PDB-2nyi: Crystal Structure of an Unknown Protein from Galdieria sulphuraria

ID or keywords:

Entry

Database: PDB / ID: 2nyi

Title

Crystal Structure of an Unknown Protein from Galdieria sulphuraria

Components

unknown protein

Keywords

STRUCTURAL GENOMICS / UNKNOWN FUNCTION / Protein Structure Initiative / PSI / Center for Eukaryotic Structural Genomics / CESG

Function / homology

Function and homology information

: / ACT domain / ACT domain / ACT domain profile. / ACT domain / ACT-like domain / Alpha-Beta Plaits / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology

Biological species

Galdieria sulphuraria (eukaryote)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MAD / Resolution: 1.8 Å

Authors

Bitto, E. / Wesenberg, G.E. / Phillips Jr., G.N. / McCoy, J.G. / Bingman, C.A. / Center for Eukaryotic Structural Genomics (CESG)

Citation

Journal: Proteins / Year: 2012
Title: Crystal structure of tandem ACT domain-containing protein ACTP from Galdieria sulphuraria.
Authors: Bitto, E. / Kim, D.J. / Bingman, C.A. / Kim, H.J. / Han, B.W. / Phillips, G.N.

History

Deposition	Nov 20, 2006	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Dec 12, 2006	Provider: repository / Type: Initial release
Revision 1.1	May 1, 2008	Group: Version format compliance
Revision 1.2	Jul 13, 2011	Group: Version format compliance
Revision 1.3	Jul 25, 2012	Group: Database references
Revision 1.4	Oct 18, 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 1.5	Dec 27, 2023	Group: Data collection / Database references / Derived calculations Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_conn Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag
Revision 1.6	Nov 13, 2024	Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

Remark 999

SEQUENCE THE SEQUENCE OF THIS PROTEIN WAS NOT AVAILABLE AT THE UNIPROT SEQUENCE DATABASE AT THE ...

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	2nyi.cif.gz	89.5 KB	Display	PDBx/mmCIF format
PDB format	pdb2nyi.ent.gz	65.9 KB	Display	PDB format
PDBx/mmJSON format	2nyi.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	2nyi_validation.pdf.gz	427.3 KB	Display	wwPDB validaton report
Full document	2nyi_full_validation.pdf.gz	429.4 KB	Display
Data in XML	2nyi_validation.xml.gz	18 KB	Display
Data in CIF	2nyi_validation.cif.gz	27.2 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/ny/2nyi ftp://data.pdbj.org/pub/pdb/validation_reports/ny/2nyi	HTTPS FTP

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Related structure data

Similar structure data	1p1m-d 6c3i-1 4pun-d 4l56-d 3e7d-2 1p4o-2 5ulj-1 6imw-1 4nrw-2 1wkf-d Search similar-shape structures by Omokage search (details) Similarity search - Function & homologyF&H Search Similarity search - HomologyF&H Search
Other databases	TargetDB: GO.80004

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Links

PDB pages	PDBj / wwPDB / NCBI
Related items in Molecule of the Month	#61 - Jan 2005 Phenylalanine Hydroxylase similarity (2) #263 - Nov 2021 Acetohydroxyacid Synthase similarity (2)

Deposited unit

A: unknown protein

B: unknown protein

42.4 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)	55.013, 79.991, 55.530
Angle α, β, γ (deg.)	90.000, 111.250, 90.000
Int Tables number	4
Space group name H-M	P12₁1

