PDB-1tr0: Crystal Structure of a boiling stable protein SP1

ID or keywords:

Entry

Database: PDB / ID: 1tr0

Title

Crystal Structure of a boiling stable protein SP1

Components

stable protein 1

Keywords

PLANT PROTEIN

Function / homology

Function and homology information

Stress-response A/B barrel domain-containing protein HS1/DABB1-like / Stress responsive alpha-beta barrel / Stress responsive A/B Barrel Domain / Stress-response A/B barrel domain profile. / Stress responsive A/B Barrel Domain / Alpha-Beta Plaits - #100 / Dimeric alpha-beta barrel / Alpha-Beta Plaits / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology

Biological species

Populus tremula (European aspen)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 1.8 Å

Authors

Almog, O. / Gonzalez, A. / Sofer, O. / Dgany, O. / Shoseyov, O.

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	Jun 18, 2004	Deposition site: RCSB / Processing site: PDBJ
Revision 1.0	Sep 21, 2004	Provider: repository / Type: Initial release
Revision 1.1	Apr 30, 2008	Group: Version format compliance
Revision 1.2	Jul 13, 2011	Group: Non-polymer description / Version format compliance
Revision 1.3	Oct 25, 2023	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_initial_refinement_model / 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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Download

PDBx/mmCIF format	1tr0.cif.gz	584.1 KB	Display	PDBx/mmCIF format
PDB format	pdb1tr0.ent.gz	475 KB	Display	PDB format
PDBx/mmJSON format	1tr0.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	1tr0_validation.pdf.gz	607.7 KB	Display	wwPDB validaton report
Full document	1tr0_full_validation.pdf.gz	653.6 KB	Display
Data in XML	1tr0_validation.xml.gz	133.5 KB	Display
Data in CIF	1tr0_validation.cif.gz	185.4 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/tr/1tr0 ftp://data.pdbj.org/pub/pdb/validation_reports/tr/1tr0	HTTPS FTP

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Related structure data

Related structure data	1si9SC S: Starting model for refinement C: citing same article (ref.)
Similar structure data	1si9-2 6icp-d 2f6i-d 6ico-d 3vcp-1 3gcf-1 3gcf-4 3vg8-d 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 - HomologyF&H Search

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Links

PDB pages	PDBj / wwPDB / NCBI

Deposited unit

A: stable protein 1

B: stable protein 1

C: stable protein 1

D: stable protein 1

E: stable protein 1

F: stable protein 1

G: stable protein 1

H: stable protein 1

I: stable protein 1

J: stable protein 1

K: stable protein 1

L: stable protein 1

M: stable protein 1

N: stable protein 1

O: stable protein 1

P: stable protein 1

R: stable protein 1

S: stable protein 1

T: stable protein 1

U: stable protein 1

V: stable protein 1

W: stable protein 1

X: stable protein 1

Y: stable protein 1

hetero molecules

300 kDa, 24 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

A: stable protein 1

B: stable protein 1

C: stable protein 1

D: stable protein 1

E: stable protein 1

F: stable protein 1

G: stable protein 1

H: stable protein 1

I: stable protein 1

J: stable protein 1

K: stable protein 1

L: stable protein 1

hetero molecules

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

2

M: stable protein 1

N: stable protein 1

O: stable protein 1

P: stable protein 1

R: stable protein 1

S: stable protein 1

T: stable protein 1

U: stable protein 1

V: stable protein 1

W: stable protein 1

X: stable protein 1

Y: stable protein 1

hetero molecules

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

Unit cell

Length a, b, c (Å)	97.028, 94.750, 168.029
Angle α, β, γ (deg.)	90.00, 90.11, 90.00
Int Tables number	4
Space group name H-M	P12₁1

Noncrystallographic symmetry (NCS)

