PDB-3kev: X-ray crystal structure of a DCUN1 domain-containing protein from...

ID or keywords:

Entry

Database: PDB / ID: 3kev

Title

X-ray crystal structure of a DCUN1 domain-containing protein from Galdieria sulfuraria

Components

Galieria sulfuraria DCUN1 domain-containing protein

Keywords

structural genomics / unknown function / cullin / neddylation / DCUN1 / DCN-1 / E3 / Center for Eukaryotic Structural Genomics / PSI / Protein Structure Initiative / CESG

Function / homology

Function and homology information

ubiquitin-like protein binding / protein neddylation / ubiquitin conjugating enzyme binding / cullin family protein binding / ubiquitin ligase complex / plasma membrane
Similarity search - Function

Biological species

Galdieria sulphuraria (eukaryote)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MAD,

molecular replacement /

MAD /

molecular replacement / Resolution: 1.3 Å

Authors

Burgie, E.S. / Bingman, C.A. / Phillips Jr., G.N. / Center for Eukaryotic Structural Genomics (CESG)

Citation

Journal: Proteins / Year: 2011
Title: Structural architecture of Galdieria sulphuraria DCN1L.
Authors: Burgie, E.S. / Bingman, C.A. / Makino, S. / Wesenberg, G.E. / Pan, X. / Fox, B.G. / Phillips, G.N.

History

Deposition	Oct 26, 2009	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Dec 1, 2009	Provider: repository / Type: Initial release
Revision 1.1	Jul 13, 2011	Group: Version format compliance
Revision 1.2	Nov 1, 2017	Group: Refinement description / Category: software Item: _software.classification / _software.contact_author ..._software.classification / _software.contact_author / _software.contact_author_email / _software.date / _software.language / _software.location / _software.name / _software.type / _software.version
Revision 1.3	Oct 16, 2024	Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / struct_conn / struct_site Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	3kev.cif.gz	109.1 KB	Display	PDBx/mmCIF format
PDB format	pdb3kev.ent.gz	82.6 KB	Display	PDB format
PDBx/mmJSON format	3kev.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	3kev_validation.pdf.gz	451.8 KB	Display	wwPDB validaton report
Full document	3kev_full_validation.pdf.gz	453.3 KB	Display
Data in XML	3kev_validation.xml.gz	12.6 KB	Display
Data in CIF	3kev_validation.cif.gz	17.6 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/ke/3kev ftp://data.pdbj.org/pub/pdb/validation_reports/ke/3kev	HTTPS FTP

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Related structure data

Similar structure data	4gao-2 1u2w-2 4gao-4 5xhm-d 4gba-1 4cso-4 2lm5-d 3np2-d 4igk-1 1hrs-d Search similar-shape structures by Omokage search (details) Similarity search - Function & homologyF&H Search Similarity search - FunctionF&H Search Similarity search - HomologyF&H Search
Other databases	TargetDB: go.88344

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Links

PDB pages	PDBj / wwPDB / NCBI

Deposited unit

A: Galieria sulfuraria DCUN1 domain-containing protein

hetero molecules

23.5 kDa, 1 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)	36.743, 52.422, 49.113
Angle α, β, γ (deg.)	90.000, 111.170, 90.000
Int Tables number	4
Space group name H-M	P12₁1

#1: Protein	Galieria sulfuraria DCUN1 domain-containing protein Mass: 23325.146 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Galdieria sulphuraria (eukaryote) / Description: Wheat germ cell free / Plasmid: pEU-His-Flexi / Production host: CELL-FREE SYNTHESIS (others) / References: UniProt: D1MPT4*PLUS
#2: Chemical	ChemComp-SO4 / SULFATE ION Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO₄
#3: Chemical	ChemComp-ACT / ACETATE ION Mass: 59.044 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C₂H₃O₂
#4: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 176 / Source method: isolated from a natural source / Formula: H₂O
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

ID	Density Matthews (Å³/Da)	Density % sol (%)
1	1.89	34.95
2

Crystal grow

Temperature (K)	Crystal-ID	Method	pH	Details
293	1	vapor diffusion, sitting drop	5	30% PEG 1500, 100 mM sodium acetate pH 5.0, 150 mM MgCl2, 50 mM NaCl, 5 mM HEPES pH 7.0, 0.3 mM TCEP, VAPOR DIFFUSION, SITTING DROP, temperature 293K
293	2	vapor diffusion, sitting drop	5	27% PEG 1500, 100 mM sodium acetate pH 5.0, 150 mM LiCl2, 50 mM NaCl, 5 mM HEPES pH 7.0, 0.3 mM TCEP, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

