PDB-1xy7: X-RAY STRUCTURE OF GENE PRODUCT FROM ARABIDOPSIS THALIANA AT5G48480

ID or keywords:

Entry

Database: PDB / ID: 1xy7

Title

X-RAY STRUCTURE OF GENE PRODUCT FROM ARABIDOPSIS THALIANA AT5G48480

Components

unknown protein

Keywords

STRUCTURAL GENOMICS / UNKNOWN FUNCTION / PROTEIN STRUCTURE INITIATIVE / PSI / CESG / AT5G48480 / REDUCTIVELY METHYLATED PROTEIN / CATH 3.10.180 FOLD / DIMER / Center for Eukaryotic Structural Genomics

Function / homology

2,3-Dihydroxybiphenyl 1,2-Dioxygenase, domain 1 / 2,3-Dihydroxybiphenyl 1,2-Dioxygenase; domain 1 / Glyoxalase/Bleomycin resistance protein/Dihydroxybiphenyl dioxygenase / Roll / cytosol / Alpha Beta / Uncharacterized protein At5g48480

Function and homology information

Biological species

Arabidopsis thaliana (thale cress)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MAD / Resolution: 1.8 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 GENE PRODUCT FROM ARABIDOPSIS THALIANA AT5G48480
Authors: Center for Eukaryotic Structural Genomics (CESG)

History

Deposition	Nov 9, 2004	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Nov 16, 2004	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

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	1xy7.cif.gz	63.5 KB	Display	PDBx/mmCIF format
PDB format	pdb1xy7.ent.gz	47.2 KB	Display	PDB format
PDBx/mmJSON format	1xy7.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	1xy7_validation.pdf.gz	434.3 KB	Display	wwPDB validaton report
Full document	1xy7_full_validation.pdf.gz	437.4 KB	Display
Data in XML	1xy7_validation.xml.gz	13.8 KB	Display
Data in CIF	1xy7_validation.cif.gz	19.8 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/xy/1xy7 ftp://data.pdbj.org/pub/pdb/validation_reports/xy/1xy7	HTTPS FTP

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Related structure data

Similar structure data	2q48-d 3d3f-3 5d2k-1 2rtg-d 5ump-d 1xfj-d 4g6v-4 4ws8-d 3rhe-2 1sv6-4 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.22340

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Links

PDB pages	PDBj / wwPDB / NCBI

Deposited unit

A: unknown protein

B: unknown protein

35.3 kDa, 2 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)	55.871, 55.871, 147.341
Angle α, β, γ (deg.)	90.00, 90.00, 120.00
Int Tables number	154
Space group name H-M	P3₂21

Noncrystallographic symmetry (NCS)

NCS domain:

ID	Ens-ID	Details
1	1	A
2	1	B
3	1	A
4	1	B
5	1	A
6	1	B

NCS domain segments:

Ens-ID: 1 / Refine code: 4

Dom-ID	Component-ID	Beg label comp-ID	End label comp-ID	Auth asym-ID	Label asym-ID	Auth seq-ID	Label seq-ID
1	1	VAL	SER	A	A	22 - 53	22 - 53
2	1	VAL	SER	B	B	22 - 53	22 - 53
3	2	VAL	SER	A	A	70 - 98	70 - 98
4	2	VAL	SER	B	B	70 - 98	70 - 98
5	3	GLY	GLU	A	A	102 - 154	102 - 154
6	3	GLY	GLU	B	B	102 - 154	102 - 154

#1: Protein	unknown protein Mass: 17668.604 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Arabidopsis thaliana (thale cress) / Gene: At5g48480 / Plasmid: PVP-13 / Production host: Escherichia coli (E. coli) / Strain (production host): B834(DE3) P(LACI+RARE) / References: UniProt: Q9LV66
#2: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 252 / Source method: isolated from a natural source / Formula: H₂O

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Experiment

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

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Sample preparation

Crystal	Density Matthews: 1.88 Å³/Da / Density % sol: 34.53 %
Crystal grow	Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5.5 Details: 12.2 MG/ML REDUCTIVELY METHYLATED PROTEIN, 2.03 M AMMONIUM SULFATE, 0.100 M MES/ACETATE, PH 5.5, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 293K

