PDB-2a13: X-ray structure of protein from Arabidopsis thaliana AT1G79260

ID or keywords:

Entry

Database: PDB / ID: 2a13

Title

X-ray structure of protein from Arabidopsis thaliana AT1G79260

Components

At1g79260

Keywords

STRUCTURAL GENOMICS / UNKNOWN FUNCTION / AT1G79260 / PROTEIN STRUCTURE INITIATIVE / PSI / CENTER FOR EUKARYOTIC STRUCTURAL GENOMICS / CESG

Function / homology

Function and homology information

Isomerases; Other isomerases / isomerase activity / metal ion binding / cytosol
Similarity search - Function

Biological species

Arabidopsis thaliana (thale cress)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MAD / Resolution: 1.32 Å

Authors

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

Citation

Journal: Proteins / Year: 2010
Title: The structure and NO binding properties of the nitrophorin-like heme-binding protein from Arabidopsis thaliana gene locus At1g79260.1.
Authors: Bianchetti, C.M. / Blouin, G.C. / Bitto, E. / Olson, J.S. / Phillips, G.N.

History

Deposition	Jun 17, 2005	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Jul 12, 2005	Provider: repository / Type: Initial release
Revision 1.1	Apr 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	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_ref_seq_dif 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

Remark 300

BIOMOLECULE: 1 THIS ENTRY CONTAINS THE CRYSTALLOGRAPHIC ASYMMETRIC UNIT WHICH CONSISTS OF 1 CHAIN(S) ...

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	2a13.cif.gz	91.5 KB	Display	PDBx/mmCIF format
PDB format	pdb2a13.ent.gz	66.5 KB	Display	PDB format
PDBx/mmJSON format	2a13.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/a1/2a13 ftp://data.pdbj.org/pub/pdb/validation_reports/a1/2a13	HTTPS FTP

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Related structure data

Related structure data	3emmC C: citing same article (ref.)
Similar structure data	3gkv-d 6wly-d 3fh9-d 4odc-d 3tux-d 2fr7-d 5w4w-3 3mfg-d 5xtj-d 3fqg-d Search similar-shape structures by Omokage search (details) 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.6462

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Links

PDB pages	PDBj / wwPDB / NCBI
Related items in Molecule of the Month	#193 - Jan 2016 Siderocalin similarity (1) #78 - Jun 2006 Luciferase similarity (1)

Deposited unit

A: At1g79260

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

1

A: At1g79260

defined by author&software
37.1 kDa, 2 polymers
Search similar-shape structures of this assembly by Omokage search (details)

Unit cell

Length a, b, c (Å)	60.056, 80.026, 36.886
Angle α, β, γ (deg.)	90.00, 90.00, 90.00
Int Tables number	18
Space group name H-M	P2₁2₁2

Details

POSSIBLE DIMER ALONG A TWO-FOLD SPACE GOURP SYMMETRY AXIS

#1: Protein	At1g79260 Mass: 18557.629 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Arabidopsis thaliana (thale cress) / Gene: AT1G79260 / Plasmid: PVP-16 / Production host: Escherichia coli (E. coli) / Strain (production host): B834 P(RARE2) / References: UniProt: O64527
#2: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 329 / 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: 2

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Sample preparation

Crystal

ID	Density Matthews (Å³/Da)	Density % sol (%)
1	2.4	48.5
2	2.4	48.5

Crystal grow

Temperature: 277 K / Method: vapor diffusion, hanging drop / pH: 8
Details: 10 MG/ML PROTEIN, 18% PEG2K, 0.025 M TRIS, pH 8.0, vapor diffusion, hanging drop, temperature 277K

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Data collection

Diffraction

ID	Mean temperature (K)	Crystal-ID
1	100	1
2	100	1
3		1

Diffraction source

Source	Site	Beamline	ID	Wavelength	Wavelength (Å)
SYNCHROTRON	APS	22-ID	1	0.97166
SYNCHROTRON	APS	22-ID	2		0.97934, 0.96863

Detector

Type	ID	Detector	Date	Details
MARMOSAIC 300 mm CCD	1	CCD	Jun 13, 2005	HORIZONTAL SAGITALLY FOCUSING 2ND BENT MONOCHROMATOR CRYSTAL, VERTICAL BENT FOCUSING MIRROR
MARMOSAIC 300 mm CCD	2	CCD	Jun 13, 2005	HORIZONTAL SAGITALLY FOCUSING 2ND BENT MONOCHROMATOR CRYSTAL, VERTICAL BENT FOCUSING MIRROR

