PDB-3ha9: The 1.7A Crystal Structure of a Thioredoxin-like Protein from Aer...

ID or keywords:

Entry

Database: PDB / ID: 3ha9

Title

The 1.7A Crystal Structure of a Thioredoxin-like Protein from Aeropyrum pernix

Components

uncharacterized Thioredoxin-like protein

Keywords

structural genomics / unknown function /

thioredoxin-like /

aeropyrum / pernix / PSI / MCSG / Midwest Center for Structural Genomics /

Protein Structure Initiative

Function / homology

Function and homology information

antioxidant activity /

oxidoreductase activity
Similarity search - Function

Biological species

Aeropyrum pernix (archaea)

Method

X-RAY DIFFRACTION /

SYNCHROTRON / Resolution: 1.7 Å

Authors

Stein, A.J. / Cuff, M.E. / Sather, A. / Hendricks, R. / Freeman, L. / Joachimiak, A. / Midwest Center for Structural Genomics (MCSG)

Citation

Journal: To be Published
Title: The 1.7A Crystal Structure of a Thioredoxin-like Protein from Aeropyrum pernix
Authors: Stein, A.J. / Cuff, M.E. / Sather, A. / Hendricks, R. / Freeman, L. / Joachimiak, A.

History

Deposition	May 1, 2009	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	May 19, 2009	Provider: repository / Type: Initial release
Revision 1.1	Jul 13, 2011	Group: Advisory / Version format compliance
Revision 1.2	Nov 1, 2017	Group: Refinement description / Category: software

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	3ha9.cif.gz	45.5 KB	Display	PDBx/mmCIF format
PDB format	pdb3ha9.ent.gz	36.3 KB	Display	PDB format
PDBx/mmJSON format	3ha9.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/ha/3ha9 ftp://data.pdbj.org/pub/pdb/validation_reports/ha/3ha9	HTTPS FTP

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Related structure data

Similar structure data	6pi4-d 5j8e-2 1o4w-d 2gsb-d 2gm2-d 3eoi-2 7by2-d 5j8e-1 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: APC61419.1

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Links

PDB pages	PDBj / wwPDB / NCBI

Deposited unit

A: uncharacterized Thioredoxin-like protein

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

1

Idetical with deposited unit
defined by author

2

A: uncharacterized Thioredoxin-like protein

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

Unit cell

Length a, b, c (Å)	74.742, 74.742, 59.451
Angle α, β, γ (deg.)	90.000, 90.000, 90.000
Int Tables number	96
Space group name H-M	P4₃2₁2

Details

biological unit is the same as asymmetric unit.

#1: Protein	uncharacterized Thioredoxin-like protein Mass: 18172.656 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Aeropyrum pernix (archaea) / Strain: K1 / Gene: APE2568, APE_2568.1 / Plasmid: pMCSG19 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q9Y8R5
#2: Water	ChemComp-HOH / water / Water Mass: 18.015 Da / Num. of mol.: 130 / Source method: isolated from a natural source / Formula: H₂O

#1: Protein

uncharacterized Thioredoxin-like protein

Mass: 18172.656 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.)

Aeropyrum pernix (archaea) / Strain: K1 / Gene: APE2568, APE_2568.1 / Plasmid: pMCSG19 / Production host:

Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q9Y8R5

#2: Water

ChemComp-HOH / water /

Water

Mass: 18.015 Da / Num. of mol.: 130 / 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: 2.32 Å³/Da / Density % sol: 47.6 %
Crystal grow	Temperature: 277 K / Method: vapor diffusion / pH: 4.6 Details: 3.5M Sodium formate, 0.1M Sodium acetate, pH 4.6, vapor diffusion, temperature 277K

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Data collection

Diffraction

Mean temperature: 100 K

Diffraction source

Source:

SYNCHROTRON / Site:

APS

/ Beamline: 19-ID / Wavelength: 0.97926 Å

Detector

Type: ADSC QUANTUM 315r / Detector: CCD / Date: Apr 21, 2009

Radiation

Monochromator: Double crystal / Protocol: SINGLE WAVELENGTH / Scattering type: x-ray