NCS domain:
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	THR	THR	THR	THR	5	A	A	3	3
2	1	THR	THR	THR	THR	5	B	B	3	3
3	1	THR	THR	THR	THR	5	C	C	3	3
4	1	THR	THR	THR	THR	5	D	D	3	3
5	1	THR	THR	THR	THR	5	E	E	3	3
6	1	THR	THR	THR	THR	5	F	F	3	3
7	1	THR	THR	THR	THR	5	G	G	3	3
8	1	THR	THR	THR	THR	5	H	H	3	3
9	1	THR	THR	THR	THR	5	I	I	3	3
10	1	THR	THR	THR	THR	5	J	J	3	3
11	1	THR	THR	THR	THR	5	K	K	3	3
12	1	THR	THR	THR	THR	5	L	L	3	3
13	1	THR	THR	THR	THR	5	M	M	3	3
14	1	THR	THR	THR	THR	5	N	N	3	3
15	1	THR	THR	THR	THR	5	O	O	3	3
16	1	THR	THR	THR	THR	5	P	P	3	3
17	1	THR	THR	THR	THR	5	R	Q	3	3
18	1	THR	THR	THR	THR	5	S	R	3	3
19	1	THR	THR	THR	THR	5	T	S	3	3
20	1	THR	THR	THR	THR	5	U	T	3	3
21	1	THR	THR	THR	THR	5	V	U	3	3
22	1	THR	THR	THR	THR	5	W	V	3	3
23	1	THR	THR	THR	THR	5	X	W	3	3
24	1	THR	THR	THR	THR	5	Y	X	3	3
25	2	ARG	ARG	THR	THR	4	A	A	4 - 22	4 - 22
26	2	ARG	ARG	THR	THR	4	B	B	4 - 22	4 - 22
27	2	ARG	ARG	THR	THR	4	C	C	4 - 22	4 - 22
28	2	ARG	ARG	THR	THR	4	D	D	4 - 22	4 - 22
29	2	ARG	ARG	THR	THR	4	E	E	4 - 22	4 - 22
30	2	ARG	ARG	THR	THR	4	F	F	4 - 22	4 - 22
31	2	ARG	ARG	THR	THR	4	G	G	4 - 22	4 - 22
32	2	ARG	ARG	THR	THR	4	H	H	4 - 22	4 - 22
33	2	ARG	ARG	THR	THR	4	I	I	4 - 22	4 - 22
34	2	ARG	ARG	THR	THR	4	J	J	4 - 22	4 - 22
35	2	ARG	ARG	THR	THR	4	K	K	4 - 22	4 - 22
36	2	ARG	ARG	THR	THR	4	L	L	4 - 22	4 - 22
37	2	ARG	ARG	THR	THR	4	M	M	4 - 22	4 - 22
38	2	ARG	ARG	THR	THR	4	N	N	4 - 22	4 - 22
39	2	ARG	ARG	THR	THR	4	O	O	4 - 22	4 - 22
40	2	ARG	ARG	THR	THR	4	P	P	4 - 22	4 - 22
41	2	ARG	ARG	THR	THR	4	R	Q	4 - 22	4 - 22
42	2	ARG	ARG	THR	THR	4	S	R	4 - 22	4 - 22
43	2	ARG	ARG	THR	THR	4	T	S	4 - 22	4 - 22
44	2	ARG	ARG	THR	THR	4	U	T	4 - 22	4 - 22
45	2	ARG	ARG	THR	THR	4	V	U	4 - 22	4 - 22
46	2	ARG	ARG	THR	THR	4	W	V	4 - 22	4 - 22
47	2	ARG	ARG	THR	THR	4	X	W	4 - 22	4 - 22
48	2	ARG	ARG	THR	THR	4	Y	X	4 - 22	4 - 22
49	3	ARG	ARG	ARG	ARG	5	A	A	23	23
