PDB-1si9: Boiling stable protein isolated from Populus tremula

ID or keywords:

Entry

Database: PDB / ID: 1si9

Title

Boiling stable protein isolated from Populus tremula

Components

stable protein 1

Keywords

PLANT PROTEIN / stress / heat shock responsive / boiling-soluble

Function / homology

Function and homology information

pollen tube adhesion
Similarity search - Function

Biological species

Populus tremula (European aspen)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MAD / Resolution: 2.27 Å

Authors

Almog, O. / Gonzales, A. / Shoseyov, O. / Dgany, O. / Sofer, O. / Wolf, S.G.

Citation

Journal: J.Biol.Chem. / Year: 2004
Title: The Structural Basis of the Thermostability of SP1, a Novel Plant (Populus tremula) Boiling Stable Protein.
Authors: Dgany, O. / Gonzalez, A. / Sofer, O. / Wang, W. / Zolotnitsky, G. / Wolf, A. / Shoham, Y. / Altman, A. / Wolf, S.G. / Shoseyov, O. / Almog, O.

History

Deposition	Feb 29, 2004	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Sep 21, 2004	Provider: repository / Type: Initial release
Revision 1.1	Apr 29, 2008	Group: Version format compliance
Revision 1.2	Jul 13, 2011	Group: Advisory / Derived calculations ...Advisory / Derived calculations / Refinement description / Version format compliance
Revision 1.3	Feb 14, 2024	Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_special_symmetry / struct_ncs_dom_lim / struct_site Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.end_auth_comp_id / _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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PDBx/mmCIF format	1si9.cif.gz	86.9 KB	Display	PDBx/mmCIF format
PDB format	pdb1si9.ent.gz	67.8 KB	Display	PDB format
PDBx/mmJSON format	1si9.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/si/1si9 ftp://data.pdbj.org/pub/pdb/validation_reports/si/1si9	HTTPS FTP

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Related structure data

Related structure data	1tr0C C: citing same article (ref.)
Similar structure data	5u7q-4 3qtn-d 3etb-2 5u7q-1 6ed6-2 2h9v-d 6ed6-1 2jbh-d 4mnf-d 3qtm-1 Search similar-shape structures by Omokage search (details) Search similar-shape structures by Omokage search (details) 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

Related structure data

1tr0C

C: citing same article (ref.)

Similar structure data

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Links

PDB pages	PDBj / wwPDB / NCBI

Deposited unit

A: stable protein 1

B: stable protein 1

C: stable protein 1

hetero molecules

37.5 kDa, 3 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

Idetical with deposited unit
defined by author

2

B: stable protein 1

hetero molecules

B: stable protein 1

hetero molecules

B: stable protein 1

hetero molecules

B: stable protein 1

hetero molecules

A: stable protein 1

C: stable protein 1

hetero molecules

A: stable protein 1

C: stable protein 1

hetero molecules

A: stable protein 1

C: stable protein 1

hetero molecules

A: stable protein 1

C: stable protein 1

hetero molecules

defined by software
150 kDa, 12 polymers
Search similar-shape structures of this assembly by Omokage search (details)

Type	Name	Symmetry operation	Number
crystal symmetry operation	3_555	-y,x,z	1
crystal symmetry operation	4_565	y,-x+1,z	1
crystal symmetry operation	13_555	-x+1/2,y+1/2,-z+1/2	1
crystal symmetry operation	14_455	x-1/2,-y+1/2,-z+1/2	1
identity operation	1_555	x,y,z	1
crystal symmetry operation	2_565	-x,-y+1,z	1
crystal symmetry operation	15_455	y-1/2,x+1/2,-z+1/2	1
crystal symmetry operation	16_555	-y+1/2,-x+1/2,-z+1/2	1

3

A: stable protein 1

C: stable protein 1

hetero molecules

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

4

B: stable protein 1

hetero molecules

B: stable protein 1

hetero molecules

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

Unit cell

Length a, b, c (Å)	90.501, 90.501, 186.302
Angle α, β, γ (deg.)	90.00, 90.00, 90.00
Int Tables number	97
Space group name H-M	I422

Components on special symmetry positions

ID	Model	Components
1	1	A-165- HOH
2	1	B-212- HOH
3	1	B-223- HOH

Noncrystallographic symmetry (NCS)

NCS domain:

ID	Ens-ID	Details
1	1	A
2	1	B
3	1	C
4	1	A
5	1	B
6	1	C
7	1	A
8	1	B
9	1	C
10	1	A
11	1	B
12	1	C

NCS domain segments:

Ens-ID: 1

Dom-ID	Component-ID	Beg auth comp-ID	Beg label comp-ID	End auth comp-ID	End label comp-ID	Refine code	Auth asym-ID	Label asym-ID	Auth seq-ID	Label seq-ID
1	1	ARG	ARG	LYS	LYS	2	A	A	4 - 18	4 - 18
2	1	ARG	ARG	LYS	LYS	2	B	B	4 - 18	4 - 18
3	1	ARG	ARG	LYS	LYS	2	C	C	4 - 18	4 - 18
4	2	ASP	ASP	ARG	ARG	5	A	A	19 - 23	19 - 23
5	2	ASP	ASP	ARG	ARG	5	B	B	19 - 23	19 - 23
6	2	ASP	ASP	ARG	ARG	5	C	C	19 - 23	19 - 23
7	3	GLU	GLU	GLN	GLN	2	A	A	24 - 99	24 - 99
8	3	GLU	GLU	GLN	GLN	2	B	B	24 - 99	24 - 99
9	3	GLU	GLU	GLN	GLN	2	C	C	24 - 99	24 - 99
10	4	LEU	LEU	TYR	TYR	2	A	A	101 - 108	101 - 108
11	4	LEU	LEU	TYR	TYR	2	B	B	101 - 108	101 - 108
12	4	LEU	LEU	TYR	TYR	2	C	C	101 - 108	101 - 108

#1: Protein	stable protein 1 Mass: 12422.962 Da / Num. of mol.: 3 / Source method: isolated from a natural source / Source: (natural) Populus tremula (European aspen) / References: UniProt: Q9AR79
#2: Chemical	ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol Mass: 92.094 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C₃H₈O₃
#3: Water	ChemComp-HOH / water / Water Mass: 18.015 Da / Num. of mol.: 409 / 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: 2.56 Å³/Da / Density % sol: 51.93 %

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Data collection

Diffraction source

Source:

SYNCHROTRON / Site:

SSRL

/ Beamline: BL9-2 / Wavelength: 0.979, 0.905, 0.980

Radiation

Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray

Radiation wavelength

ID	Wavelength (Å)	Relative weight
1	0.979	1
2	0.905	1
3	0.98	1

Reflection

Resolution: 2.27→91.29 Å / Num. all: 17318 / Num. obs: 17318 / % possible obs: 99.36 %

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Processing

Software

Name: REFMAC / Version: 5.1.24 / Classification: refinement

Refinement

Method to determine structure:

MAD / Resolution: 2.27→91.29 Å / Cor.coef. F_o:F_c: 0.949 / Cor.coef. F_o:F_c free: 0.931 / SU B: 10.259 / SU ML: 0.232 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.378 / ESU R Free: 0.252
Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.25808	910	5 %	RANDOM
R_work	0.20624	-	-	-
obs	0.20874	17318	99.36 %	-

Solvent computation

Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK

Displacement parameters

B_iso mean: 17.344 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	3.39 Å²	0 Å²	0 Å²
2-	-	3.39 Å²	0 Å²
3-	-	-	-6.78 Å²

Refinement step

Cycle: LAST / Resolution: 2.27→91.29 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	2589	0	18	409	3016

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.006	0.021	2738
X-RAY DIFFRACTION	r_bond_other_d	0	0.02	2428
X-RAY DIFFRACTION	r_angle_refined_deg	0.909	1.966	3708
X-RAY DIFFRACTION	r_angle_other_deg	3.597	3	5666
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	6.56	5	324
X-RAY DIFFRACTION	r_dihedral_angle_2_deg
X-RAY DIFFRACTION	r_dihedral_angle_3_deg
X-RAY DIFFRACTION	r_dihedral_angle_4_deg
X-RAY DIFFRACTION	r_chiral_restr	0.057	0.2	413
X-RAY DIFFRACTION	r_gen_planes_refined	0.003	0.02	3018
X-RAY DIFFRACTION	r_gen_planes_other	0.004	0.02	589
X-RAY DIFFRACTION	r_nbd_refined	0.212	0.3	602
X-RAY DIFFRACTION	r_nbd_other	0.298	0.3	2750
X-RAY DIFFRACTION	r_nbtor_refined
X-RAY DIFFRACTION	r_nbtor_other	0.143	0.5	1344
X-RAY DIFFRACTION	r_xyhbond_nbd_refined	0.246	0.5	407
X-RAY DIFFRACTION	r_xyhbond_nbd_other
X-RAY DIFFRACTION	r_metal_ion_refined
X-RAY DIFFRACTION	r_metal_ion_other
X-RAY DIFFRACTION	r_symmetry_vdw_refined	0.236	0.3	56
X-RAY DIFFRACTION	r_symmetry_vdw_other	0.318	0.3	191
X-RAY DIFFRACTION	r_symmetry_hbond_refined	0.259	0.5	75
X-RAY DIFFRACTION	r_symmetry_hbond_other
X-RAY DIFFRACTION	r_mcbond_it	0.534	1.5	1618
X-RAY DIFFRACTION	r_mcbond_other
X-RAY DIFFRACTION	r_mcangle_it	0.985	2	2618
X-RAY DIFFRACTION	r_scbond_it	1.058	3	1120
X-RAY DIFFRACTION	r_scangle_it	1.809	4.5	1088
X-RAY DIFFRACTION	r_rigid_bond_restr
X-RAY DIFFRACTION	r_sphericity_free
X-RAY DIFFRACTION	r_sphericity_bonded