Radiation

ID	Monochromator	Protocol	Monochromatic (M) / Laue (L)	Scattering type	Wavelength-ID
1	CRYOGENICALLY COOLED SI (220) DOUBLE BOUNCE	SINGLE WAVELENGTH	M	x-ray	1
2	CRYOGENICALLY COOLED SI (220) DOUBLE BOUNCE	MAD	M	x-ray	1

Radiation wavelength

ID	Wavelength (Å)	Relative weight
1	0.97166	1
2	0.97934	1
3	0.96863	1

Reflection

D res low: 50 Å

Redundancy (%)	ID	Number	R_merge(I) obs	Χ²	D res high (Å)	% possible obs
7.5	1	41019	0.066	1.169	1.31	96.3
14	2	29610	0.07	1.212	1.46	95.3
9.8	3	28976	0.059	0.865	1.46	93.2

Diffraction reflection shell

Highest resolution (Å)	Lowest resolution (Å)	% possible obs (%)	ID	R_merge(I) obs	Chi squared	Redundancy
3.23	50	97	1	0.058	0.907	7.1
2.56	3.23	98.1	1	0.056	0.902	7.5
2.24	2.56	98.2	1	0.06	0.975	7.8
2.04	2.24	98.7	1	0.062	1.159	7.7
1.89	2.04	96.6	1	0.066	1.293	7.6
1.78	1.89	97.1	1	0.074	1.343	7.6
1.69	1.78	96.8	1	0.088	1.277	7.6
1.62	1.69	96.6	1	0.098	1.236	7.5
1.55	1.62	96.3	1	0.106	1.305	7.5
1.5	1.55	95.7	1	0.118	1.311	7.5
1.45	1.5	95.1	1	0.142	1.282	7.5
1.41	1.45	95.9	1	0.158	1.273	7.4
1.37	1.41	94.2	1	0.185	1.163	7.4
1.34	1.37	94.2	1	0.206	1.077	7.4
1.31	1.34	93.1	1	0.24	1.043	6.8
3.6	50	97.8	2	0.065	1.241	12
2.86	3.6	99.8	2	0.061	1.183	13.9
2.5	2.86	99.8	2	0.066	1.141	14.2
2.27	2.5	99.7	2	0.066	1.295	14.3
2.11	2.27	99.8	2	0.069	1.218	14.2
1.98	2.11	99.4	2	0.075	1.294	14.3
1.88	1.98	99.4	2	0.081	1.322	14.3
1.8	1.88	99.4	2	0.085	1.287	14.3
1.73	1.8	99.3	2	0.092	1.236	14.3
1.67	1.73	98.8	2	0.099	1.193	14.4
1.62	1.67	99	2	0.104	1.164	14.3
1.57	1.62	98.5	2	0.111	1.173	14.3
1.53	1.57	98.9	2	0.122	1.127	14.3
1.49	1.53	98.2	2	0.131	1.123	13.9
1.46	1.49	40.8	2	0.144	1.097	12.1
3.6	50	82.2	3	0.055	0.715	9.3
2.86	3.6	89.8	3	0.052	0.799	10.2
2.5	2.86	91.6	3	0.057	0.802	10.3
2.27	2.5	92.9	3	0.056	0.853	10.2
2.11	2.27	93.8	3	0.057	0.805	10.1
1.98	2.11	94.4	3	0.063	0.895	10.1
1.88	1.98	94.9	3	0.069	0.948	10
1.8	1.88	95.5	3	0.072	0.908	9.9
1.73	1.8	95.7	3	0.078	0.88	9.9
1.67	1.73	96	3	0.085	0.87	9.8
1.62	1.67	96.6	3	0.09	0.865	9.8
1.57	1.62	96.4	3	0.098	0.895	9.7
1.53	1.57	96.6	3	0.109	0.895	9.8
1.49	1.53	96.5	3	0.124	0.941	9.7
1.46	1.49	86.3	3	0.14	0.905	8.7