Details

biological unit appeats to be a dimer (chains A & B) in the asymmetric unit

#1: Protein	unknown protein Mass: 21212.041 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Galdieria sulphuraria (eukaryote) / Gene: c855_101305g34.t1(MSU_Galdi) / Plasmid: PVP16 / Production host: Escherichia coli (E. coli) / Strain (production host): B834P(RARE2) / References: UniProt: J3QW32*PLUS
#2: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 370 / 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	Density Matthews: 2.68 Å³/Da / Density % sol: 54.16 %
Crystal grow	Temperature: 293 K / Method: vapor diffusion, hanging drop Details: Protein solution (10 mg/mL protein, 0.050 M Sodium chloride, 0.0003 M TCEP, 0.005 M MES pH 6.0) mixed in a 1:1 ratio with the well solution (24% PEG 8000, 0.04 M Magnesium chloride, 0.2 M ...Details: Protein solution (10 mg/mL protein, 0.050 M Sodium chloride, 0.0003 M TCEP, 0.005 M MES pH 6.0) mixed in a 1:1 ratio with the well solution (24% PEG 8000, 0.04 M Magnesium chloride, 0.2 M Sodium fluoride, 0.10 M PIPES pH 6.5). Cryoprotection: well solution supplemented with up to 20% ethylene glycol, vapor diffusion, hanging drop, temperature 293K

Crystal

Density Matthews: 2.68 Å³/Da / Density % sol: 54.16 %

Crystal grow

Temperature: 293 K / Method: vapor diffusion, hanging drop
Details: Protein solution (10 mg/mL protein, 0.050 M Sodium chloride, 0.0003 M TCEP, 0.005 M MES pH 6.0) mixed in a 1:1 ratio with the well solution (24% PEG 8000, 0.04 M Magnesium chloride, 0.2 M ...

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Data collection

Diffraction

Mean temperature: 100 K

Diffraction source

Source:

SYNCHROTRON / Site:

APS

/ Beamline: 23-ID-D / Wavelength: 0.97923, 0.96400

Detector

Type: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Nov 8, 2006 / Details: Adjustable focusing mirrors in K-B geometry

Radiation

Monochromator: Si(111) Double Crystal Monochromator / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray

Radiation wavelength

ID	Wavelength (Å)	Relative weight
1	0.97923	1
2	0.964	1

Reflection

Resolution: 1.8→45.62 Å / Num. obs: 39789 / % possible obs: 96.3 % / Redundancy: 7.4 % / R_merge(I) obs: 0.071 / Χ²: 1.131 / Net I/σ(I): 11.673

Reflection shell

Diffraction-ID: 1

Resolution (Å)	Redundancy (%)	R_merge(I) obs	Mean I/σ(I) obs	Num. unique all	Χ²	% possible all
1.8-1.84	4.9	0.419	2.656	2291	0.99	83.2
1.84-1.89	5.9	0.363		2493	0.995	91.5
1.89-1.94	6.6	0.343		2610	1.21	94.6
1.94-2	7.3	0.252		2617	1.074	96.4
2-2.06	7.6	0.202		2691	1.07	97
2.06-2.13	7.8	0.172		2648	1.077	97.1
2.13-2.22	7.8	0.139		2682	1.11	97.5
2.22-2.32	7.8	0.128		2669	1.104	97.7
2.32-2.44	7.8	0.114		2678	1.122	97.9
2.44-2.6	7.8	0.094		2724	1.19	98.2
2.6-2.8	7.8	0.079		2691	1.169	98.1
2.8-3.08	7.8	0.069		2730	1.22	98.5
3.08-3.52	7.7	0.053		2718	1.116	98.8
3.52-4.44	7.7	0.045		2745	1.122	98.8
4.44-45.616	7.6	0.051		2802	1.28	99

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Phasing

Phasing

Method:

MAD

Phasing MAD set

Highest resolution: 2 Å / Lowest resolution: 45.62 Å

ID	R cullis acentric	R cullis centric	Power acentric	Power centric	Reflection acentric	Reflection centric
ISO_1	0	0	0	0	28795	986
ISO_2	0.837	0.825	0.9	0.73	28775	982
ANO_1	0.62	0	1.833	0	28765	0
ANO_2	0.815	0	0.979	0	28755	0