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Data collection

Diffraction

Mean temperature: 100 K

Diffraction source

Source:

SYNCHROTRON / Site:

APS

/ Beamline: 14-ID-B / Wavelength: 0.97919, 0.97942, 0.95653

Detector

Type: MAR CCD 165 mm / Detector: CCD / Date: Oct 24, 2004 / Details: bent cylindrical Si-mirror (Rh coating)

Radiation

Monochromator: Diamond (111) double-crystal monochromator / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray

Radiation wavelength

ID	Wavelength (Å)	Relative weight
1	0.97919	1
2	0.97942	1
3	0.95653	1

Reflection

Resolution: 1.8→27.447 Å / Num. obs: 25282 / % possible obs: 98.9 % / Redundancy: 13.6 % / R_merge(I) obs: 0.037 / Χ²: 0.981 / Net I/σ(I): 29.85

Reflection shell

Resolution (Å)	Redundancy (%)	R_merge(I) obs	Mean I/σ(I) obs	Num. measured all	Χ²	% possible all
1.8-1.84	10.9	0.123	10.84	1614	0.825	99.6
1.84-1.89		0.092		1667	0.786	99.4
1.89-1.94		0.101		1694	1.189	99.4
1.94-2		0.069		1675	0.968	99.6
2-2.06		0.06		1657	0.987	99.9
2.06-2.13		0.055		1672	1.01	99.9
2.13-2.22		0.051		1684	0.845	99.9
2.22-2.32		0.058		1669	1.153	98.4
2.32-2.44		0.044		1673	0.968	100
2.44-2.6		0.041		1709	0.929	100
2.6-2.8		0.037		1718	0.959	100
2.8-3.08		0.035		1715	1.104	100
3.08-3.52		0.03		1727	0.977	100
3.52-4.44		0.029		1728	0.98	98.9
4.44-50		0.034		1680	1.005	88.9

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Phasing

Phasing

Method:

MAD

Phasing set

ID
1
2
3

Phasing MAD

D res high: 1.79 Å / D res low: 26.13 Å / FOM : 0.691 / FOM acentric: 0.685 / FOM centric: 0.779 / Reflection: 46298

Phasing MAD set

Highest resolution: 1.79 Å / Lowest resolution: 26.13 Å

ID	R cullis	R cullis acentric	R cullis centric	R kraut	R kraut acentric	R kraut centric	FOM	FOM acentric	FOM centric	Loc	Loc acentric	Loc centric	Power (kW)	Power acentric	Power centric
f_peak	0.975	0.998	0.795	0.027	0.026	0.034	0.059	0.053	0.141	5.908	5.865	6.548	0.258	0.254	0.3
f_peak_FRIED	0.697	0.687	0.84	0.024	0.023	0.033	0.333	0.346	0.15	5.961	5.918	6.613	1.515	1.512	1.55
f_edge	0.664	0.687	0.499	0.019	0.019	0.025	0.35	0.325	0.703	5.252	5.224	5.689	1.475	1.464	1.593
f_edge_FRIED	0.529	0.531	0.513	0.019	0.018	0.025	0.434	0.415	0.697	5.378	5.347	5.839	2.304	2.288	2.478
f_hrem_FRIED	0.527	0.508	10	0.012	0.012	0.002	0.349	0.375	0	3.162	3.159	3.228	2.273	2.247	2.584

Phasing MAD set

Clust-ID	Expt-ID	Set-ID	Wavelength (Å)	Atom type	F double prime refined	F prime refined
1	1	1	0.97919	SE	3.42	-1.59
1	1	2	0.97942	SE	4.14	-6.94
1	1	3	0.95653	SE	2.19	-2

