PDB-3rnr: Crystal Structure of Stage II Sporulation E Family Protein from T...

ID or keywords:

Entry

Database: PDB / ID: 3rnr

Title

Crystal Structure of Stage II Sporulation E Family Protein from Thermanaerovibrio acidaminovorans

Components

Stage II sporulation E family protein

Keywords

STRUCTURAL GENOMICS / UNKNOWN FUNCTION / PSI-Biology / Midwest Center for Structural Genomics / MCSG / alpha-beta-alpha sandwich / phosphatase / cytosol

Function / homology

Function and homology information

protein serine/threonine phosphatase activity
Similarity search - Function

Biological species

Thermanaerovibrio acidaminovorans (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

SAD / Resolution: 2 Å

Authors

Kim, Y. / Li, H. / Clancy, S. / Joachimiak, A. / Midwest Center for Structural Genomics (MCSG)

Citation

Journal: To be Published
Title: Crystal Structure of Stage II Sporulation E Family Protein from Thermanaerovibrio acidaminovorans
Authors: Kim, Y. / Li, H. / Clancy, S. / Joachimiak, A.

History

Deposition	Apr 22, 2011	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Jun 29, 2011	Provider: repository / Type: Initial release
Revision 1.1	Jul 13, 2011	Group: Version format compliance

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	3rnr.cif.gz	173.5 KB	Display	PDBx/mmCIF format
PDB format	pdb3rnr.ent.gz	148.3 KB	Display	PDB format
PDBx/mmJSON format	3rnr.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	3rnr_validation.pdf.gz	478.6 KB	Display	wwPDB validaton report
Full document	3rnr_full_validation.pdf.gz	493 KB	Display
Data in XML	3rnr_validation.xml.gz	22.5 KB	Display
Data in CIF	3rnr_validation.cif.gz	31.4 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/rn/3rnr ftp://data.pdbj.org/pub/pdb/validation_reports/rn/3rnr	HTTPS FTP

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Related structure data

Similar structure data	2vqj-d 5ngf-1 5gsy-d 5ahs-2 3b9o-2 4m5x-1 5ahs-6 5ew1-d 3hj1-2 5ahs-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: APC100780

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Links

PDB pages	PDBj / wwPDB / NCBI
Related items in Molecule of the Month	#4 - Apr 2000 Collagen similarity (1) #116 - Aug 2009 Sulfotransferases similarity (1)

Deposited unit

A: Stage II sporulation E family protein

B: Stage II sporulation E family protein

hetero molecules

45.3 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)	65.530, 87.349, 93.364
Angle α, β, γ (deg.)	90.00, 90.00, 90.00
Int Tables number	19
Space group name H-M	P2₁2₁2₁

#1: Protein	Stage II sporulation E family protein Mass: 22000.910 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Thermanaerovibrio acidaminovorans (bacteria) Strain: DSM 6589 / Gene: Taci_1699 / Plasmid: pMCSG7 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 Magic / References: UniProt: D1B7C2
#2: Chemical	ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL Mass: 92.094 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: C₃H₈O₃
#3: Chemical	ChemComp-ACY / ACETIC ACID Mass: 60.052 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C₂H₄O₂
#4: Chemical	ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL Mass: 62.068 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C₂H₆O₂
#5: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 283 / 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: 3.04 Å³/Da / Density % sol: 59.49 %
Crystal grow	Temperature: 289 K / Method: vapor diffusion, sitting drop / pH: 7.5 Details: 0.1 M HEPES (NaOH) pH 7.5, 10 % (w/v) PEG8000, 10 % (v/v) ethylene Glycol, VAPOR DIFFUSION, SITTING DROP, temperature 289K

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Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: SYNCHROTRON / Site: APS / Beamline: 19-BM / Wavelength: 0.97903 Å
Detector	Type: ADSC QUANTUM 210r / Detector: CCD / Date: Dec 18, 2010 / Details: mirrors
Radiation	Monochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.97903 Å / Relative weight: 1
Reflection	Resolution: 2→50 Å / Num. all: 37141 / Num. obs: 37141 / % possible obs: 100 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 8.8 % / R_merge(I) obs: 0.092 / Net I/σ(I): 10
Reflection shell	Resolution: 2→2.03 Å / Redundancy: 8.9 % / Mean I/σ(I) obs: 5.2 / R_sym value: 0.607 / % possible all: 100

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Processing

Software

Name	Version	Classification
SBC-Collect		data collection
HKL-3000		data collection
HKL-3000		phasing
SHELXS		phasing
MLPHARE		phasing
BUCCANEER		model building
PHENIX	(phenix.refine: 1.7_650)	refinement
HKL-3000		data reduction
HKL-3000		data scaling
BUCCANEER		phasing