Phasing MAD set shell

ID	Resolution (Å)	R cullis acentric	R cullis centric	Power acentric	Power centric	Reflection acentric	Reflection centric
ISO_1	8.79-45.62	0	0	0	0	311	52
ISO_1	6.27-8.79	0	0	0	0	595	50
ISO_1	5.14-6.27	0	0	0	0	761	54
ISO_1	4.46-5.14	0	0	0	0	908	54
ISO_1	3.99-4.46	0	0	0	0	1025	44
ISO_1	3.64-3.99	0	0	0	0	1137	54
ISO_1	3.37-3.64	0	0	0	0	1235	48
ISO_1	3.16-3.37	0	0	0	0	1340	50
ISO_1	2.98-3.16	0	0	0	0	1399	49
ISO_1	2.83-2.98	0	0	0	0	1505	50
ISO_1	2.69-2.83	0	0	0	0	1556	51
ISO_1	2.58-2.69	0	0	0	0	1658	52
ISO_1	2.48-2.58	0	0	0	0	1682	45
ISO_1	2.39-2.48	0	0	0	0	1784	49
ISO_1	2.31-2.39	0	0	0	0	1832	44
ISO_1	2.24-2.31	0	0	0	0	1927	47
ISO_1	2.17-2.24	0	0	0	0	1926	50
ISO_1	2.11-2.17	0	0	0	0	2010	49
ISO_1	2.05-2.11	0	0	0	0	2073	44
ISO_1	2-2.05	0	0	0	0	2131	50
ANO_1	8.79-45.62	0.493	0	2.578	0	309	0
ANO_1	6.27-8.79	0.389	0	3.335	0	595	0
ANO_1	5.14-6.27	0.446	0	2.954	0	761	0
ANO_1	4.46-5.14	0.551	0	2.386	0	907	0
ANO_1	3.99-4.46	0.475	0	2.695	0	1023	0
ANO_1	3.64-3.99	0.525	0	2.495	0	1136	0
ANO_1	3.37-3.64	0.546	0	2.319	0	1233	0
ANO_1	3.16-3.37	0.478	0	2.518	0	1339	0
ANO_1	2.98-3.16	0.507	0	2.386	0	1396	0
ANO_1	2.83-2.98	0.504	0	2.347	0	1505	0
ANO_1	2.69-2.83	0.55	0	2.119	0	1555	0
ANO_1	2.58-2.69	0.597	0	1.9	0	1656	0
ANO_1	2.48-2.58	0.638	0	1.703	0	1680	0
ANO_1	2.39-2.48	0.675	0	1.514	0	1782	0
ANO_1	2.31-2.39	0.723	0	1.332	0	1831	0
ANO_1	2.24-2.31	0.785	0	1.103	0	1927	0
ANO_1	2.17-2.24	0.813	0	1.035	0	1924	0
ANO_1	2.11-2.17	0.857	0	0.893	0	2008	0
ANO_1	2.05-2.11	0.89	0	0.765	0	2072	0
ANO_1	2-2.05	0.904	0	0.685	0	2126	0
ISO_2	8.79-45.62	0.636	0.542	1.543	0.979	310	52
ISO_2	6.27-8.79	0.662	0.667	1.673	1.308	595	50
ISO_2	5.14-6.27	0.745	0.839	1.379	0.964	761	54
ISO_2	4.46-5.14	0.791	0.833	1.183	1.105	908	54
ISO_2	3.99-4.46	0.823	0.927	1.019	0.577	1025	43
ISO_2	3.64-3.99	0.847	0.856	0.895	0.627	1137	54
ISO_2	3.37-3.64	0.844	0.877	0.802	0.568	1235	48
ISO_2	3.16-3.37	0.865	0.972	0.916	0.712	1340	49
ISO_2	2.98-3.16	0.841	0.891	0.864	0.614	1399	49
ISO_2	2.83-2.98	0.858	0.929	0.917	0.722	1505	50
ISO_2	2.69-2.83	0.871	0.903	0.885	0.558	1555	51
ISO_2	2.58-2.69	0.861	0.798	0.83	0.527	1658	51
ISO_2	2.48-2.58	0.881	0.87	0.795	0.525	1681	45
ISO_2	2.39-2.48	0.877	1.013	0.767	0.511	1783	49
ISO_2	2.31-2.39	0.889	1.02	0.709	0.498	1832	44
ISO_2	2.24-2.31	0.882	0.96	0.613	0.441	1922	47
ISO_2	2.17-2.24	0.884	0.974	0.545	0.446	1924	50
ISO_2	2.11-2.17	0.884	0.925	0.497	0.383	2008	49
ISO_2	2.05-2.11	0.883	0.907	0.444	0.316	2068	43
ISO_2	2-2.05	0.889	0.92	0.409	0.252	2129	50
ANO_2	8.79-45.62	0.595	0	1.69	0	310	0
ANO_2	6.27-8.79	0.486	0	2.329	0	595	0
ANO_2	5.14-6.27	0.522	0	2.196	0	761	0
ANO_2	4.46-5.14	0.628	0	1.795	0	908	0
ANO_2	3.99-4.46	0.61	0	1.794	0	1021	0
ANO_2	3.64-3.99	0.657	0	1.681	0	1137	0
ANO_2	3.37-3.64	0.704	0	1.515	0	1234	0
ANO_2	3.16-3.37	0.668	0	1.495	0	1340	0
ANO_2	2.98-3.16	0.705	0	1.349	0	1397	0
ANO_2	2.83-2.98	0.716	0	1.335	0	1504	0
ANO_2	2.69-2.83	0.775	0	1.079	0	1554	0
ANO_2	2.58-2.69	0.838	0	0.885	0	1658	0
ANO_2	2.48-2.58	0.869	0	0.785	0	1680	0
ANO_2	2.39-2.48	0.894	0	0.716	0	1782	0
ANO_2	2.31-2.39	0.92	0	0.606	0	1831	0
ANO_2	2.24-2.31	0.937	0	0.482	0	1921	0
ANO_2	2.17-2.24	0.955	0	0.441	0	1924	0
ANO_2	2.11-2.17	0.97	0	0.378	0	2008	0
ANO_2	2.05-2.11	0.98	0	0.319	0	2068	0
ANO_2	2-2.05	0.984	0	0.293	0	2122	0