Phasing MAD set shell

ID	Resolution (Å)	R cullis	R cullis acentric	R cullis centric	R kraut	R kraut acentric	R kraut centric	FOM	FOM acentric	FOM centric	Loc	Loc acentric	Loc centric	Power (kW)	Power acentric	Power centric
f_peak	3.58-26.13	0.991	1.031	0.802	0.019	0.017	0.029	0.12	0.103	0.238	9.618	9.628	9.645	0.362	0.36	0.372
f_peak	2.84-3.58	0.989	1.017	0.78	0.021	0.021	0.032	0.09	0.082	0.184	7.774	7.778	7.784	0.261	0.259	0.279
f_peak	2.48-2.84	1.007	1.034	0.775	0.024	0.024	0.033	0.079	0.073	0.159	5.741	5.744	5.75	0.236	0.235	0.249
f_peak	2.26-2.48	1.002	1.024	0.779	0.027	0.027	0.036	0.059	0.055	0.119	5.141	5.143	5.15	0.186	0.186	0.182
f_peak	2.09-2.26	0.978	0.995	0.781	0.032	0.031	0.038	0.041	0.039	0.083	5.085	5.087	5.094	0.134	0.135	0.131
f_peak	1.97-2.09	0.97	0.983	0.79	0.036	0.035	0.043	0.034	0.033	0.068	4.465	4.466	4.47	0.115	0.116	0.109
f_peak	1.87-1.97	0.914	0.916	0.871	0.049	0.049	0.05	0.022	0.021	0.044	4.751	4.752	4.761	0.082	0.082	0.082
f_peak	1.79-1.87	0.845	0.845	0.839	0.065	0.065	0.066	0.016	0.015	0.028	4.465	4.466	4.471	0.068	0.068	0.067
f_peak_FRIED	3.58-26.13	0.667	0.648	0.879	0.018	0.017	0.027	0.363	0.391	0.167	9.789	9.798	9.813	1.595	1.601	1.558
f_peak_FRIED	2.84-3.58	0.724	0.717	0.829	0.021	0.02	0.031	0.357	0.374	0.164	8.049	8.053	8.06	1.501	1.493	1.589
f_peak_FRIED	2.48-2.84	0.687	0.681	0.792	0.023	0.022	0.033	0.383	0.398	0.18	5.841	5.844	5.85	1.706	1.698	1.806
f_peak_FRIED	2.26-2.48	0.679	0.673	0.785	0.024	0.024	0.036	0.373	0.387	0.167	5.18	5.182	5.189	1.63	1.632	1.601
f_peak_FRIED	2.09-2.26	0.703	0.699	0.794	0.027	0.027	0.038	0.344	0.356	0.138	5.046	5.047	5.055	1.415	1.417	1.385
f_peak_FRIED	1.97-2.09	0.719	0.715	0.782	0.03	0.029	0.043	0.324	0.335	0.136	4.443	4.444	4.448	1.407	1.411	1.332
f_peak_FRIED	1.87-1.97	0.746	0.741	0.872	0.04	0.039	0.051	0.269	0.277	0.101	4.776	4.777	4.786	1.142	1.142	1.138
f_peak_FRIED	1.79-1.87	0.725	0.722	0.812	0.049	0.049	0.067	0.228	0.236	0.075	4.329	4.331	4.335	1.117	1.119	1.088
f_edge	3.58-26.13	0.6	0.631	0.466	0.013	0.012	0.022	0.441	0.395	0.756	7.976	7.984	7.998	1.718	1.717	1.723
f_edge	2.84-3.58	0.653	0.676	0.491	0.014	0.013	0.025	0.423	0.393	0.781	6.431	6.434	6.443	1.593	1.584	1.696
f_edge	2.48-2.84	0.626	0.648	0.457	0.016	0.015	0.026	0.435	0.41	0.784	4.686	4.689	4.693	1.76	1.753	1.858