50	3	ARG	ARG	ARG	ARG	5	B	B	23	23
51	3	ARG	ARG	ARG	ARG	5	C	C	23	23
52	3	ARG	ARG	ARG	ARG	5	D	D	23	23
53	3	ARG	ARG	ARG	ARG	5	E	E	23	23
54	3	ARG	ARG	ARG	ARG	5	F	F	23	23
55	3	ARG	ARG	ARG	ARG	5	G	G	23	23
56	3	ARG	ARG	ARG	ARG	5	H	H	23	23
57	3	ARG	ARG	ARG	ARG	5	I	I	23	23
58	3	ARG	ARG	ARG	ARG	5	J	J	23	23
59	3	ARG	ARG	ARG	ARG	5	K	K	23	23
60	3	ARG	ARG	ARG	ARG	5	L	L	23	23
61	3	ARG	ARG	ARG	ARG	5	M	M	23	23
62	3	ARG	ARG	ARG	ARG	5	N	N	23	23
63	3	ARG	ARG	ARG	ARG	5	O	O	23	23
64	3	ARG	ARG	ARG	ARG	5	P	P	23	23
65	3	ARG	ARG	ARG	ARG	5	R	Q	23	23
66	3	ARG	ARG	ARG	ARG	5	S	R	23	23
67	3	ARG	ARG	ARG	ARG	5	T	S	23	23
68	3	ARG	ARG	ARG	ARG	5	U	T	23	23
69	3	ARG	ARG	ARG	ARG	5	V	U	23	23
70	3	ARG	ARG	ARG	ARG	5	W	V	23	23
71	3	ARG	ARG	ARG	ARG	5	X	W	23	23
72	3	ARG	ARG	ARG	ARG	5	Y	X	23	23
73	4	GLU	GLU	TYR	TYR	4	A	A	24 - 108	24 - 108
74	4	GLU	GLU	TYR	TYR	4	B	B	24 - 108	24 - 108
75	4	GLU	GLU	TYR	TYR	4	C	C	24 - 108	24 - 108
76	4	GLU	GLU	TYR	TYR	4	D	D	24 - 108	24 - 108
77	4	GLU	GLU	TYR	TYR	4	E	E	24 - 108	24 - 108
78	4	GLU	GLU	TYR	TYR	4	F	F	24 - 108	24 - 108
79	4	GLU	GLU	TYR	TYR	4	G	G	24 - 108	24 - 108
80	4	GLU	GLU	TYR	TYR	4	H	H	24 - 108	24 - 108
81	4	GLU	GLU	TYR	TYR	4	I	I	24 - 108	24 - 108
82	4	GLU	GLU	TYR	TYR	4	J	J	24 - 108	24 - 108
83	4	GLU	GLU	TYR	TYR	4	K	K	24 - 108	24 - 108
84	4	GLU	GLU	TYR	TYR	4	L	L	24 - 108	24 - 108
85	4	GLU	GLU	TYR	TYR	4	M	M	24 - 108	24 - 108
86	4	GLU	GLU	TYR	TYR	4	N	N	24 - 108	24 - 108
87	4	GLU	GLU	TYR	TYR	4	O	O	24 - 108	24 - 108
88	4	GLU	GLU	TYR	TYR	4	P	P	24 - 108	24 - 108
89	4	GLU	GLU	TYR	TYR	4	R	Q	24 - 108	24 - 108
90	4	GLU	GLU	TYR	TYR	4	S	R	24 - 108	24 - 108
91	4	GLU	GLU	TYR	TYR	4	T	S	24 - 108	24 - 108
92	4	GLU	GLU	TYR	TYR	4	U	T	24 - 108	24 - 108
93	4	GLU	GLU	TYR	TYR	4	V	U	24 - 108	24 - 108
94	4	GLU	GLU	TYR	TYR	4	W	V	24 - 108	24 - 108
95	4	GLU	GLU	TYR	TYR	4	X	W	24 - 108	24 - 108
96	4	GLU	GLU	TYR	TYR	4	Y	X	24 - 108	24 - 108