Refinement

Method to determine structure:

SAD / Resolution: 2→38.021 Å / SU ML: 0.5 / Isotropic thermal model: mixed / σ(F): 1.34 / Phase error: 17.95 / Stereochemistry target values: MLHL

	R_factor	Num. reflection	% reflection
R_free	0.2022	1827	4.97 %
R_work	0.1692	-	-
obs	0.1708	36788	99.69 %
all	-	36788	-

Solvent computation

Shrinkage radii: 0.95 Å / VDW probe radii: 1.2 Å / Solvent model: FLAT BULK SOLVENT MODEL / B_sol: 52.874 Å² / k_sol: 0.362 e/Å³

Displacement parameters

	B_aniso -1	B_aniso -2	B_aniso -3
1-	3.1442 Å²	-0 Å²	-0 Å²
2-	-	-1.976 Å²	0 Å²
3-	-	-	-1.1681 Å²

Refinement step

Cycle: LAST / Resolution: 2→38.021 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	2999	0	84	283	3366

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.009	3240
X-RAY DIFFRACTION	f_angle_d	1.282	4386
X-RAY DIFFRACTION	f_dihedral_angle_d	14.09	1183
X-RAY DIFFRACTION	f_chiral_restr	0.11	502
X-RAY DIFFRACTION	f_plane_restr	0.007	582

LS refinement shell

Resolution (Å)	R_factor R_free	Num. reflection R_free	R_factor R_work	Num. reflection R_work	Refine-ID	% reflection obs (%)
2-2.0541	0.2621	152	0.2021	2624	X-RAY DIFFRACTION	99
2.0541-2.1145	0.2264	140	0.1897	2644	X-RAY DIFFRACTION	99
2.1145-2.1828	0.2103	119	0.175	2660	X-RAY DIFFRACTION	100
2.1828-2.2608	0.209	131	0.1639	2656	X-RAY DIFFRACTION	100
2.2608-2.3513	0.2064	135	0.1726	2660	X-RAY DIFFRACTION	100
2.3513-2.4583	0.1899	151	0.1747	2644	X-RAY DIFFRACTION	100
2.4583-2.5879	0.1966	130	0.1755	2676	X-RAY DIFFRACTION	100
2.5879-2.7499	0.2171	139	0.1672	2681	X-RAY DIFFRACTION	100
2.7499-2.9622	0.2095	145	0.1673	2684	X-RAY DIFFRACTION	100
2.9622-3.2601	0.1872	157	0.1574	2693	X-RAY DIFFRACTION	100
3.2601-3.7315	0.2221	152	0.1535	2697	X-RAY DIFFRACTION	100
3.7315-4.7	0.1674	133	0.1523	2767	X-RAY DIFFRACTION	100
4.7-38.0279	0.2121	143	0.1924	2875	X-RAY DIFFRACTION	100