Diffraction

ID	Mean temperature (K)	Crystal-ID
1	100	1
2	100	2

Diffraction source

Source	Site	Beamline	ID	Wavelength (Å)
SYNCHROTRON	APS	21-ID-D	1	0.97625
SYNCHROTRON	APS	23-ID-D	2	0.96426, 0.97949, 0.97965, 0.99522

Detector

Type	ID	Detector	Date
MARMOSAIC 300 mm CCD	1	CCD	Oct 12, 2009
MARMOSAIC 300 mm CCD	2	CCD	Oct 18, 2009

Radiation

ID	Monochromator	Protocol	Scattering type	Wavelength-ID
1	Si(111)	SINGLE WAVELENGTH	x-ray	1
2	Si(111)	MAD	x-ray	1

Radiation wavelength

ID	Wavelength (Å)	Relative weight
1	0.97625	1
2	0.96426	1
3	0.97949	1
4	0.97965	1
5	0.99522	1

Reflection

Redundancy: 7.5 % / Av σ(I) over netI: 23.15 / Number: 112798 / R_merge(I) obs: 0.075 / Χ²: 1.24 / D res high: 1.81 Å / D res low: 50 Å / Num. obs: 15091 / % possible obs: 97.7

Diffraction reflection shell

Highest resolution (Å)	Lowest resolution (Å)	% possible obs (%)	ID	R_merge(I) obs	Chi squared	Redundancy
4.91	50	97.5	1	0.08	1.332	7.3
3.9	4.91	99.2	1	0.046	0.88	7.5
3.41	3.9	99	1	0.041	0.892	7.3
3.09	3.41	98.8	1	0.043	0.912	7.3
2.87	3.09	99	1	0.046	0.944	7.4
2.7	2.87	99	1	0.053	1.049	7.4
2.57	2.7	98.4	1	0.061	1.183	7.5
2.46	2.57	98.3	1	0.073	1.262	7.6
2.36	2.46	98.2	1	0.076	1.31	7.7
2.28	2.36	98.2	1	0.076	1.234	7.7
2.21	2.28	99.2	1	0.085	1.289	7.6
2.15	2.21	97.2	1	0.094	1.295	7.7
2.09	2.15	97.7	1	0.105	1.26	7.7
2.04	2.09	98.3	1	0.112	1.346	7.7
1.99	2.04	96.9	1	0.131	1.387	7.7
1.95	1.99	98.8	1	0.132	1.396	7.6
1.91	1.95	96.1	1	0.16	1.46	7.6
1.87	1.91	98.4	1	0.185	1.44	7.5
1.84	1.87	96	1	0.192	1.408	7.4
1.81	1.84	89.7	1	0.231	1.587	6.3

Reflection

Resolution: 1.3→50 Å / Num. all: 42886 / Num. obs: 42243 / % possible obs: 98.5 % / Redundancy: 4 % / R_merge(I) obs: 0.04 / Χ²: 1.012 / Net I/σ(I): 16

Reflection shell

Resolution: 1.3→1.32 Å / Redundancy: 3 % / R_merge(I) obs: 0.388 / Mean I/σ(I) obs: 2.6 / Num. unique all: 1849 / Χ²: 1.114 / % possible all: 87.2

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Phasing

Phasing

Method
MAD
molecular replacement

Phasing MAD set

ID	R cullis acentric	R cullis centric	Highest resolution (Å)	Lowest resolution (Å)	Reflection acentric	Reflection centric
ISO_1	0	0	1.79	34.22	14383	695
ISO_2	0.481	0.488	1.79	34.22	14378	692
ISO_3	0.731	0.734	1.79	34.22	13794	660
ISO_4	0.642	0.67	1.79	34.22	14360	692
ANO_1	0.958	0	1.79	34.22	14323	0
ANO_2	0.974	0	1.79	34.22	14950	0
ANO_3	0.999	0	1.79	34.22	13742	0
ANO_4	0.994	0	1.79	34.22	14418	0

