PDB-1zxu: X-ray structure of protein from arabidopsis thaliana AT5G01750

ID or keywords:

Entry

Database: PDB / ID: 1zxu

Title

X-ray structure of protein from arabidopsis thaliana AT5G01750

Components

At5g01750 protein

Keywords

STRUCTURAL GENOMICS / UNKNOWN FUNCTION / AT5G01750 / PFAM PF01167 / TULP / PROTEIN STRUCTURE INITIATIVE / PSI / CENTER FOR EUKARYOTIC STRUCTURAL GENOMICS / CESG

Function / homology

Function and homology information

protein domain specific binding / plasma membrane / cytosol
Similarity search - Function

Biological species

Arabidopsis thaliana (thale cress)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MAD / Resolution: 1.7 Å

Authors

Wesenberg, G.E. / Phillips Jr., G.N. / Bitto, E. / Bingman, C.A. / Allard, S.T.M. / Center for Eukaryotic Structural Genomics (CESG)

Citation

Journal: To be published
Title: X-ray structure of protein from arabidopsis thaliana AT5G01750
Authors: Center for Eukaryotic Structural Genomics (CESG)

History

Deposition	Jun 8, 2005	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Jun 21, 2005	Provider: repository / Type: Initial release
Revision 1.1	Feb 1, 2008	Group: Version format compliance
Revision 1.2	Jul 13, 2011	Group: Version format compliance
Revision 1.3	Oct 11, 2017	Group: Refinement description / Category: software
Revision 1.4	Jan 24, 2018	Group: Database references / Category: citation_author / Item: _citation_author.name
Revision 1.5	Nov 20, 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_ref_seq_dif / 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_ref_seq_dif.details / _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	1zxu.cif.gz	52.6 KB	Display	PDBx/mmCIF format
PDB format	pdb1zxu.ent.gz	34 KB	Display	PDB format
PDBx/mmJSON format	1zxu.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	1zxu_validation.pdf.gz	442.2 KB	Display	wwPDB validaton report
Full document	1zxu_full_validation.pdf.gz	443.7 KB	Display
Data in XML	1zxu_validation.xml.gz	11 KB	Display
Data in CIF	1zxu_validation.cif.gz	14.4 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/zx/1zxu ftp://data.pdbj.org/pub/pdb/validation_reports/zx/1zxu	HTTPS FTP

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Related structure data

Similar structure data	2q4m-d 4hio-d 3g7x-2 3hbw-2 5brj-d 4hj7-d 1twe-d 1cwf-d 6izk-1 5r8c-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.24556

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Links

PDB pages	PDBj / wwPDB / NCBI

Deposited unit

A: At5g01750 protein

hetero molecules

24.8 kDa, 1 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

Idetical with deposited unit
defined by author

Unit cell

Length a, b, c (Å)	41.066, 57.499, 75.359
Angle α, β, γ (deg.)	90.00, 90.00, 90.00
Int Tables number	19
Space group name H-M	P2₁2₁2₁

#1: Protein	At5g01750 protein Mass: 24702.094 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Arabidopsis thaliana (thale cress) / Gene: AT5G01750 / Plasmid: PVP-13 / Production host: Escherichia coli (E. coli) / Strain (production host): BL834(DE3) PLACI+RARE / References: UniProt: Q9LZX1
#2: Chemical	ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C₂H₆O₂
#3: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 127 / 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: 2.5 Å³/Da / Density % sol: 50.2 %
Crystal grow	Temperature: 293 K / Method: batch seeding / pH: 5.5 Details: 10 MG/ML PROTEIN, 25% PEG 3350, 0.2 M AMMONIUM ACETATE, 0.1 M BISTRIS, temperature 293K, pH 5.5, BATCH SEEDING

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Data collection

Diffraction

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

Diffraction source

Source:

SYNCHROTRON / Site:

NSLS

/ Beamline: X29A / Wavelength: 0.97900, 0.96110

Detector

Type: ADSC / Detector: CCD / Date: May 25, 2005
Details: HORIZONTAL SAGITALLY FOCUSING 2ND BENT MONOCHROMATOR CRYSTAL, VERTICAL BENT FOCUSING MIRROR

Radiation

Monochromator: CRYOGENICALLY COOLED SI (111) DOUBLE BOUNCE / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray

Radiation wavelength

ID	Wavelength (Å)	Relative weight
1	0.979	1
2	0.9611	1

Reflection

D res high: 1.7 Å / D res low: 50 Å

Redundancy (%)	ID	Number	R_merge(I) obs	Χ²	% possible obs
13.6	1	20314	0.08	1.535	100
12.3	2	20052	0.078	1.278	97.3

Diffraction reflection shell

Highest resolution (Å)	Lowest resolution (Å)	% possible obs (%)	ID	R_merge(I) obs	Chi squared	Redundancy
3.66	50	99.8	1	0.058	1.784	12.9
2.91	3.66	100	1	0.071	1.724	13.7
2.54	2.91	100	1	0.086	1.877	13.9
2.31	2.54	100	1	0.097	1.814	14.1
2.14	2.31	100	1	0.105	1.616	14.2
2.02	2.14	100	1	0.128	1.585	14.2
1.91	2.02	100	1	0.169	1.421	14.2
1.83	1.91	100	1	0.241	1.276	14.2
1.76	1.83	100	1	0.342	1.097	13.4
1.7	1.76	99.9	1	0.454	0.995	11.1
3.66	50	99.8	2	0.049	1.04	13
2.91	3.66	100	2	0.072	1.284	13.8
2.54	2.91	100	2	0.091	1.367	14
2.31	2.54	100	2	0.12	1.461	14.2
2.14	2.31	100	2	0.149	1.524	14.1
2.02	2.14	100	2	0.203	1.433	14.2
1.91	2.02	100	2	0.295	1.22	13.9
1.83	1.91	99.9	2	0.43	1.082	11.8
1.76	1.83	96.8	2	0.567	0.944	7.5
1.7	1.76	76.4	2	0.674	0.897	4.2

Reflection

Resolution: 1.7→50 Å / Num. obs: 20314 / % possible obs: 100 % / Redundancy: 13.6 % / R_merge(I) obs: 0.08 / Χ²: 1.535 / Net I/σ(I): 18.016

Reflection shell

Resolution (Å)	% possible obs (%)	Redundancy (%)	R_merge(I) obs	Mean I/σ(I) obs	Num. measured obs	Χ²	% possible all
1.7-1.76	99.9	11.1	0.454	4.422	1976	0.995	99.9
1.76-1.83	100	13.4	0.342		1992	1.097
1.83-1.91	100	14.2	0.241		2005	1.276
1.91-2.02	100	14.2	0.169		1984	1.421
2.02-2.14	100	14.2	0.128		2030	1.585
2.14-2.31	100	14.2	0.105		2001	1.616
2.31-2.54	100	14.1	0.097		2027	1.814
2.54-2.91	100	13.9	0.086		2039	1.877
2.91-3.66	100	13.7	0.071		2062	1.724
3.66-50	99.8	12.9	0.058		2198	1.784

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Phasing

Phasing

Method:

MAD

Phasing MAD set

Highest resolution: 1.7 Å / Lowest resolution: 14.62 Å

ID	R cullis acentric	R cullis centric	Power acentric	Power centric	Reflection acentric	Reflection centric
ISO_1	0	0	0	0	17300	2335
ISO_2	0.871	0.879	0.62	0.502	17194	2324
ANO_1	0.806	0	1.11	0	16737	0
ANO_2	0.543	0	2.239	0	17194	0

