2F2G | pdb_00002f2g

X-Ray Structure of Gene Product From Arabidopsis Thaliana AT3G16990

PDB DOI: https://doi.org/10.2210/pdb2F2G/pdb
Entry: 2F2G supersedes: 1Q4M

Classification: PLANT PROTEIN
Organism(s): Arabidopsis thaliana
Expression System: Escherichia coli
Mutation(s): Yes

Deposited: 2005-11-16 Released: 2005-12-13
Deposition Author(s): Wesenberg, G.W., Smith, D.W., Phillips Jr., G.N., Johnson, K.A., Bitto, E., Bingman, C.A., Center for Eukaryotic Structural Genomics (CESG)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.10 Å
R-Value Free:
0.234 (Depositor), 0.232 (DCC)
R-Value Work:
0.170 (Depositor), 0.172 (DCC)
R-Value Observed:
0.173 (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: 2Q4X

Literature

Crystal structure of gene locus At3g16990 from Arabidopsis thaliana

Blommel, P.G., Smith, D.W., Bingman, C.A., Dyer, D.H., Rayment, I., Holden, H.M., Fox, B.G., Phillips Jr., G.N.

(2004) Proteins 57: 221-222

PubMed: 15326608 Search on PubMed
DOI: https://doi.org/10.1002/prot.20213
Primary Citation Related Structures:
2F2G

Organizational Affiliation

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

Macromolecule Content

Total Structure Weight: 51.33 kDa
Atom Count: 3,896
Modeled Residue Count: 426
Deposited Residue Count: 442
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
SEED MATURATION PROTEIN PM36 HOMOLOG	A, B	221	Arabidopsis thaliana	Mutation(s): 5 Gene Names: At3g16990 EC: 3.5.1 (UniProt), 3.5.99.2 (UniProt)
UniProt
Find proteins for Q9ASY9 (Arabidopsis thaliana) Explore Q9ASY9 Go to UniProtKB: Q9ASY9
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q9ASY9
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
HMH Query on HMH Download:Ideal Coordinates CCD File SDF format, chain H [auth B] SDF format, chain D [auth A] MOL2 format, chain H [auth B] MOL2 format, chain D [auth A] mmCIF format, chain H [auth B] mmCIF format, chain D [auth A]	D [auth A], H [auth B]	4-AMINO-5-HYDROXYMETHYL-2-METHYLPYRIMIDINE C₆ H₉ N₃ O VUTBELPREDJDDH-UHFFFAOYSA-N		Interactions Focus chain D [auth A] Focus chain H [auth B] Interactions & Density Focus chain D [auth A] Focus chain H [auth B]
SO4 Query on SO4 Download:Ideal Coordinates CCD File SDF format, chain G [auth B] SDF format, chain F [auth B] SDF format, chain E [auth B] SDF format, chain C [auth A] MOL2 format, chain G [auth B] MOL2 format, chain F [auth B] MOL2 format, chain E [auth B] MOL2 format, chain C [auth A] mmCIF format, chain G [auth B] mmCIF format, chain F [auth B] mmCIF format, chain E [auth B] mmCIF format, chain C [auth A]	C [auth A], E [auth B], F [auth B], G [auth B]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain C [auth A] Focus chain E [auth B] Focus chain F [auth B] Focus chain G [auth B] Interactions & Density Focus chain C [auth A] Focus chain E [auth B] Focus chain F [auth B] Focus chain G [auth B]

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: 2.10 Å
R-Value Free: 0.234 (Depositor), 0.232 (DCC)
R-Value Work: 0.170 (Depositor), 0.172 (DCC)
R-Value Observed: 0.173 (Depositor)

Space Group: P 4₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 62.7	α = 90
b = 62.7	β = 90
c = 287.621	γ = 90

Software Package:

Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
SOLVE	phasing
RESOLVE	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction
MAR345	data collection

Structure Validation

View Full Validation Report

View more in-depth experimental data

Entry History

Deposition Data

Released Date: 2005-12-13

Deposition Author(s):

Center for Eukaryotic Structural Genomics (CESG)

This entry supersedes: 1Q4M

Revision History (Full details and data files)

Version 1.0: 2005-12-13
Type: Initial release
Version 1.1: 2008-02-01
Changes: Version format compliance
Version 1.2: 2011-07-13
Changes: Advisory, Version format compliance
Version 1.3: 2017-10-18
Changes: Refinement description
Version 1.4: 2024-11-06
Changes: Data collection, Database references, Derived calculations, Refinement description, Structure summary