Radiation wavelength

Wavelength: 0.97926 Å / Relative weight: 1

Reflection

Resolution: 1.65→50 Å / Num. obs: 20769 / % possible obs: 99.4 % / Redundancy: 9.3 % / R_merge(I) obs: 0.088 / Χ²: 2.821 / Net I/σ(I): 13

Reflection shell

Resolution (Å)	Redundancy (%)	R_merge(I) obs	Num. unique all	Χ²	Diffraction-ID	% possible all
1.65-1.71	9.5	0.752	2046	1.177	1	100
1.71-1.78	9.5	0.526	2027	1.169	1	100
1.78-1.86	9.5	0.35	2050	1.176	1	100
1.86-1.96	9.5	0.217	2059	1.328	1	100
1.96-2.08	9.5	0.151	2062	1.68	1	100
2.08-2.24	9.5	0.112	2056	2.07	1	100
2.24-2.46	9.4	0.096	2096	2.701	1	100
2.46-2.82	9.3	0.095	2094	4.427	1	100
2.82-3.55	9	0.073	2116	5.131	1	99.5
3.55-50	8.3	0.069	2163	7.882	1	95.1

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Processing

Software

Name	Version	Classification
DENZO		data reduction
SCALEPACK		data scaling
REFMAC	refmac_5.5.0054	refinement
PDB_EXTRACT	3.004	data extraction
SBC-Collect		data collection
HKL-3000		data reduction
HKL-3000		data scaling
HKL-3000		phasing
SHELX		phasing
MLPHARE		phasing
DM		phasing
ARP/wARP		model building
Coot		model building

Refinement

Resolution: 1.7→27.62 Å / Cor.coef. F_o:F_c: 0.956 / Cor.coef. F_o:F_c free: 0.936 / WR_factor R_free: 0.242 / WR_factor R_work: 0.203 / SU B: 4.705 / SU ML: 0.071 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.112 / ESU R Free: 0.112 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : RESIDUAL ONLY

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.232	978	5.2 %	RANDOM
R_work	0.194	-	-	-
obs	0.196	18952	99.35 %	-

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: 16.861 Å²

	B_aniso -1	B_aniso -2
1-	0 Å²	0 Å²
2-	-	0 Å²
3-	-	-

Refinement step

Cycle: LAST / Resolution: 1.7→27.62 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	1245	0	0	130	1375

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.011	0.022	1288
X-RAY DIFFRACTION	r_angle_refined_deg	1.198	1.968	1761
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	5.361	5	166
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	36.422	24.423	52
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	13.366	15	210
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	15.427	15	6
X-RAY DIFFRACTION	r_chiral_restr	0.08	0.2	202
X-RAY DIFFRACTION	r_gen_planes_refined	0.007	0.021	970
X-RAY DIFFRACTION	r_mcbond_it	0.555	1.5	812
X-RAY DIFFRACTION	r_mcangle_it	0.981	2	1319
X-RAY DIFFRACTION	r_scbond_it	2.098	3	476
X-RAY DIFFRACTION	r_scangle_it	2.79	4.5	439

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	0.247	76	0.225	1292	1372	99.708
1.744-1.792	0.283	64	0.21	1274	1340	99.851
1.792-1.843	0.249	68	0.197	1230	1298	100
1.843-1.9	0.244	75	0.187	1201	1276	100
1.9-1.962	0.23	68	0.185	1170	1239	99.919
1.962-2.03	0.212	56	0.183	1147	1203	100
2.03-2.106	0.191	66	0.186	1070	1136	100
2.106-2.192	0.229	62	0.174	1063	1125	100
2.192-2.289	0.217	46	0.183	1032	1078	100
2.289-2.4	0.224	55	0.176	970	1025	100
2.4-2.528	0.243	61	0.192	928	989	100
2.528-2.68	0.264	40	0.209	891	931	100
2.68-2.863	0.234	37	0.225	842	879	100
2.863-3.09	0.241	40	0.217	787	828	99.879
3.09-3.381	0.193	34	0.202	728	766	99.478
3.381-3.773	0.284	42	0.179	647	701	98.288
3.773-4.343	0.238	31	0.161	575	628	96.497
4.343-5.286	0.179	28	0.179	496	545	96.147
5.286-7.343	0.305	16	0.224	413	434	98.848
7.343-27.618	0.217	13	0.248	218	283	81.625

Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

ID	L11 (°²)	L12 (°²)	L13 (°²)	L22 (°²)	L23 (°²)	L33 (°²)	S11 (Å °)	S12 (Å °)	S13 (Å °)	S21 (Å °)	S22 (Å °)	S23 (Å °)	S31 (Å °)	S32 (Å °)	S33 (Å °)	T11 (Å²)	T12 (Å²)	T13 (Å²)	T22 (Å²)	T23 (Å²)	T33 (Å²)	Origin x (Å)	Origin y (Å)	Origin z (Å)
1	5.809	-2.4132	-1.9392	4.5765	-3.6906	9.3625	-0.1137	-0.1291	0.3123	0.3813	0.2239	0.3816	-0.3546	-0.5064	-0.1102	0.1532	0.0333	0.0342	0.1765	0.006	0.2531	7.6181	39.394	44.258
2	8.3388	-3.3735	-1.5368	3.9794	0.0883	0.3923	0.0458	0.1783	-0.0395	-0.0379	-0.0135	0.2275	-0.0094	-0.0494	-0.0323	0.1372	0.0607	-0.0188	0.1481	0.005	0.1759	11.5695	37.4508	36.8415
3	4.3787	-4.5501	-1.7443	8.8933	3.0204	12.4362	0.0565	0.3103	-0.0735	-0.3087	-0.0154	-0.0401	-0.0232	0.077	-0.0411	0.1436	-0.0109	0.0031	0.1555	-0.0042	0.1488	17.5749	34.3653	31.827
4	1.1441	-1.2748	-0.3852	1.4335	0.2967	5.4506	-0.0285	-0.0728	0.0018	-0.0146	0.0509	0.0202	-0.6719	0.1137	-0.0224	0.2488	-0.0272	-0.0285	0.1711	0.0166	0.148	21.2793	30.344	16.8436
5	4.1712	1.0989	-2.0876	1.9605	0.777	7.3833	0.3732	0.0639	0.4274	-0.1807	-0.2057	0.217	-1.1592	-0.581	-0.1675	0.2398	0.0833	-0.0465	0.1275	0.0064	0.15	17.1269	30.6223	12.7177
6	4.1242	-0.1039	-1.07	0.8796	0.7779	3.3192	0.0041	-0.0205	0.023	-0.0715	-0.0584	0.102	0.0131	-0.4612	0.0543	0.125	-0.0116	-0.014	0.159	-0.0144	0.1404	16.4572	19.2342	17.9369
7	1.2977	1.3983	0.2395	1.5293	0.317	0.2127	-0.0192	0.119	-0.0989	0.0596	0.0946	-0.1199	0.1963	0.0038	-0.0754	0.2423	-0.0023	-0.0234	0.1234	-0.0184	0.149	29.6761	11.8332	12.0393
8	1.8855	0.1836	-1.2106	0.6993	0.9792	3.1759	-0.0737	0.0043	-0.1233	0.1344	-0.0207	0.1213	0.3887	-0.2239	0.0944	0.1758	-0.0818	0.0274	0.1311	-0.0068	0.1919	17.0227	8.3878	12.2079
9	2.9159	-4.3897	3.9138	8.0257	-5.1282	5.7267	0.0639	-0.053	-0.2019	-0.1303	0.0776	0.3632	0.0783	-0.1887	-0.1415	0.0676	-0.0919	0.0083	0.322	-0.0418	0.284	6.3838	13.1608	12.3335
10	4.254	0.6344	1.2433	0.7146	0.2609	1.6504	0.0526	-0.1204	0.0022	0.0024	-0.0444	0.0653	-0.0406	-0.1682	-0.0082	0.1157	0.0182	-0.0124	0.1277	-0.0079	0.1433	23.4125	20.7014	14.3156
11	7.3442	-2.8309	-0.5439	7.2665	-3.1387	5.2864	-0.0488	0.0167	0.1663	0.0563	0.1781	-0.0783	-0.2299	0.2619	-0.1293	0.0833	-0.0132	-0.0248	0.1278	-0.0246	0.1472	39.4922	24.2429	18.3719
12	4.6688	-1.0044	3.3521	1.5472	-0.8831	2.4667	-0.1353	0.1869	0.1644	-0.0162	0.0545	-0.0876	-0.0577	0.1964	0.0808	0.0976	0.0314	-0.0009	0.1844	-0.0242	0.145	39.6039	18.844	11.2843
13	8.1656	-0.3054	-0.587	5.9088	0.9424	5.2778	-0.0791	0.4168	-0.004	-0.4051	0.0186	0.0751	-0.1229	0.1024	0.0605	0.1122	-0.0105	-0.0164	0.1173	-0.0021	0.1077	28.1112	19.6967	2.8761
14	2.8579	3.0583	0.9843	5.0898	-0.1538	1.1413	0.0004	-0.0422	-0.013	-0.0708	-0.0583	-0.1047	0.0538	-0.0128	0.0579	0.1265	-0.011	0.0009	0.1249	-0.0236	0.1513	23.4523	13.0298	4.3886
15	0.7322	1.5723	0.1708	3.684	1.0067	2.2978	-0.1222	0.0193	0.1431	-0.3213	-0.051	0.2807	-0.0986	-0.3433	0.1732	0.1272	0.0261	-0.0248	0.148	-0.0169	0.1312	20.0298	21.5848	9.2333
16	4.767	-0.5965	-3.5398	3.8504	-3.9521	9.239	0.0376	-0.15	0.2321	0.1847	-0.0106	-0.1335	-0.3923	0.339	-0.027	0.1369	-0.0127	-0.0068	0.1284	-0.0076	0.1356	29.4542	26.8037	21.7833
17	1.9484	0.8399	-0.2578	0.438	0.2848	2.4025	-0.0262	-0.0099	0.0677	0.0472	-0.0276	0.055	0.1367	-0.1488	0.0538	0.1453	0.0064	0.01	0.1271	-0.0054	0.1413	22.07	18.9048	23.417
18	6.4363	-4.5725	-0.8657	8.3876	0.9428	3.8019	0.0424	0.1807	-0.1316	-0.101	-0.1469	0.372	-0.0027	-0.345	0.1046	0.1371	-0.0177	-0.0071	0.1793	-0.0144	0.1354	14.308	19.1485	27.3479
19	6.841	-0.2233	5.0013	3.6247	2.2203	5.2541	0.4672	-0.2941	-0.3747	0.1982	-0.1466	-0.0819	0.5729	-0.2961	-0.3206	0.3083	-0.0479	0.0667	0.1147	0.0033	0.1165	19.9676	7.7059	21.5135
20	5.1563	-0.5346	-2.3344	5.3496	1.6173	7.2391	0.0965	-0.1837	0.1019	0.0697	-0.1061	0.4473	-0.1535	-0.5355	0.0097	0.1952	-0.0517	0.0161	0.2088	-0.0141	0.1963	9.9842	10.2439	23.0655