Phasing MAD set shell

ID	Resolution (Å)	R cullis acentric	R cullis centric	Reflection acentric	Reflection centric
ISO_1	7.81-34.22	0	0	158	34
ISO_1	5.6-7.81	0	0	304	39
ISO_1	4.59-5.6	0	0	398	37
ISO_1	3.98-4.59	0	0	469	39
ISO_1	3.57-3.98	0	0	535	37
ISO_1	3.26-3.57	0	0	591	40
ISO_1	3.02-3.26	0	0	637	34
ISO_1	2.83-3.02	0	0	708	35
ISO_1	2.67-2.83	0	0	735	39
ISO_1	2.53-2.67	0	0	774	34
ISO_1	2.41-2.53	0	0	817	35
ISO_1	2.31-2.41	0	0	871	37
ISO_1	2.22-2.31	0	0	899	36
ISO_1	2.14-2.22	0	0	922	31
ISO_1	2.07-2.14	0	0	961	33
ISO_1	2-2.07	0	0	992	38
ISO_1	1.94-2	0	0	1017	31
ISO_1	1.89-1.94	0	0	1058	41
ISO_1	1.84-1.89	0	0	1075	26
ISO_1	1.79-1.84	0	0	462	19
ANO_1	7.81-34.22	0.769	0	157	0
ANO_1	5.6-7.81	0.66	0	304	0
ANO_1	4.59-5.6	0.807	0	398	0
ANO_1	3.98-4.59	0.868	0	469	0
ANO_1	3.57-3.98	0.872	0	531	0
ANO_1	3.26-3.57	0.894	0	587	0
ANO_1	3.02-3.26	0.858	0	633	0
ANO_1	2.83-3.02	0.88	0	706	0
ANO_1	2.67-2.83	0.888	0	733	0
ANO_1	2.53-2.67	0.923	0	772	0
ANO_1	2.41-2.53	0.937	0	817	0
ANO_1	2.31-2.41	0.965	0	871	0
ANO_1	2.22-2.31	0.973	0	898	0
ANO_1	2.14-2.22	0.984	0	922	0
ANO_1	2.07-2.14	0.99	0	959	0
ANO_1	2-2.07	0.992	0	992	0
ANO_1	1.94-2	0.995	0	1016	0
ANO_1	1.89-1.94	0.997	0	1057	0
ANO_1	1.84-1.89	0.998	0	1072	0
ANO_1	1.79-1.84	0.999	0	429	0
ISO_2	7.81-34.22	0.57	0.871	155	34
ISO_2	5.6-7.81	0.43	0.537	304	39
ISO_2	4.59-5.6	0.459	0.43	398	37
ISO_2	3.98-4.59	0.417	0.389	469	39
ISO_2	3.57-3.98	0.445	0.275	535	37
ISO_2	3.26-3.57	0.359	0.398	591	40
ISO_2	3.02-3.26	0.329	0.399	637	34
ISO_2	2.83-3.02	0.339	0.333	708	35
ISO_2	2.67-2.83	0.357	0.432	735	39
ISO_2	2.53-2.67	0.353	0.406	774	34
ISO_2	2.41-2.53	0.355	0.4	817	35
ISO_2	2.31-2.41	0.4	0.414	871	37
ISO_2	2.22-2.31	0.406	0.58	899	36
ISO_2	2.14-2.22	0.455	0.57	922	31
ISO_2	2.07-2.14	0.487	0.619	961	33
ISO_2	2-2.07	0.516	0.66	992	38
ISO_2	1.94-2	0.53	0.57	1017	31
ISO_2	1.89-1.94	0.577	0.551	1058	41
ISO_2	1.84-1.89	0.634	0.65	1074	24
ISO_2	1.79-1.84	0.599	0.458	461	18
ANO_2	7.81-34.22	0.786	0	152	0
ANO_2	5.6-7.81	0.674	0	304	0
ANO_2	4.59-5.6	0.808	0	398	0
ANO_2	3.98-4.59	0.887	0	469	0
ANO_2	3.57-3.98	0.881	0	535	0
ANO_2	3.26-3.57	0.884	0	590	0
ANO_2	3.02-3.26	0.891	0	640	0
ANO_2	2.83-3.02	0.901	0	708	0
ANO_2	2.67-2.83	0.907	0	735	0
ANO_2	2.53-2.67	0.944	0	774	0
ANO_2	2.41-2.53	0.957	0	817	0
ANO_2	2.31-2.41	0.977	0	870	0
ANO_2	2.22-2.31	0.982	0	899	0
ANO_2	2.14-2.22	0.99	0	923	0
ANO_2	2.07-2.14	0.994	0	963	0
ANO_2	2-2.07	0.996	0	992	0
ANO_2	1.94-2	0.997	0	1016	0
ANO_2	1.89-1.94	0.998	0	1058	0
ANO_2	1.84-1.89	0.999	0	1075	0
ANO_2	1.79-1.84	1.001	0	1032	0