f_edge	2.26-2.48	0.656	0.672	0.498	0.019	0.018	0.028	0.401	0.38	0.733	4.345	4.347	4.352	1.577	1.579	1.548
f_edge	2.09-2.26	0.717	0.729	0.57	0.022	0.022	0.027	0.34	0.319	0.695	4.454	4.456	4.462	1.276	1.278	1.247
f_edge	1.97-2.09	0.742	0.751	0.617	0.027	0.027	0.029	0.309	0.292	0.637	4.225	4.226	4.229	1.161	1.164	1.097
f_edge	1.87-1.97	0.775	0.78	0.677	0.041	0.041	0.043	0.235	0.219	0.55	4.802	4.803	4.812	0.877	0.877	0.888
f_edge	1.79-1.87	0.806	0.804	0.836	0.058	0.059	0.05	0.169	0.159	0.4	5.09	5.091	5.097	0.724	0.724	0.707
f_edge_FRIED	3.58-26.13	0.468	0.466	0.482	0.013	0.012	0.022	0.519	0.485	0.75	8.243	8.252	8.266	2.65	2.649	2.657
f_edge_FRIED	2.84-3.58	0.519	0.521	0.504	0.014	0.013	0.025	0.494	0.47	0.771	6.59	6.594	6.603	2.485	2.471	2.645
f_edge_FRIED	2.48-2.84	0.484	0.486	0.465	0.016	0.015	0.027	0.508	0.488	0.783	4.766	4.769	4.774	2.774	2.762	2.927
f_edge_FRIED	2.26-2.48	0.522	0.522	0.521	0.019	0.018	0.027	0.479	0.464	0.725	4.542	4.543	4.549	2.422	2.424	2.378
f_edge_FRIED	2.09-2.26	0.565	0.564	0.578	0.022	0.021	0.027	0.441	0.426	0.691	4.508	4.51	4.516	2.028	2.03	1.982
f_edge_FRIED	1.97-2.09	0.616	0.615	0.631	0.027	0.026	0.03	0.404	0.392	0.632	4.322	4.323	4.326	1.829	1.834	1.728
f_edge_FRIED	1.87-1.97	0.676	0.675	0.703	0.04	0.039	0.043	0.325	0.314	0.54	4.993	4.994	5.004	1.361	1.36	1.377
f_edge_FRIED	1.79-1.87	0.713	0.709	0.82	0.054	0.054	0.05	0.254	0.247	0.41	5.014	5.015	5.021	1.186	1.187	1.159
f_hrem_FRIED	3.58-26.13	0.407	0.38	10	0.006	0.006	0.002	0.424	0.488	0	3.89	3.894	3.901	3.123	3.12	3.138
f_hrem_FRIED	2.84-3.58	0.448	0.43	10	0.006	0.006	0.002	0.438	0.477	0	3.027	3.029	3.034	3.064	3.048	3.244
f_hrem_FRIED	2.48-2.84	0.465	0.449	10	0.009	0.009	0.003	0.438	0.47	0	2.568	2.57	2.572	2.961	2.949	3.122
f_hrem_FRIED	2.26-2.48	0.511	0.495	10	0.012	0.012	0.003	0.403	0.429	0	2.628	2.629	2.632	2.437	2.44	2.386
f_hrem_FRIED	2.09-2.26	0.588	0.571	10	0.016	0.016	0.003	0.35	0.371	0	3.001	3.002	3.006	1.796	1.799	1.757
f_hrem_FRIED	1.97-2.09	0.656	0.639	10	0.02	0.021	0.003	0.299	0.315	0	3.025	3.026	3.028	1.557	1.562	1.471
f_hrem_FRIED	1.87-1.97	0.701	0.683	10	0.031	0.032	0.004	0.224	0.235	0	3.53	3.53	3.537	1.154	1.154	1.151
f_hrem_FRIED	1.79-1.87	0.743	0.726	10	0.045	0.047	0.005	0.173	0.181	0	3.797	3.799	3.803	0.95	0.951	0.927