Phasing MAD set shell

ID	Resolution (Å)	R cullis acentric	R cullis centric	Power acentric	Power centric	Reflection acentric	Reflection centric
ISO_1	6.78-14.62	0	0	0	0	206	123
ISO_1	5.08-6.78	0	0	0	0	354	125
ISO_1	4.23-5.08	0	0	0	0	455	127
ISO_1	3.7-4.23	0	0	0	0	536	131
ISO_1	3.33-3.7	0	0	0	0	627	128
ISO_1	3.06-3.33	0	0	0	0	689	123
ISO_1	2.84-3.06	0	0	0	0	754	126
ISO_1	2.66-2.84	0	0	0	0	811	103
ISO_1	2.51-2.66	0	0	0	0	854	106
ISO_1	2.39-2.51	0	0	0	0	913	106
ISO_1	2.28-2.39	0	0	0	0	957	106
ISO_1	2.18-2.28	0	0	0	0	1025	110
ISO_1	2.1-2.18	0	0	0	0	1050	98
ISO_1	2.03-2.1	0	0	0	0	1093	130
ISO_1	1.96-2.03	0	0	0	0	1133	121
ISO_1	1.9-1.96	0	0	0	0	1186	130
ISO_1	1.84-1.9	0	0	0	0	1225	128
ISO_1	1.79-1.84	0	0	0	0	1223	123
ISO_1	1.74-1.79	0	0	0	0	1224	106
ISO_1	1.7-1.74	0	0	0	0	985	85
ANO_1	6.78-14.62	0.468	0	2.173	0	206	0
ANO_1	5.08-6.78	0.441	0	2.859	0	354	0
ANO_1	4.23-5.08	0.67	0	1.82	0	455	0
ANO_1	3.7-4.23	0.601	0	2.12	0	536	0
ANO_1	3.33-3.7	0.595	0	2.237	0	627	0
ANO_1	3.06-3.33	0.584	0	2.278	0	689	0
ANO_1	2.84-3.06	0.567	0	2.402	0	754	0
ANO_1	2.66-2.84	0.602	0	2.178	0	811	0
ANO_1	2.51-2.66	0.643	0	1.873	0	854	0
ANO_1	2.39-2.51	0.685	0	1.56	0	913	0
ANO_1	2.28-2.39	0.76	0	1.246	0	957	0
ANO_1	2.18-2.28	0.814	0	1.048	0	1025	0
ANO_1	2.1-2.18	0.859	0	0.845	0	1050	0
ANO_1	2.03-2.1	0.89	0	0.695	0	1093	0
ANO_1	1.96-2.03	0.924	0	0.62	0	1133	0
ANO_1	1.9-1.96	0.948	0	0.485	0	1186	0
ANO_1	1.84-1.9	0.967	0	0.402	0	1223	0
ANO_1	1.79-1.84	0.984	0	0.331	0	1185	0
ANO_1	1.74-1.79	0.987	0	0.301	0	1022	0
ANO_1	1.7-1.74	0.991	0	0.288	0	664	0
ISO_2	6.78-14.62	0.802	0.783	0.843	0.648	206	123
ISO_2	5.08-6.78	0.856	0.913	0.821	0.718	354	125
ISO_2	4.23-5.08	0.843	0.859	0.599	0.505	455	127
ISO_2	3.7-4.23	0.891	0.876	0.558	0.461	536	131
ISO_2	3.33-3.7	0.894	0.883	0.527	0.399	627	128
ISO_2	3.06-3.33	0.917	0.925	0.589	0.335	689	123
ISO_2	2.84-3.06	0.92	0.911	0.644	0.452	754	126
ISO_2	2.66-2.84	0.927	0.965	0.662	0.592	811	103
ISO_2	2.51-2.66	0.942	0.95	0.66	0.519	854	106
ISO_2	2.39-2.51	0.953	0.954	0.674	0.565	913	106
ISO_2	2.28-2.39	0.941	0.915	0.664	0.467	957	106
ISO_2	2.18-2.28	0.911	0.915	0.618	0.445	1025	110
ISO_2	2.1-2.18	0.902	0.923	0.571	0.46	1050	98
ISO_2	2.03-2.1	0.894	0.907	0.592	0.451	1093	130
ISO_2	1.96-2.03	0.872	0.905	0.593	0.396	1133	121
ISO_2	1.9-1.96	0.846	0.97	0.577	0.412	1186	130
ISO_2	1.84-1.9	0.809	0.798	0.558	0.376	1225	127
ISO_2	1.79-1.84	0.723	0.758	0.519	0.385	1223	123
ISO_2	1.74-1.79	0.616	0.767	0.478	0.385	1224	106
ISO_2	1.7-1.74	0.581	0.706	0.45	0.324	879	75
ANO_2	6.78-14.62	0.418	0	2.555	0	206	0
ANO_2	5.08-6.78	0.371	0	3.378	0	354	0
ANO_2	4.23-5.08	0.547	0	2.35	0	455	0
ANO_2	3.7-4.23	0.511	0	2.489	0	536	0
ANO_2	3.33-3.7	0.485	0	2.82	0	627	0
ANO_2	3.06-3.33	0.458	0	2.977	0	689	0
ANO_2	2.84-3.06	0.423	0	3.245	0	754	0
ANO_2	2.66-2.84	0.429	0	3.278	0	811	0
ANO_2	2.51-2.66	0.435	0	3.027	0	854	0
ANO_2	2.39-2.51	0.463	0	2.811	0	913	0
ANO_2	2.28-2.39	0.486	0	2.631	0	957	0
ANO_2	2.18-2.28	0.529	0	2.352	0	1025	0
ANO_2	2.1-2.18	0.585	0	1.965	0	1050	0
ANO_2	2.03-2.1	0.628	0	1.779	0	1093	0
ANO_2	1.96-2.03	0.67	0	1.533	0	1133	0
ANO_2	1.9-1.96	0.73	0	1.271	0	1186	0
ANO_2	1.84-1.9	0.785	0	1.109	0	1225	0
ANO_2	1.79-1.84	0.846	0	0.937	0	1223	0
ANO_2	1.74-1.79	0.895	0	0.831	0	1224	0
ANO_2	1.7-1.74	0.917	0	0.74	0	879	0