ISO_3	7.81-34.22	0.77	0.841	144	33
ISO_3	5.6-7.81	0.743	0.778	304	38
ISO_3	4.59-5.6	0.725	0.677	398	37
ISO_3	3.98-4.59	0.7	0.693	469	39
ISO_3	3.57-3.98	0.707	0.673	535	37
ISO_3	3.26-3.57	0.706	0.731	590	40
ISO_3	3.02-3.26	0.704	0.701	637	34
ISO_3	2.83-3.02	0.713	0.675	708	35
ISO_3	2.67-2.83	0.702	0.752	735	39
ISO_3	2.53-2.67	0.71	0.803	774	34
ISO_3	2.41-2.53	0.705	0.751	817	35
ISO_3	2.31-2.41	0.718	0.69	870	37
ISO_3	2.22-2.31	0.713	0.777	899	36
ISO_3	2.14-2.22	0.735	0.802	922	31
ISO_3	2.07-2.14	0.746	0.721	961	33
ISO_3	2-2.07	0.76	0.833	992	38
ISO_3	1.94-2	0.771	0.713	1017	29
ISO_3	1.89-1.94	0.796	0.849	1050	38
ISO_3	1.84-1.89	0.855	0.711	970	16
ISO_3	1.79-1.84	1.376	0.969	2	1
ANO_3	7.81-34.22	0.969	0	142	0
ANO_3	5.6-7.81	0.948	0	304	0
ANO_3	4.59-5.6	0.972	0	397	0
ANO_3	3.98-4.59	0.982	0	469	0
ANO_3	3.57-3.98	0.989	0	534	0
ANO_3	3.26-3.57	0.983	0	589	0
ANO_3	3.02-3.26	0.989	0	641	0
ANO_3	2.83-3.02	0.998	0	708	0
ANO_3	2.67-2.83	0.999	0	736	0
ANO_3	2.53-2.67	0.999	0	774	0
ANO_3	2.41-2.53	0.999	0	817	0
ANO_3	2.31-2.41	0.999	0	870	0
ANO_3	2.22-2.31	0.999	0	899	0
ANO_3	2.14-2.22	1	0	921	0
ANO_3	2.07-2.14	1	0	960	0
ANO_3	2-2.07	1	0	991	0
ANO_3	1.94-2	1	0	1016	0
ANO_3	1.89-1.94	1	0	1044	0
ANO_3	1.84-1.89	1	0	929	0
ANO_3	1.79-1.84	1	0	1	0
ISO_4	7.81-34.22	0.777	0.863	141	32
ISO_4	5.6-7.81	0.713	0.776	304	39
ISO_4	4.59-5.6	0.66	0.607	398	37
ISO_4	3.98-4.59	0.599	0.621	468	39
ISO_4	3.57-3.98	0.597	0.592	535	37
ISO_4	3.26-3.57	0.593	0.646	589	40
ISO_4	3.02-3.26	0.595	0.61	637	34
ISO_4	2.83-3.02	0.613	0.541	708	35
ISO_4	2.67-2.83	0.6	0.65	735	39
ISO_4	2.53-2.67	0.615	0.734	774	34
ISO_4	2.41-2.53	0.611	0.615	817	35
ISO_4	2.31-2.41	0.624	0.611	871	37
ISO_4	2.22-2.31	0.611	0.648	899	36
ISO_4	2.14-2.22	0.643	0.751	922	31
ISO_4	2.07-2.14	0.647	0.654	961	33
ISO_4	2-2.07	0.665	0.732	992	38
ISO_4	1.94-2	0.671	0.654	1017	31
ISO_4	1.89-1.94	0.703	0.743	1057	41
ISO_4	1.84-1.89	0.767	0.785	1075	26
ISO_4	1.79-1.84	0.816	0.737	460	18
ANO_4	7.81-34.22	0.897	0	138	0
ANO_4	5.6-7.81	0.771	0	304	0
ANO_4	4.59-5.6	0.901	0	396	0
ANO_4	3.98-4.59	0.939	0	466	0
ANO_4	3.57-3.98	0.936	0	534	0
ANO_4	3.26-3.57	0.944	0	588	0
ANO_4	3.02-3.26	0.958	0	640	0
ANO_4	2.83-3.02	0.955	0	709	0
ANO_4	2.67-2.83	0.987	0	735	0
ANO_4	2.53-2.67	0.982	0	774	0
ANO_4	2.41-2.53	0.989	0	817	0
ANO_4	2.31-2.41	0.99	0	871	0
ANO_4	2.22-2.31	0.996	0	899	0
ANO_4	2.14-2.22	0.997	0	922	0
ANO_4	2.07-2.14	0.998	0	963	0
ANO_4	2-2.07	0.999	0	992	0
ANO_4	1.94-2	0.999	0	1017	0
ANO_4	1.89-1.94	1	0	1057	0
ANO_4	1.84-1.89	1	0	1068	0
ANO_4	1.79-1.84	1	0	528	0