Phasing MAD set site

ID	Cartn x (Å)	Cartn y (Å)	Cartn z (Å)	Atom type symbol	B iso	Occupancy
1	-15.25	-37.756	-26.212	SE	18.18	1.56
2	-11.547	-0.474	-20.772	SE	34.8	1.87
3	-13.175	-40.016	-31.075	SE	36.5	2.01
4	-3.025	-29.132	-34.591	SE	20.7	1.33
5	-4.309	-26.117	-43.709	SE	31.3	1.23
6	-8.231	-26.81	-34.392	SE	32.48	1.34

Phasing dm

Method: Solvent flattening and Histogram matching / Reflection: 29781

Phasing dm shell

Resolution (Å)	Delta phi final	FOM	Reflection
7.9-100	49.2	0.859	501
6.26-7.9	48.2	0.926	511
5.42-6.26	48.4	0.94	541
4.85-5.42	50.6	0.949	597
4.43-4.85	50.9	0.954	680
4.1-4.43	51.2	0.943	740
3.83-4.1	52.8	0.952	781
3.61-3.83	52	0.956	802
3.43-3.61	52	0.947	884
3.27-3.43	49.8	0.947	910
3.13-3.27	52.5	0.943	961
3.01-3.13	54.1	0.946	1022
2.9-3.01	51.4	0.931	1013
2.8-2.9	55	0.933	1082
2.71-2.8	56.5	0.935	1103
2.63-2.71	54.1	0.929	1124
2.56-2.63	59.5	0.921	1192
2.49-2.56	58.7	0.925	1180
2.42-2.49	58.2	0.927	1227
2.37-2.42	59.6	0.924	1282
2.31-2.37	59.5	0.927	1273
2.26-2.31	60.3	0.915	1329
2.21-2.26	63.7	0.923	1328
2.17-2.21	64.5	0.925	1397
2.13-2.17	67.9	0.914	1385
2.09-2.13	67.2	0.911	1438
2.05-2.09	71	0.893	1447
2-2.05	73	0.839	2051