Refine LS restraints NCS

Ens-ID: 1 / Refine-ID: X-RAY DIFFRACTION

Dom-ID	Auth asym-ID	Number	Type	Rms dev position (Å)	Weight position
1	A	562	tight positional	0.07	0.12
2	B	562	tight positional	0.08	0.12
3	C	562	tight positional	0.07	0.12
1	A	862	medium positional	0.36	0.6
2	B	862	medium positional	0.58	0.6
3	C	862	medium positional	0.4	0.6
1	A	23	loose positional	1.8	5
2	B	23	loose positional	1.06	5
3	C	23	loose positional	1.3	5
1	A	562	tight thermal	0.31	1
2	B	562	tight thermal	0.46	1
3	C	562	tight thermal	0.26	1
1	A	862	medium thermal	1.31	5
2	B	862	medium thermal	1.52	5
3	C	862	medium thermal	0.89	5
1	A	23	loose thermal	1.53	10
2	B	23	loose thermal	0.53	10
3	C	23	loose thermal	1.83	10

LS refinement shell

Resolution: 2.27→2.329 Å / Total num. of bins used: 20 /

	R_factor	Num. reflection
R_free	0.341	72
R_work	0.32	1247

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	4.1392	-4.8142	0.0577	11.6165	-1.3606	2.3581	0.135	-0.1784	0.0314	-0.0398	0.0157	-0.0805	-0.1116	0.4659	-0.1507	0.1251	-0.0051	0.0306	0.2352	-0.0429	0.511	30.927	27.941	44.668
2	1.6862	-1.2386	-0.0087	3.4707	-1.5033	1.0517	0.228	0.1213	0.4445	-0.3109	-0.3598	-0.5453	-0.0646	0.3457	0.1318	0.2194	-0.0282	0.0962	0.1619	-0.0486	0.5504	31.908	35.022	34.629
3	4.4772	-0.7924	-2.7481	2.3545	0.2188	4.7971	0.4118	0.2332	-0.3744	-0.7163	-0.3125	0.2855	-0.2626	-0.125	-0.0993	0.4694	0.0847	-0.1336	0.1141	-0.0562	0.4718	6.592	25.21	17.975
4	3.9717	0.8064	-0.6473	1.2953	-1.0453	3.8383	0.169	-0.0026	-0.6663	-0.3645	-0.1631	0.2368	0.261	-0.5102	-0.0059	0.3089	0.0402	-0.158	0.006	-0.0016	0.5687	7.198	16.57	26.591
5	1.4786	-0.6885	-0.0828	2.0794	-0.1383	1.1854	0.1949	-0.0023	-0.0842	-0.4449	-0.0371	0.003	0.1485	0.0906	-0.1578	0.3002	0.0408	-0.0282	0.1069	-0.029	0.4666	16.267	26.491	28.082
6	1.0064	-0.0114	0.5668	0.245	-0.5534	1.1404	0.118	-0.0614	-0.0455	-0.0649	-0.0079	-0.0539	0.0113	0.0961	-0.1101	0.2446	0.0299	0.0179	0.1405	-0.0114	0.4944	21.388	26.569	34.312
7	5.1352	1.4987	-2.765	2.5991	0.2815	1.7184	-0.461	0.9914	-0.1077	-0.2035	0.2707	0.1171	0.0677	-0.1032	0.1903	0.1204	-0.1325	0.0044	0.6039	0.1242	0.4517	46.337	12.086	15.978
8	5.7237	0.8513	0.667	2.3211	-0.739	1.2808	-0.2442	1.3628	0.8293	0.1429	0.4324	0.5392	-0.1393	0.015	-0.1882	0.0884	-0.1469	-0.0546	0.6812	0.3002	0.4659	37.658	14.198	14.512
9	3.3279	2.1882	-0.7267	2.7194	0.0176	0.3206	-0.4567	1.0641	0.1191	-0.2113	0.6498	0.0388	0.0423	-0.1731	-0.1931	0.1599	-0.1648	-0.0061	0.6068	-0.0276	0.3443	49.243	3.59	14.838

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Auth asym-ID	Auth seq-ID
1	X-RAY DIFFRACTION	1	A	18 - 43
2	X-RAY DIFFRACTION	2	A	72 - 97
3	X-RAY DIFFRACTION	3	C	18 - 43
4	X-RAY DIFFRACTION	4	C	72 - 97
5	X-RAY DIFFRACTION	5	C	3 - 17
6	X-RAY DIFFRACTION	5	C	44 - 71
7	X-RAY DIFFRACTION	5	C	98 - 108
8	X-RAY DIFFRACTION	6	A	3 - 17
9	X-RAY DIFFRACTION	6	A	44 - 71
10	X-RAY DIFFRACTION	6	A	98 - 108
11	X-RAY DIFFRACTION	7	B	18 - 43
12	X-RAY DIFFRACTION	8	B	72 - 97
13	X-RAY DIFFRACTION	9	B	3 - 17
14	X-RAY DIFFRACTION	9	B	44 - 71
15	X-RAY DIFFRACTION	9	B	98 - 108

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