Phasing MAD set site

Cartn x: 5.162 Å / Cartn y: 0.052 Å / Cartn z: 12.191 Å / Atom type symbol: SE / B iso: 36.84 / Occupancy: 0.83

Phasing MR

	Highest resolution	Lowest resolution
Rotation	1.6 Å	20.99 Å
Translation	1.6 Å	20.99 Å

Phasing dm

Method: Solvent flattening and Histogram matching / Reflection: 15703

Phasing dm shell

Resolution (Å)	Delta phi final	FOM	Reflection
5.72-100	54	0.782	504
4.53-5.72	47.6	0.915	502
3.94-4.53	54.5	0.914	515
3.59-3.94	55.6	0.914	506
3.32-3.59	60.4	0.878	503
3.13-3.32	71.6	0.878	504
2.97-3.13	62.4	0.861	507
2.84-2.97	70.7	0.882	516
2.72-2.84	63.5	0.875	519
2.62-2.72	68.7	0.881	532
2.53-2.62	63.7	0.876	572
2.45-2.53	69.6	0.877	573
2.38-2.45	66.7	0.865	608
2.31-2.38	67.7	0.876	620
2.24-2.31	70.4	0.86	620
2.19-2.24	71.5	0.875	652
2.13-2.19	70.2	0.886	666
2.08-2.13	73.2	0.865	679
2.04-2.08	75.1	0.858	685
1.99-2.04	75.2	0.867	726
1.95-1.99	76.6	0.848	733
1.91-1.95	80.3	0.833	694
1.88-1.91	81.8	0.81	792
1.84-1.88	85.4	0.791	730
1.79-1.84	87.2	0.743	1245

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Processing

Software

Name	Version	Classification
DENZO		data reduction
SCALEPACK		data scaling
MOLREP		phasing
SHARP		phasing
DM	6.1	phasing
PHENIX	1.5_2	refinement
PDB_EXTRACT	3.005	data extraction
HKL-2000		data collection
HKL-2000		data scaling

Refinement

Method to determine structure:

MAD,

molecular replacement / Resolution: 1.3→20.984 Å / Occupancy max: 1.4 / Occupancy min: 0.19 / FOM work R set: 0.922 / SU ML: 0.16 / σ(F): 1.35 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.178	2111	5.01 %	random
R_work	0.155	-	-	-
all	0.156	42820	-	-
obs	0.156	42161	98.46 %	-

Solvent computation

Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / B_sol: 60.058 Å² / k_sol: 0.4 e/Å³

Displacement parameters

B_iso max: 52.77 Å² / B_iso mean: 20.012 Å² / B_iso min: 7.22 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	-1.285 Å²	-0 Å²	2.593 Å²
2-	-	-2.06 Å²	-0 Å²
3-	-	-	3.345 Å²

Refinement step

Cycle: LAST / Resolution: 1.3→20.984 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	1525	0	13	176	1714

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.018	1800
X-RAY DIFFRACTION	f_angle_d	1.566	2465
X-RAY DIFFRACTION	f_chiral_restr	0.101	259
X-RAY DIFFRACTION	f_plane_restr	0.007	328
X-RAY DIFFRACTION	f_dihedral_angle_d	17.426	679

LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 15

Resolution (Å)	R_factor R_free	Num. reflection R_free	R_factor R_work	Num. reflection R_work	Num. reflection all	% reflection obs (%)
1.3-1.33	0.197	124	0.183	2388	2512	88
1.33-1.363	0.21	143	0.173	2599	2742	96
1.363-1.4	0.2	148	0.156	2640	2788	99
1.4-1.442	0.194	141	0.147	2687	2828	100
1.442-1.488	0.192	126	0.134	2741	2867	100
1.488-1.541	0.163	161	0.122	2669	2830	100
1.541-1.603	0.16	139	0.116	2717	2856	100
1.603-1.676	0.178	137	0.113	2709	2846	100
1.676-1.764	0.125	137	0.116	2696	2833	100
1.764-1.875	0.172	144	0.118	2710	2854	100
1.875-2.019	0.153	133	0.13	2706	2839	100
2.019-2.222	0.143	138	0.125	2723	2861	100
2.222-2.543	0.178	139	0.142	2718	2857	100
2.543-3.203	0.186	151	0.159	2729	2880	100
3.203-20.987	0.171	150	0.169	2618	2768	94

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