins for Q94EG6 (Arabidopsis thaliana) Explore Q94EG6 Go to UniProtKB: Q94EG6
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q94EG6
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
NAP Query on NAP Download:Ideal Coordinates CCD File SDF format, chain D [auth B] SDF format, chain C [auth A] MOL2 format, chain D [auth B] MOL2 format, chain C [auth A] mmCIF format, chain D [auth B] mmCIF format, chain C [auth A]	C [auth A], D [auth B]	NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE C₂₁ H₂₈ N₇ O₁₇ P₃ XJLXINKUBYWONI-NNYOXOHSSA-N		Interactions Focus chain C [auth A] Focus chain D [auth B] Interactions & Density Focus chain C [auth A] Focus chain D [auth B]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.80 Å
R-Value Free: 0.278 (Depositor), 0.278 (DCC)
R-Value Work: 0.218 (Depositor), 0.221 (DCC)
R-Value Observed: 0.221 (Depositor)

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 46.75	α = 90
b = 69.799	β = 96.01
c = 83.828	γ = 90

Software Package:

Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
SOLVE	phasing
RESOLVE	phasing
REFMAC	refinement
ARP/wARP	model building

Structure Validation

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Ligand Structure Quality Assessment

View more in-depth experimental data

Entry History

Deposition Data

Released Date: 2004-10-19

Deposition Author(s):

Wesenberg, G.E.

Phillips Jr., G.N.

Center for Eukaryotic Structural Genomics (CESG)

Revision History (Full details and data files)

Version 1.0: 2004-10-19
Type: Initial release
Version 1.1: 2008-02-01
Changes: Version format compliance
Version 1.2: 2011-07-13
Changes: Version format compliance
Version 1.3: 2017-10-11
Changes: Refinement description
Version 1.4: 2024-02-14
Changes: Data collection, Database references, Derived calculations

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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.