Reflection

Resolution: 1.31→50 Å / Num. obs: 41019 / % possible obs: 96.3 % / Redundancy: 7.5 % / R_merge(I) obs: 0.066 / Χ²: 1.169 / Net I/σ(I): 14.91

Reflection shell

Resolution: 1.31→1.34 Å / % possible obs: 93.1 % / Redundancy: 6.8 % / R_merge(I) obs: 0.24 / Mean I/σ(I) obs: 6.178 / Num. measured obs: 2588 / Χ²: 1.043 / % possible all: 93.1

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Phasing

Phasing

Method:

MAD

Phasing MAD set

Highest resolution: 1.46 Å / Lowest resolution: 32.86 Å

ID	R cullis acentric	R cullis centric	Power acentric	Power centric	Reflection acentric	Reflection centric
ISO_1	0	0	0	0	25975	3048
ISO_2	0.908	0.916	0.589	0.469	25204	2291
ANO_1	0.677	0	1.654	0	25960	0
ANO_2	0.854	0	0.81	0	25105	0

Phasing MAD set shell

ID	Resolution (Å)	R cullis acentric	R cullis centric	Power acentric	Power centric	Reflection acentric	Reflection centric
ISO_1	6.41-32.86	0	0	0	0	240	149
ISO_1	4.58-6.41	0	0	0	0	475	158
ISO_1	3.75-4.58	0	0	0	0	638	158
ISO_1	3.25-3.75	0	0	0	0	771	166
ISO_1	2.91-3.25	0	0	0	0	901	157
ISO_1	2.66-2.91	0	0	0	0	993	168
ISO_1	2.46-2.66	0	0	0	0	1110	162
ISO_1	2.31-2.46	0	0	0	0	1208	170
ISO_1	2.17-2.31	0	0	0	0	1254	159
ISO_1	2.06-2.17	0	0	0	0	1357	167
ISO_1	1.97-2.06	0	0	0	0	1415	156
ISO_1	1.88-1.97	0	0	0	0	1496	162
ISO_1	1.81-1.88	0	0	0	0	1552	152
ISO_1	1.74-1.81	0	0	0	0	1630	150
ISO_1	1.69-1.74	0	0	0	0	1680	146
ISO_1	1.63-1.69	0	0	0	0	1743	138
ISO_1	1.58-1.63	0	0	0	0	1800	134
ISO_1	1.54-1.58	0	0	0	0	1858	127
ISO_1	1.5-1.54	0	0	0	0	1912	133
ISO_1	1.46-1.5	0	0	0	0	1942	136
ANO_1	6.41-32.86	0.616	0	1.448	0	237	0
ANO_1	4.58-6.41	0.646	0	1.697	0	472	0
ANO_1	3.75-4.58	0.751	0	1.419	0	638	0
ANO_1	3.25-3.75	0.718	0	1.545	0	771	0
ANO_1	2.91-3.25	0.661	0	1.872	0	901	0
ANO_1	2.66-2.91	0.628	0	2.088	0	993	0
ANO_1	2.46-2.66	0.638	0	2.032	0	1110	0
ANO_1	2.31-2.46	0.615	0	2.036	0	1208	0
ANO_1	2.17-2.31	0.656	0	1.846	0	1254	0
ANO_1	2.06-2.17	0.672	0	1.753	0	1357	0
ANO_1	1.97-2.06	0.651	0	1.752	0	1415	0
ANO_1	1.88-1.97	0.649	0	1.678	0	1496	0
ANO_1	1.81-1.88	0.655	0	1.714	0	1552	0
ANO_1	1.74-1.81	0.655	0	1.666	0	1630	0
ANO_1	1.69-1.74	0.662	0	1.534	0	1680	0
ANO_1	1.63-1.69	0.703	0	1.476	0	1743	0
ANO_1	1.58-1.63	0.727	0	1.348	0	1799	0
ANO_1	1.54-1.58	0.764	0	1.2	0	1856	0
ANO_1	1.5-1.54	0.8	0	1.118	0	1912	0
ANO_1	1.46-1.5	0.847	0	0.926	0	1936	0
ISO_2	6.41-32.86	0.952	0.976	0.744	0.634	218	84
ISO_2	4.58-6.41	0.938	0.944	0.663	0.603	431	100
ISO_2	3.75-4.58	0.887	0.876	0.522	0.386	587	99
ISO_2	3.25-3.75	0.876	0.927	0.548	0.481	718	114
ISO_2	2.91-3.25	0.892	0.898	0.618	0.393	848	107
ISO_2	2.66-2.91	0.901	0.891	0.649	0.531	937	121
ISO_2	2.46-2.66	0.925	0.956	0.692	0.495	1055	118
ISO_2	2.31-2.46	0.92	0.913	0.624	0.539	1156	125
ISO_2	2.17-2.31	0.905	0.906	0.572	0.403	1210	119
ISO_2	2.06-2.17	0.909	0.902	0.571	0.344	1303	129
ISO_2	1.97-2.06	0.911	0.903	0.559	0.43	1375	123
ISO_2	1.88-1.97	0.916	0.92	0.545	0.341	1455	127
ISO_2	1.81-1.88	0.936	0.92	0.573	0.382	1515	119
ISO_2	1.74-1.81	0.929	0.93	0.578	0.411	1598	122
ISO_2	1.69-1.74	0.932	0.959	0.58	0.468	1653	122
ISO_2	1.63-1.69	0.928	0.924	0.555	0.397	1720	112
ISO_2	1.58-1.63	0.927	0.921	0.542	0.334	1770	113
ISO_2	1.54-1.58	0.922	0.914	0.504	0.337	1836	104
ISO_2	1.5-1.54	0.916	0.908	0.473	0.276	1892	117
ISO_2	1.46-1.5	0.91	0.977	0.447	0.29	1927	116
ANO_2	6.41-32.86	0.781	0	0.842	0	199	0
ANO_2	4.58-6.41	0.843	0	0.876	0	413	0
ANO_2	3.75-4.58	0.879	0	0.708	0	564	0
ANO_2	3.25-3.75	0.862	0	0.757	0	708	0
ANO_2	2.91-3.25	0.853	0	0.864	0	847	0
ANO_2	2.66-2.91	0.805	0	1.047	0	935	0
ANO_2	2.46-2.66	0.781	0	1.108	0	1055	0
ANO_2	2.31-2.46	0.792	0	1.039	0	1156	0
ANO_2	2.17-2.31	0.839	0	0.941	0	1206	0
ANO_2	2.06-2.17	0.857	0	0.851	0	1303	0
ANO_2	1.97-2.06	0.825	0	0.871	0	1372	0
ANO_2	1.88-1.97	0.852	0	0.808	0	1454	0
ANO_2	1.81-1.88	0.855	0	0.816	0	1510	0
ANO_2	1.74-1.81	0.854	0	0.826	0	1598	0
ANO_2	1.69-1.74	0.864	0	0.751	0	1651	0
ANO_2	1.63-1.69	0.89	0	0.661	0	1720	0
ANO_2	1.58-1.63	0.907	0	0.608	0	1769	0
ANO_2	1.54-1.58	0.937	0	0.535	0	1833	0
ANO_2	1.5-1.54	0.942	0	0.452	0	1890	0
ANO_2	1.46-1.5	0.96	0	0.389	0	1922	0