Phasing MAD set site

ID	Cartn x (Å)	Cartn y (Å)	Cartn z (Å)	Atom type symbol	B iso	Occupancy
1	-15.975	-37.937	-7.328	SE	26.48	1.95
2	-5.218	-33.968	-4.121	SE	21.87	1.61
3	-34.548	-23.113	-7.276	SE	49.34	0.5
4	-35.109	-38.548	-7.469	SE	31.57	0.41
5	-24.201	-33.977	-4.102	SE	24.19	0.09

Phasing dm

Method: Solvent flattening and Histogram matching / Reflection: 19901

Phasing dm shell

Resolution (Å)	Delta phi final	FOM	Reflection
5.93-100	62.3	0.795	506
4.71-5.93	55.7	0.855	514
4.11-4.71	59.2	0.856	504
3.73-4.11	58.8	0.854	508
3.45-3.73	53.9	0.871	517
3.23-3.45	57.7	0.849	540
3.05-3.23	59.6	0.834	578
2.9-3.05	57.2	0.85	609
2.76-2.9	56.7	0.846	625
2.65-2.76	56.4	0.832	655
2.54-2.65	63.9	0.804	690
2.45-2.54	56.8	0.82	699
2.37-2.45	56.5	0.824	748
2.3-2.37	62.5	0.824	739
2.23-2.3	59.3	0.821	788
2.16-2.23	57.8	0.818	796
2.11-2.16	58.1	0.83	836
2.05-2.11	60.5	0.82	839
2.01-2.05	61.4	0.803	869
1.96-2.01	62.6	0.784	871
1.92-1.96	62.7	0.76	904
1.88-1.92	65.2	0.729	915
1.84-1.88	67.2	0.735	961
1.8-1.84	69.5	0.728	923
1.77-1.8	70.1	0.68	958
1.74-1.77	75.4	0.669	904
1.7-1.74	76.2	0.594	905

