PDB-9c7o: Crystal Structure of the Maize R ACT-like Domain

ID or keywords:

Entry

Database: PDB / ID: 9c7o

Title

Crystal Structure of the Maize R ACT-like Domain

Components

Anthocyanin regulatory Lc protein

Keywords

LIPID BINDING PROTEIN / LBP / CRBPII

Function / homology

Function and homology information

regulation of biosynthetic process / regulation of primary metabolic process / protein dimerization activity / DNA binding / nucleus
Similarity search - Function

Biological species

Zea mays (maize)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

SAD / Resolution: 2.292 Å

Authors

Silwal, J. / Ghanbarpour, A. / Lee, Y.S. / Geiger, J.H. / Grotewold, E.

Funding support

United States, 2items

Citation

Journal: To Be Published
Title: Crystal Structure of Maize R ACT-like domain
Authors: Silwal, J. / Ghanbarpour, A. / Lee, Y.S. / Geiger, J.H. / Grotewold, E.

History

Deposition	Jun 10, 2024	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Oct 8, 2025	Provider: repository / Type: Initial release

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	9c7o.cif.gz	76.5 KB	Display	PDBx/mmCIF format
PDB format	pdb9c7o.ent.gz	56.7 KB	Display	PDB format
PDBx/mmJSON format	9c7o.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	9c7o_validation.pdf.gz	432.1 KB	Display	wwPDB validaton report
Full document	9c7o_full_validation.pdf.gz	434.6 KB	Display
Data in XML	9c7o_validation.xml.gz	8.9 KB	Display
Data in CIF	9c7o_validation.cif.gz	11.2 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/c7/9c7o ftp://data.pdbj.org/pub/pdb/validation_reports/c7/9c7o	HTTPS FTP

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Related structure data

Similar structure data	Similarity search - Function & homologyF&H Search Similarity search - FunctionF&H Search Similarity search - HomologyF&H Search

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Links

PDB pages	PDBj / wwPDB / NCBI
Related items in Molecule of the Month	#240 - Dec 2019 Hypoxia-Inducible Factors similarity (5) #122 - Feb 2010 Enhanceosome similarity (4) #258 - Jun 2021 Glucocorticoid Receptor and Dexamethasone similarity (4) #112 - Apr 2009 Oct and Sox Transcription Factors similarity (5)

Deposited unit

A: Anthocyanin regulatory Lc protein

B: Anthocyanin regulatory Lc protein

18.8 kDa, 2 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

Idetical with deposited unit
defined by author&software

Unit cell

Length a, b, c (Å)	74.124, 74.124, 90.144
Angle α, β, γ (deg.)	90.00, 90.00, 90.00
Int Tables number	96
Space group name H-M	P4₃2₁2

#1: Protein	Anthocyanin regulatory Lc protein Mass: 9397.415 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Zea mays (maize) / Gene: LC / Production host: Escherichia coli (E. coli) / References: UniProt: P13526
#2: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 17 / Source method: isolated from a natural source / Formula: H₂O
Has ligand of interest	Y
Has protein modification	Y

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Experiment

Experiment	Method: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

Crystal	Density Matthews: 3.34 Å³/Da / Density % sol: 63.22 %
Crystal grow	Temperature: 298 K / Method: vapor diffusion, hanging drop / Details: 0.2M Sodium Thiocyanate, 20%PEG 3350

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Data collection

Diffraction

Mean temperature: 100 K / Serial crystal experiment: N

Diffraction source

Source:

SYNCHROTRON / Site:

APS

/ Beamline: 21-ID-D / Wavelength: 0.97849 Å

Detector

Type: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Jun 21, 2019

Radiation

Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray

Radiation wavelength

Wavelength: 0.97849 Å / Relative weight: 1

Reflection

Resolution: 2.29→40 Å / Num. obs: 11190 / % possible obs: 94.4 % / Redundancy: 18.7 % / R_merge(I) obs: 0.133 / R_rim(I) all: 0.158 / Net I/σ(I): 3.9