Phasing MAD set site

ID	Cartn x (Å)	Cartn y (Å)	Cartn z (Å)	Atom type symbol	B iso	Occupancy
1	-14.432	-35.732	-5.592	SE	18.65	0.87
2	-18.473	-0.471	-16.742	SE	16	0.65

Phasing dm

Method: Solvent flattening and Histogram matching / Reflection: 27380

Phasing dm shell

Resolution (Å)	Delta phi final	FOM	Reflection
5.84-100	69.1	0.758	511
4.63-5.84	66.5	0.884	508
4.02-4.63	63.6	0.916	504
3.6-4.02	70.6	0.893	574
3.3-3.6	64.7	0.892	624
3.05-3.3	63.7	0.902	694
2.86-3.05	61.4	0.911	734
2.7-2.86	64.2	0.908	770
2.56-2.7	64.3	0.912	802
2.44-2.56	62.8	0.905	851
2.34-2.44	63.1	0.923	898
2.25-2.34	67.5	0.902	911
2.17-2.25	65	0.917	957
2.09-2.17	64.1	0.92	984
2.03-2.09	62.3	0.918	1018
1.97-2.03	64.5	0.913	1048
1.91-1.97	64.5	0.918	1084
1.86-1.91	67	0.9	1101
1.81-1.86	61.7	0.906	1130
1.77-1.81	63.7	0.889	1165
1.73-1.77	63.9	0.892	1155
1.69-1.73	64.6	0.887	1223
1.66-1.69	64.4	0.881	1245
1.62-1.66	64.5	0.871	1251
1.59-1.62	65.3	0.878	1284
1.56-1.59	66.1	0.862	1290
1.53-1.56	67.1	0.84	1330
1.5-1.53	71.9	0.779	1734