#1: Protein	... stable protein 1 / boling stable protein Mass: 12422.962 Da / Num. of mol.: 24 / 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 Mass: 92.094 Da / Num. of mol.: 24 / Source method: obtained synthetically / Formula: C₃H₈O₃
#3: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 3179 / 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: 2.7 Å³/Da / Density % sol: 53.8 %
Crystal grow	Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5 Details: PEG 3000, Sodium Chloride, Hepes, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: SYNCHROTRON / Site: SSRL / Beamline: BL9-2 / Wavelength: 0.954 Å
Detector	Type: ADSC QUANTUM 4 / Detector: CCD / Date: Apr 28, 2002
Radiation	Monochromator: Si 111 double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.954 Å / Relative weight: 1
Reflection	Resolution: 1.8→48.5 Å / Num. all: 246060 / Num. obs: 246060 / % possible obs: 92.5 % / Observed criterion σ(F): 7 / Observed criterion σ(I): 2.8 / Redundancy: 1.9 % / R_sym value: 0.087
Reflection shell	Resolution: 1.8→1.9 Å / Redundancy: 1.9 % / R_merge(I) obs: 0.447 / Mean I/σ(I) obs: 2.8 / % possible all: 88.4

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Processing

Software

Name	Version	Classification
REFMAC	5.1.24	refinement
Blu-Ice		data collection
CCP4	(SCALA)	data scaling
MOLREP		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: pdb entry 1SI9

1si9

Resolution: 1.8→48.5 Å / Cor.coef. F_o:F_c: 0.963 / Cor.coef. F_o:F_c free: 0.94 / SU B: 2.623 / SU ML: 0.079 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.119 / ESU R Free: 0.116
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	0.20192	13491	5.2 %	RANDOM
R_work	0.16234	-	-	-
all	0.164	246060	-	-
obs	0.16447	246060	100 %	-

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: 7.848 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	-0.81 Å²	0 Å²	-0.03 Å²
2-	-	1.68 Å²	0 Å²
3-	-	-	-0.87 Å²

Refinement step

Cycle: LAST / Resolution: 1.8→48.5 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	20712	0	144	3179	24035

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.017	0.021	21348
X-RAY DIFFRACTION	r_bond_other_d	0.002	0.02	18870
X-RAY DIFFRACTION	r_angle_refined_deg	1.588	1.964	28851
X-RAY DIFFRACTION	r_angle_other_deg	0.991	3	43953
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	6.699	5	2520
X-RAY DIFFRACTION	r_chiral_restr	0.102	0.2	3192
X-RAY DIFFRACTION	r_gen_planes_refined	0.009	0.02	23532
X-RAY DIFFRACTION	r_gen_planes_other	0.009	0.02	4560
X-RAY DIFFRACTION	r_nbd_refined	0.217	0.2	4345
X-RAY DIFFRACTION	r_nbd_other	0.256	0.2	22963
X-RAY DIFFRACTION	r_nbtor_other	0.089	0.2	12620
X-RAY DIFFRACTION	r_xyhbond_nbd_refined	0.171	0.2	2647
X-RAY DIFFRACTION	r_symmetry_vdw_refined	0.117	0.2	8
X-RAY DIFFRACTION	r_symmetry_vdw_other	0.352	0.2	91
X-RAY DIFFRACTION	r_symmetry_hbond_refined	0.192	0.2	67
X-RAY DIFFRACTION	r_mcbond_it	0.829	1.5	12672
X-RAY DIFFRACTION	r_mcangle_it	1.464	2	20415
X-RAY DIFFRACTION	r_scbond_it	2.526	3	8676
X-RAY DIFFRACTION	r_scangle_it	3.711	4.5	8436