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Auth asym-ID	Auth seq-ID
1	X-RAY DIFFRACTION	1	A	27 - 32
2	X-RAY DIFFRACTION	2	A	33 - 37
3	X-RAY DIFFRACTION	3	A	38 - 43
4	X-RAY DIFFRACTION	4	A	44 - 49
5	X-RAY DIFFRACTION	5	A	50 - 61
6	X-RAY DIFFRACTION	6	A	62 - 69
7	X-RAY DIFFRACTION	7	A	70 - 78
8	X-RAY DIFFRACTION	8	A	79 - 87
9	X-RAY DIFFRACTION	9	A	88 - 92
10	X-RAY DIFFRACTION	10	A	93 - 104
11	X-RAY DIFFRACTION	11	A	105 - 113
12	X-RAY DIFFRACTION	12	A	114 - 123
13	X-RAY DIFFRACTION	13	A	124 - 128
14	X-RAY DIFFRACTION	14	A	129 - 134
15	X-RAY DIFFRACTION	15	A	135 - 143
16	X-RAY DIFFRACTION	16	A	144 - 149
17	X-RAY DIFFRACTION	17	A	150 - 164
18	X-RAY DIFFRACTION	18	A	165 - 171
19	X-RAY DIFFRACTION	19	A	172 - 178
20	X-RAY DIFFRACTION	20	A	179 - 187

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