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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: 1.32→48.06 Å / Cor.coef. F_o:F_c: 0.967 / Cor.coef. F_o:F_c free: 0.958 / SU B: 1.226 / SU ML: 0.025 / Cross valid method: THROUGHOUT / ESU R: 0.053 / ESU R Free: 0.051 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS, SELENIUM C COEFFICIENT FOR STRUCTURE FACTOR CALCULATION SET TO -9.00

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.186	2068	5.1 %	RANDOM
R_work	0.156	-	-	-
all	0.157	-	-	-
obs	0.15708	38582	95.4 %	-

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: 17.287 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	0.07 Å²	0 Å²	0 Å²
2-	-	-0.1 Å²	0 Å²
3-	-	-	0.03 Å²

Refinement step

Cycle: LAST / Resolution: 1.32→48.06 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	1220	0	0	329	1549

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.011	0.022	1251
X-RAY DIFFRACTION	r_angle_refined_deg	1.311	1.975	1697
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	6.37	5	152
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	35.693	23.846	52
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	11.941	15	221
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	18.235	15	7
X-RAY DIFFRACTION	r_chiral_restr	0.09	0.2	188
X-RAY DIFFRACTION	r_gen_planes_refined	0.006	0.02	934
X-RAY DIFFRACTION	r_nbd_refined	0.192	0.2	501
X-RAY DIFFRACTION	r_nbtor_refined	0.292	0.2	840
X-RAY DIFFRACTION	r_xyhbond_nbd_refined	0.179	0.2	229
X-RAY DIFFRACTION	r_symmetry_vdw_refined	0.16	0.2	34
X-RAY DIFFRACTION	r_symmetry_hbond_refined	0.109	0.2	37
X-RAY DIFFRACTION	r_mcbond_it	1.329	1.5	803
X-RAY DIFFRACTION	r_mcangle_it	1.834	2	1256
X-RAY DIFFRACTION	r_scbond_it	2.751	3	524
X-RAY DIFFRACTION	r_scangle_it	3.552	4.5	441
X-RAY DIFFRACTION	r_sphericity_free	3.111	3	329
X-RAY DIFFRACTION	r_sphericity_bonded	3.071	3	1220
X-RAY DIFFRACTION	r_rigid_bond_restr	2.309	3	1327

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 (%)
1.32-1.354	0.21	136	0.16	2641	3109	89.321
1.354-1.391	0.187	147	0.15	2666	2983	94.301
1.391-1.431	0.192	134	0.149	2654	2985	93.4
1.431-1.475	0.17	143	0.141	2548	2850	94.421
1.475-1.524	0.165	146	0.14	2469	2762	94.678
1.524-1.577	0.194	118	0.134	2437	2697	94.735
1.577-1.637	0.164	137	0.135	2359	2611	95.596
1.637-1.703	0.173	111	0.144	2276	2486	96.018
1.703-1.779	0.188	124	0.154	2188	2414	95.775
1.779-1.866	0.197	105	0.156	2115	2308	96.187
1.866-1.966	0.172	102	0.156	2016	2199	96.317
1.966-2.085	0.212	92	0.156	1933	2077	97.496
2.085-2.229	0.177	100	0.155	1828	1969	97.918
2.229-2.407	0.193	94	0.169	1704	1834	98.037
2.407-2.636	0.245	87	0.185	1581	1714	97.316
2.636-2.946	0.199	84	0.191	1443	1550	98.516
2.946-3.4	0.19	70	0.178	1257	1378	96.299
3.4-4.159	0.17	57	0.174	1101	1181	98.052
4.159-5.86	0.188	53	0.173	858	935	97.433
5.86-48.057	0.257	28	0.227	508	570	94.035

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