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	1612	medium positional	0.3	0.5
2	B	1612	medium positional	0.38	0.5
3	C	1612	medium positional	0.35	0.5
4	D	1612	medium positional	0.39	0.5
5	E	1612	medium positional	0.43	0.5
6	F	1612	medium positional	0.3	0.5
7	G	1612	medium positional	0.29	0.5
8	H	1612	medium positional	0.31	0.5
9	I	1612	medium positional	0.33	0.5
10	J	1612	medium positional	0.31	0.5
11	K	1612	medium positional	0.34	0.5
12	L	1612	medium positional	0.38	0.5
13	M	1612	medium positional	0.25	0.5
14	N	1612	medium positional	0.33	0.5
15	O	1612	medium positional	0.36	0.5
16	P	1612	medium positional	0.33	0.5
17	R	1612	medium positional	0.28	0.5
18	S	1612	medium positional	0.31	0.5
19	T	1612	medium positional	0.25	0.5
20	U	1612	medium positional	0.35	0.5
21	V	1612	medium positional	0.41	0.5
22	W	1612	medium positional	0.35	0.5
23	X	1612	medium positional	0.45	0.5
24	Y	1612	medium positional	0.32	0.5
1	A	25	loose positional	2.41	5
2	B	25	loose positional	1.37	5
3	C	25	loose positional	1.74	5
4	D	25	loose positional	1.61	5
5	E	25	loose positional	1.78	5
6	F	25	loose positional	1.64	5
7	G	25	loose positional	1.42	5
8	H	25	loose positional	1.83	5
9	I	25	loose positional	1.93	5
10	J	25	loose positional	1.69	5
11	K	25	loose positional	1.42	5
12	L	25	loose positional	1.81	5
13	M	25	loose positional	1.99	5
14	N	25	loose positional	1.89	5
15	O	25	loose positional	1.78	5
16	P	25	loose positional	1.77	5
17	R	25	loose positional	1.6	5
18	S	25	loose positional	2.12	5
19	T	25	loose positional	2.45	5
20	U	25	loose positional	1.51	5
21	V	25	loose positional	1.72	5
22	W	25	loose positional	1.99	5
23	X	25	loose positional	1.7	5
24	Y	25	loose positional	2.32	5
1	A	1612	medium thermal	0.7	2
2	B	1612	medium thermal	0.6	2
3	C	1612	medium thermal	0.66	2
4	D	1612	medium thermal	0.69	2
5	E	1612	medium thermal	0.83	2
6	F	1612	medium thermal	1.14	2
7	G	1612	medium thermal	1.4	2
8	H	1612	medium thermal	1.07	2
9	I	1612	medium thermal	0.82	2
10	J	1612	medium thermal	0.81	2
11	K	1612	medium thermal	0.78	2
12	L	1612	medium thermal	0.84	2
13	M	1612	medium thermal	0.96	2
14	N	1612	medium thermal	0.88	2
15	O	1612	medium thermal	0.76	2
16	P	1612	medium thermal	0.72	2
17	R	1612	medium thermal	0.68	2
18	S	1612	medium thermal	0.78	2
19	T	1612	medium thermal	0.64	2
20	U	1612	medium thermal	0.72	2
21	V	1612	medium thermal	0.88	2
22	W	1612	medium thermal	1.02	2
23	X	1612	medium thermal	0.82	2
24	Y	1612	medium thermal	1.27	2
1	A	25	loose thermal	1.28	10
2	B	25	loose thermal	3.44	10
3	C	25	loose thermal	1.14	10
4	D	25	loose thermal	0.8	10
5	E	25	loose thermal	1.9	10
6	F	25	loose thermal	6.61	10
7	G	25	loose thermal	5.99	10
8	H	25	loose thermal	6.08	10
9	I	25	loose thermal	5.47	10
10	J	25	loose thermal	4.61	10
11	K	25	loose thermal	6.85	10
12	L	25	loose thermal	5.98	10
13	M	25	loose thermal	9.79	10
14	N	25	loose thermal	3.6	10
15	O	25	loose thermal	5.71	10
16	P	25	loose thermal	2.47	10
17	R	25	loose thermal	1.42	10
18	S	25	loose thermal	2.62	10
19	T	25	loose thermal	3.62	10
20	U	25	loose thermal	1.27	10
21	V	25	loose thermal	1.89	10
22	W	25	loose thermal	2.2	10
23	X	25	loose thermal	5.66	10
24	Y	25	loose thermal	1.52	10

LS refinement shell

Resolution: 1.8→1.847 Å / Total num. of bins used: 20 /

	R_factor	Num. reflection
R_work	0.231	17385
R_free	-	0

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