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Processing

Software

Name	Version	Classification
DENZO		data reduction
SCALEPACK		data scaling
SHARP		phasing
DM	5	phasing
REFMAC	refmac_5.2.0005	refinement
PDB_EXTRACT	1.6	data extraction
SOLOMON		phasing
ARP/wARP		model building

Refinement

Method to determine structure:

MAD / Resolution: 1.7→45.69 Å / Cor.coef. F_o:F_c: 0.956 / Cor.coef. F_o:F_c free: 0.939 / SU B: 1.921 / SU ML: 0.066 / Cross valid method: THROUGHOUT / ESU R: 0.106 / ESU R Free: 0.109 / Stereochemistry target values: MAXIMUM LIKELIHOOD

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.231	1037	5.1 %	RANDOM
R_work	0.189	-	-	-
all	0.191	-	-	-
obs	0.191	19200	99.88 %	-

Solvent computation

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

Displacement parameters

B_iso mean: 24.682 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	0.05 Å²	0 Å²	0 Å²
2-	-	0.38 Å²	0 Å²
3-	-	-	-0.43 Å²

Refinement step

Cycle: LAST / Resolution: 1.7→45.69 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	1287	0	4	127	1418

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.02	0.022	1311
X-RAY DIFFRACTION	r_angle_refined_deg	1.723	1.957	1764
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	6.437	5	156
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	34.366	23.065	62
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	16.004	15	226
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	13.154	15	12
X-RAY DIFFRACTION	r_chiral_restr	0.148	0.2	199
X-RAY DIFFRACTION	r_gen_planes_refined	0.008	0.02	974
X-RAY DIFFRACTION	r_nbd_refined	0.217	0.2	592
X-RAY DIFFRACTION	r_nbtor_refined	0.313	0.2	893
X-RAY DIFFRACTION	r_xyhbond_nbd_refined	0.193	0.2	105
X-RAY DIFFRACTION	r_symmetry_vdw_refined	0.239	0.2	34
X-RAY DIFFRACTION	r_symmetry_hbond_refined	0.203	0.2	14
X-RAY DIFFRACTION	r_mcbond_it	2.333	2	811
X-RAY DIFFRACTION	r_mcangle_it	3.871	4	1287
X-RAY DIFFRACTION	r_scbond_it	5.548	6	556
X-RAY DIFFRACTION	r_scangle_it	7.906	8	477

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 (%)
1.7-1.744	0.341	86	0.235	1351	1451	99.035
1.744-1.791	0.348	71	0.21	1379	1450	100
1.791-1.843	0.256	71	0.19	1298	1369	100
1.843-1.9	0.226	69	0.192	1292	1362	99.927
1.9-1.962	0.213	71	0.182	1257	1328	100
1.962-2.031	0.245	63	0.186	1214	1277	100
2.031-2.107	0.229	74	0.179	1158	1232	100
2.107-2.193	0.182	49	0.171	1137	1186	100
2.193-2.291	0.23	65	0.182	1090	1155	100
2.291-2.402	0.234	68	0.182	1021	1089	100
2.402-2.532	0.226	64	0.202	971	1035	100
2.532-2.685	0.195	46	0.204	942	988	100
2.685-2.869	0.298	40	0.198	915	955	100
2.869-3.098	0.245	45	0.192	817	863	99.884
3.098-3.392	0.215	44	0.182	779	823	100
3.392-3.79	0.233	32	0.172	703	735	100
3.79-4.371	0.221	30	0.171	623	654	99.847
4.371-5.342	0.169	25	0.162	552	577	100
5.342-7.503	0.34	13	0.244	436	449	100
7.503-45.691	0.199	11	0.228	265	284	97.183

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