Phasing MAD set site

ID	Cartn x (Å)	Cartn y (Å)	Cartn z (Å)	Atom type symbol	B iso	Occupancy
1	-12.6819	28.5399	10.7678	SE	23.9015	1
2	-0.483237	13.513	12.0231	SE	23.6252	1

Phasing MAD shell

Resolution (Å)	FOM	FOM acentric	FOM centric	Reflection
3.58-26.13	0.7891	0.7858	0.8183	5801
2.84-3.58	0.8025	0.7984	0.8569	6042
2.48-2.84	0.8122	0.809	0.8621	6035
2.26-2.48	0.7685	0.7652	0.8239	5932
2.09-2.26	0.6957	0.6909	0.7834	5904
1.97-2.09	0.646	0.6421	0.722	5923
1.87-1.97	0.5342	0.53	0.6232	5690
1.79-1.87	0.4252	0.4221	0.4968	4971

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Processing

Software

Name	Version	Classification
DENZO		data reduction
SCALEPACK		data scaling
CNS		phasing
REFMAC	refmac_5.2.0005	refinement

Refinement

Method to determine structure:

MAD / Resolution: 1.8→49.088 Å / Cor.coef. F_o:F_c: 0.954 / Cor.coef. F_o:F_c free: 0.931 / WR_factor R_free: 0.242 / WR_factor R_work: 0.192 / SU B: 2.256 / SU ML: 0.073 / SU R Cruickshank DPI: 0.121 / Cross valid method: THROUGHOUT / ESU R: 0.121 / ESU R Free: 0.123 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.228	1282	5.093 %	RANDOM
R_work	0.1817	-	-	-
all	0.184	-	-	-
obs	0.184	25171	98.629 %	-

Solvent computation

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

Displacement parameters

B_iso mean: 26.655 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	0.767 Å²	0.384 Å²	0 Å²
2-	-	0.767 Å²	0 Å²
3-	-	-	-1.151 Å²

Refinement step

Cycle: LAST / Resolution: 1.8→49.088 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	1803	0	0	252	2055

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.019	0.022	1833
X-RAY DIFFRACTION	r_angle_refined_deg	1.689	1.951	2480
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	5.161	5	238
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	39.755	25.882	68
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	13.068	15	302
X-RAY DIFFRACTION	r_chiral_restr	0.148	0.2	301
X-RAY DIFFRACTION	r_gen_planes_refined	0.009	0.02	1328
X-RAY DIFFRACTION	r_nbd_refined	0.212	0.2	855
X-RAY DIFFRACTION	r_nbtor_refined	0.313	0.2	1283
X-RAY DIFFRACTION	r_xyhbond_nbd_refined	0.177	0.2	192
X-RAY DIFFRACTION	r_symmetry_vdw_refined	0.245	0.2	29
X-RAY DIFFRACTION	r_symmetry_hbond_refined	0.184	0.2	12
X-RAY DIFFRACTION	r_mcbond_it	2.086	2	1209
X-RAY DIFFRACTION	r_mcangle_it	3.527	5	1910
X-RAY DIFFRACTION	r_scbond_it	5.903	8	688
X-RAY DIFFRACTION	r_scangle_it	8.572	12	570

Refine LS restraints NCS

Dom-ID: 1 / Auth asym-ID: A / Ens-ID: 1 / Number: 818 / Refine-ID: X-RAY DIFFRACTION

Type	Rms dev position (Å)	Weight position
medium positional	0.95	0.5
medium thermal	2.88	2

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 (%)
1.8-1.847	0.3	96	0.205	1719	1826	99.398
1.847-1.897	0.236	87	0.18	1705	1805	99.28
1.897-1.952	0.235	97	0.184	1598	1742	97.302
1.952-2.012	0.238	85	0.178	1634	1722	99.826
2.012-2.078	0.23	78	0.167	1592	1671	99.94
2.078-2.151	0.222	76	0.17	1531	1609	99.876
2.151-2.232	0.22	83	0.18	1459	1550	99.484
2.232-2.323	0.203	67	0.181	1389	1495	97.391
2.323-2.426	0.222	75	0.177	1379	1455	99.931
2.426-2.544	0.197	60	0.183	1312	1372	100
2.544-2.681	0.263	86	0.184	1217	1303	100
2.681-2.843	0.216	68	0.194	1185	1253	100
2.843-3.039	0.241	66	0.178	1109	1176	99.915
3.039-3.281	0.205	59	0.181	1047	1107	99.91
3.281-3.593	0.23	47	0.166	969	1017	99.902
3.593-4.014	0.234	53	0.162	878	940	99.043
4.014-4.63	0.192	38	0.16	777	833	97.839
4.63-5.658	0.166	27	0.188	649	717	94.282
5.658-7.949	0.283	21	0.231	519	572	94.406
7.949-49.088	0.414	13	0.319	221	356	65.73

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