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	1.9043	0.41	-0.4393	0.6986	-0.4781	0.8518	-0.065	0.13	-0.1246	-0.0286	0.1911	0.0277	0.053	-0.0334	0.016	0.1905	-0.0322	-0.0166	0.1631	0.0372	0.1765	37.8739	9.0563	60.9806
2	1.3906	-0.0351	-0.9445	0.8175	-0.4628	1.0575	0.0193	-0.4308	-0.2267	0.0065	-0.0651	-0.0598	0.0011	0.3131	0.025	0.2607	-0.0209	-0.0158	0.3317	0.0587	0.2542	46.5598	5.52	75.4615
3	0.4304	-0.3547	0.766	0.7066	-0.7818	1.2681	-0.0123	-0.0567	-0.0412	-0.2174	0.2195	0.2999	0.3683	-0.7037	-0.1323	0.2144	-0.0737	-0.0234	0.2302	0.081	0.2323	27.9769	-3.7159	77.0421
4	2.2585	0.2104	-1.0673	0.7449	-0.6467	0.99	0.1949	-0.6875	-0.0137	0.2172	-0.0307	0.1299	-0.0731	-0.0503	-0.0757	0.2833	-0.0145	0.0192	0.295	0.0086	0.2437	40.745	10.9287	74.6752
5	1.3331	0.2812	-0.5783	0.8621	-0.3161	2.9757	-0.3322	-0.0127	-0.5178	-0.436	0.4543	0.1679	0.8828	0.0162	0.0626	0.4716	-0.1094	-0.033	0.2691	0.0758	0.374	50.1861	-2.1389	64.0643
6	1.1187	-0.5	0.7355	0.3676	-0.211	0.5987	-0.2474	-0.1265	-0.0421	0.4115	-0.0544	-0.2705	0.3715	0.4612	-0.3147	0.4539	-0.0862	-0.3603	0.5513	0.0509	0.2267	63.1212	0.8667	69.4335
7	0.5824	-0.0296	-0.7081	0.4061	-0.4982	1.558	-0.3082	-0.1675	-0.8634	-0.5553	0.1886	-0.8411	1.0949	-0.0481	0.0744	0.6297	-0.091	-0.0468	0.3551	0.1203	0.4259	51.1729	-4.0022	70.6126
8	1.5035	-0.7075	-0.687	1.3784	-0.1406	0.8642	0.1093	0.1035	0.0392	0.0325	-0.0259	-0.1775	-0.0696	-0.1934	-0.0062	0.1928	-0.0153	0.0191	0.2141	0.0109	0.1979	53.3041	13.9047	52.0041
9	1.3731	0.6219	-0.9833	1.0343	-0.475	1.5596	0.0684	0.3373	0.1205	0.1238	0.078	0.2616	0.0015	-0.3469	-0.0842	0.2004	0.0061	0.0023	0.2868	0.0328	0.2767	48.0914	17.6715	47.3657
10	1.1921	-0.0843	-0.2919	0.4023	0.6961	1.8137	-0.0008	0.1495	-0.074	0.0756	-0.0097	-0.1902	0.3407	-0.0146	-0.0065	0.2678	-0.0033	-0.0051	0.2292	-0.0021	0.257	62.0754	5.4506	44.6168
11	4.3645	1.2764	-0.019	4.0886	1.2393	1.7516	-0.3464	-0.4142	0.2623	-0.5488	0.0328	0.436	-0.3388	0.2466	0.2124	0.2257	-0.0189	0.0091	0.2442	0.0134	0.2326	68.9498	20.6207	31.1095
12	1.7218	-0.0485	-0.8241	0.5837	-0.1046	1.3066	0.1692	0.44	0.4955	-0.1619	0.1152	-0.0338	-0.1246	-0.1555	-0.1251	0.2854	0.0323	0.0311	0.2622	0.0269	0.3073	58.4246	22.4325	39.0152
13	2.3887	0.0746	-0.8058	0.9824	0.2196	2.2264	-0.0351	-0.1889	0.2531	0.2172	0.084	-0.0601	0.0483	0.2133	-0.0505	0.2869	0.0048	-0.0058	0.2614	0.0076	0.3159	61.0116	9.0055	51.2631
14	3.9262	-2.2256	1.7064	3.7188	0.9033	2.1919	0.0121	-0.2521	-0.6758	0.7403	-0.5406	-0.7057	1.021	1.3388	-0.1131	0.5242	0.1789	-0.0535	0.587	0.2393	0.5043	63.6994	-1.6545	60.9668
15	1.3988	-0.4959	-0.9094	1.2585	-0.8835	1.9872	0.2343	-0.8804	0.0266	0.1604	-0.6109	-0.5255	0.1029	0.6736	0.1033	0.2804	-0.0409	0.0005	0.4616	0.0755	0.4048	67.6577	8.1383	55.338

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	chain 'A' and (resseq -2:77)
2	X-RAY DIFFRACTION	2	chain 'A' and (resseq 78:109)
3	X-RAY DIFFRACTION	3	chain 'A' and (resseq 110:133)
4	X-RAY DIFFRACTION	4	chain 'A' and (resseq 134:155)
5	X-RAY DIFFRACTION	5	chain 'A' and (resseq 156:176)
6	X-RAY DIFFRACTION	6	chain 'A' and (resseq 177:190)
7	X-RAY DIFFRACTION	7	chain 'A' and (resseq 191:208)
8	X-RAY DIFFRACTION	8	chain 'B' and (resseq -2:21)
9	X-RAY DIFFRACTION	9	chain 'B' and (resseq 22:77)
10	X-RAY DIFFRACTION	10	chain 'B' and (resseq 78:109)
11	X-RAY DIFFRACTION	11	chain 'B' and (resseq 110:124)
12	X-RAY DIFFRACTION	12	chain 'B' and (resseq 125:143)
13	X-RAY DIFFRACTION	13	chain 'B' and (resseq 144:173)
14	X-RAY DIFFRACTION	14	chain 'B' and (resseq 174:190)
15	X-RAY DIFFRACTION	15	chain 'B' and (resseq 191:208)

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