1YDH | pdb_00001ydh

X-ray structure of a lysine decarboxylase-like protein from arabidopsis thaliana gene at5g11950

PDB DOI: https://doi.org/10.2210/pdb1YDH/pdb

Classification: STRUCTURAL GENOMICS, UNKNOWN FUNCTION
Organism(s): Arabidopsis thaliana
Expression System: Escherichia coli
Mutation(s): Yes

Deposited: 2004-12-23 Released: 2005-01-11
Deposition Author(s): Wesenberg, G.E., 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: 2.15 Å
R-Value Free:
0.213 (Depositor), 0.230 (DCC)
R-Value Work:
0.159 (Depositor), 0.184 (DCC)
R-Value Observed:
0.162 (Depositor)

wwPDB Validation 3D Report Full Report

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: 2Q4D

Literature

X-ray crystal structures of the conserved hypothetical proteins from Arabidopsis thaliana gene loci At5g11950 and AT2g37210.

Jeon, W.B., Allard, S.T.M., Bingman, C.A., Bitto, E., Han, B.W., Wesenberg, G.E., Phillips Jr., G.N.

(2006) Proteins 65: 1051-1054

PubMed: 17048257 Search on PubMed
DOI: https://doi.org/10.1002/prot.21166
Primary Citation Related Structures:
1YDH, 2A33

Organizational Affiliation

Center for Eukaryotic Structural Genomics, Department of Biochemistry, University of Wisconsin-Madison, Madison, Wisconsin 53706, USA.

Macromolecule Content

Total Structure Weight: 48.79 kDa
Atom Count: 3,135
Modeled Residue Count: 365
Deposited Residue Count: 432
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
At5g11950	A, B	216	Arabidopsis thaliana	Mutation(s): 9 Gene Names: AT5G11950
UniProt
Find proteins for Q84MC2 (Arabidopsis thaliana) Explore Q84MC2 Go to UniProtKB: Q84MC2
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q84MC2
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
EDO Query on EDO Download:Ideal Coordinates CCD File SDF format, chain D [auth A] SDF format, chain E [auth A] SDF format, chain F [auth B] SDF format, chain G [auth B] MOL2 format, chain D [auth A] MOL2 format, chain E [auth A] MOL2 format, chain F [auth B] MOL2 format, chain G [auth B] mmCIF format, chain D [auth A] mmCIF format, chain E [auth A] mmCIF format, chain F [auth B] mmCIF format, chain G [auth B]	D [auth A], E [auth A], F [auth B], G [auth B]	1,2-ETHANEDIOL C₂ H₆ O₂ LYCAIKOWRPUZTN-UHFFFAOYSA-N		Interactions Focus chain D [auth A] Focus chain E [auth A] Focus chain F [auth B] Focus chain G [auth B] Interactions & Density Focus chain D [auth A] Focus chain E [auth A] Focus chain F [auth B] Focus chain G [auth B]
NO3 Query on NO3 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]	NITRATE ION N O₃ NHNBFGGVMKEFGY-UHFFFAOYSA-N		Interactions Focus chain C [auth A] Interactions & Density Focus chain C [auth A]

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

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.15 Å
R-Value Free: 0.213 (Depositor), 0.230 (DCC)
R-Value Work: 0.159 (Depositor), 0.184 (DCC)
R-Value Observed: 0.162 (Depositor)

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 121.589	α = 90
b = 80.427	β = 102.97
c = 50.709	γ = 90

Software Package:

Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
SOLVE	phasing
RESOLVE	phasing
REFMAC	refinement

Structure Validation

View Full Validation Report

View more in-depth experimental data

Entry History

Deposition Data

Released Date: 2005-01-11

Deposition Author(s):

Center for Eukaryotic Structural Genomics (CESG)

Revision History (Full details and data files)

Version 1.0: 2005-01-11
Type: Initial release
Version 1.1: 2008-04-30
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: 2024-10-30
Changes: Data collection, Database references, Derived calculations, Structure summary