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Processing

Software

Name	Version	Classification
DENZO		data reduction
SCALEPACK		data scaling
SHARP		phasing
DM	5	phasing
REFMAC	5.2.0005	refinement
PDB_EXTRACT	2	data extraction
MAR345	300	data collection
HKL-2000		data reduction

Refinement

Method to determine structure:

MAD / Resolution: 1.8→45.62 Å / Cor.coef. F_o:F_c: 0.961 / Cor.coef. F_o:F_c free: 0.945 / WR_factor R_free: 0.222 / WR_factor R_work: 0.182 / SU B: 4.556 / SU ML: 0.072 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.112 / ESU R Free: 0.113 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.214	2027	5.1 %	RANDOM
R_work	0.176	-	-	-
all	0.178	39742	-	-
obs	0.178	39742	96.021 %	-

Solvent computation

Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT

Displacement parameters

B_iso mean: 27.458 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	0.248 Å²	0 Å²	0.362 Å²
2-	-	0.326 Å²	0 Å²
3-	-	-	-0.312 Å²

Refinement step

Cycle: LAST / Resolution: 1.8→45.62 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	2589	0	0	370	2959

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.017	0.022	2687
X-RAY DIFFRACTION	r_angle_refined_deg	1.287	1.966	3658
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	5.621	5	353
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	34.269	24.348	115
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	12.62	15	441
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	17.258	15	17
X-RAY DIFFRACTION	r_chiral_restr	0.096	0.2	431
X-RAY DIFFRACTION	r_gen_planes_refined	0.005	0.02	2035
X-RAY DIFFRACTION	r_nbd_refined	0.2	0.2	1229
X-RAY DIFFRACTION	r_nbtor_refined	0.299	0.2	1896
X-RAY DIFFRACTION	r_xyhbond_nbd_refined	0.16	0.2	280
X-RAY DIFFRACTION	r_symmetry_vdw_refined	0.156	0.2	72
X-RAY DIFFRACTION	r_symmetry_hbond_refined	0.177	0.2	26
X-RAY DIFFRACTION	r_mcbond_it	1.446	2	1792
X-RAY DIFFRACTION	r_mcangle_it	2.677	5	2801
X-RAY DIFFRACTION	r_scbond_it	6.255	10	1012
X-RAY DIFFRACTION	r_scangle_it	8.885	15	854

LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20

Resolution (Å)	R_factor R_free	Num. reflection R_free	R_factor R_work	Num. reflection R_work	Num. reflection all	% reflection obs (%)
1.8-1.85	0.307	127	0.24	2329	3044	80.683
1.849-1.9	0.253	135	0.212	2600	2983	91.686
1.9-1.955	0.282	137	0.217	2582	2860	95.07
1.955-2.015	0.254	138	0.175	2575	2804	96.755
2.015-2.081	0.211	142	0.167	2492	2718	96.909
2.081-2.154	0.2	135	0.169	2427	2635	97.23
2.154-2.235	0.22	130	0.165	2333	2531	97.313
2.235-2.326	0.208	103	0.176	2293	2454	97.637
2.326-2.429	0.212	124	0.187	2185	2360	97.839
2.429-2.548	0.191	99	0.184	2078	2222	97.975
2.548-2.685	0.248	104	0.179	2007	2149	98.232
2.685-2.848	0.229	106	0.177	1894	2034	98.328
2.848-3.044	0.213	97	0.179	1786	1910	98.586
3.044-3.287	0.229	95	0.167	1644	1766	98.471
3.287-3.599	0.187	84	0.158	1532	1635	98.838
3.599-4.021	0.192	77	0.16	1386	1480	98.851
4.021-4.639	0.16	62	0.156	1241	1318	98.862
4.639-5.67	0.217	52	0.164	1054	1112	99.46
5.67-7.97	0.245	58	0.228	813	875	99.543
7.97-45.616	0.207	22	0.191	464	499	97.395

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Yorodumi