Reflection shell

Diffraction-ID: 1

Resolution (Å)	Redundancy (%)	R_merge(I) obs	Num. unique obs	CC_1/2	CC star	R_pim(I) all	R_rim(I) all	Χ²	% possible all
2.29-2.33	9.1	0.425	398	0.984	0.996	0.123	0.444	0.466	68.9
2.33-2.37	9.6	0.453	418	0.984	0.996	0.128	0.472	0.426	73.1
2.37-2.42	10.6	0.477	457	0.981	0.995	0.131	0.496	0.4	80.5
2.42-2.47	11.8	0.567	498	0.968	0.992	0.147	0.587	0.378	85.4
2.47-2.52	12.8	0.628	513	0.936	0.983	0.161	0.65	0.405	89.7
2.52-2.58	14.6	0.72	554	0.945	0.986	0.175	0.742	0.441	95.7
2.58-2.64	17.1	0.638	583	0.974	0.993	0.147	0.655	0.398	99.1
2.64-2.71	19.7	0.614	578	0.983	0.996	0.136	0.63	0.391	100
2.71-2.79	21.5	0.553	569	0.981	0.995	0.12	0.566	0.45	100
2.79-2.89	22.3	0.441	591	0.99	0.997	0.094	0.451	0.498	100
2.89-2.99	21.1	0.352	594	0.978	0.994	0.078	0.36	0.643	99.8
2.99-3.11	18.7	0.26	576	0.993	0.998	0.061	0.267	0.743	99.8
3.11-3.25	23.7	0.214	595	0.991	0.998	0.045	0.219	0.712	99.8
3.25-3.42	24.6	0.181	581	0.987	0.997	0.038	0.185	1.18	99.8
3.42-3.63	23.6	0.148	595	0.958	0.989	0.033	0.152	2.299	99.8
3.63-3.91	23.2	0.124	598	0.992	0.998	0.028	0.128	2.6	99.8
3.91-4.31	22.2	0.106	597	0.98	0.995	0.024	0.109	2.489	99.3
4.31-4.93	19.9	0.088	612	0.999	1	0.023	0.091	3.189	99.8
4.93-6.21	17.3	0.097	615	0.997	0.999	0.024	0.1	3.105	98.6
6.21-40	19.9	0.095	668	0.995	0.999	0.022	0.098	6.621	97.1

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Processing

Software

Name	Version	Classification
PHENIX	(1.14_3260: ???)	refinement
HKL-2000		data scaling
HKL-2000		data reduction
PHASER		phasing
PHENIX		phasing

Refinement

Method to determine structure:

SAD / Resolution: 2.292→23.341 Å / SU ML: 0.3 / Cross valid method: FREE R-VALUE / σ(F): 0 / Phase error: 28.83 / Stereochemistry target values: MLHL

	R_factor	Num. reflection	% reflection
R_free	0.2602	1070	9.99 %
R_work	0.2086	-	-
obs	0.2136	10716	90.88 %

Solvent computation

Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL

Refinement step

Cycle: LAST / Resolution: 2.292→23.341 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	1212	0	0	17	1229

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.01	1254
X-RAY DIFFRACTION	f_angle_d	1.205	1703
X-RAY DIFFRACTION	f_dihedral_angle_d	16.242	771
X-RAY DIFFRACTION	f_chiral_restr	0.065	209
X-RAY DIFFRACTION	f_plane_restr	0.008	210

LS refinement shell

Resolution (Å)	R_factor R_free	Num. reflection R_free	R_factor R_work	Num. reflection R_work	Refine-ID	% reflection obs (%)
2.2921-2.3963	0.3521	91	0.2602	837	X-RAY DIFFRACTION	65
2.3963-2.5225	0.3082	115	0.2458	1008	X-RAY DIFFRACTION	78
2.5225-2.6803	0.3048	129	0.2525	1192	X-RAY DIFFRACTION	92
2.6803-2.8869	0.3033	143	0.2232	1279	X-RAY DIFFRACTION	98
2.8869-3.1768	0.2659	144	0.2262	1298	X-RAY DIFFRACTION	99
3.1768-3.635	0.266	147	0.1963	1320	X-RAY DIFFRACTION	99
3.635-4.5741	0.2379	149	0.1815	1330	X-RAY DIFFRACTION	99
4.5741-23.341	0.2333	152	0.2085	1382	X-RAY DIFFRACTION	96

Refinement TLS params.

Method: refined / Origin x: 53.1845 Å / Origin y: 30.9034 Å / Origin z: 36.9759 Å

	11	12	13	21	22	23	31	32	33
T	0.3855 Å²	-0.0011 Å²	0.0581 Å²	-	0.2568 Å²	-0.0282 Å²	-	-	0.346 Å²
L	1.4804 °²	-0.5062 °²	0.2244 °²	-	5.0182 °²	-0.3435 °²	-	-	1.2085 °²
S	-0.0628 Å °	-0.1455 Å °	0.0679 Å °	0.2456 Å °	0.0863 Å °	-0.0425 Å °	0.0128 Å °	-0.0253 Å °	-0.0098 Å °

Refinement TLS group

Selection details: all

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