PDB-8f01: Thaumatin Anomalous Dataset at 293 K and 7.1 keV

ID or keywords:

Entry

Database: PDB / ID: 8f01

Title

Thaumatin Anomalous Dataset at 293 K and 7.1 keV

Components

Thaumatin I

Keywords

PLANT PROTEIN / sweet-testing protein

Function / homology

Function and homology information

cytoplasmic vesicle
Similarity search - Function

Biological species

Thaumatococcus daniellii (katemfe)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

SAD / Resolution: 1.8 Å

Authors

Doukov, T. / Yabukarski, F. / Herschlag, D.

Funding support

United States,

France, 2items

Citation

Journal: Acta Crystallogr D Struct Biol / Year: 2023
Title: Obtaining anomalous and ensemble information from protein crystals from 220 K up to physiological temperatures.
Authors: Doukov, T. / Herschlag, D. / Yabukarski, F.

History

Deposition	Nov 1, 2022	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Mar 15, 2023	Provider: repository / Type: Initial release
Revision 1.1	Nov 20, 2024	Group: Data collection / Structure summary Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_entry_details / pdbx_modification_feature Item: _pdbx_entry_details.has_protein_modification

Structure viewer	Molecule: MolmilJmol/JSmol

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PDBx/mmCIF format	8f01.cif.gz	122.3 KB	Display	PDBx/mmCIF format
PDB format	pdb8f01.ent.gz	73.4 KB	Display	PDB format
PDBx/mmJSON format	8f01.json.gz		Tree view	PDBx/mmJSON format
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Validation report

Summary document	8f01_validation.pdf.gz	440 KB	Display	wwPDB validaton report
Full document	8f01_full_validation.pdf.gz	440.3 KB	Display
Data in XML	8f01_validation.xml.gz	11.1 KB	Display
Data in CIF	8f01_validation.cif.gz	15.4 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/f0/8f01 ftp://data.pdbj.org/pub/pdb/validation_reports/f0/8f01	HTTPS FTP

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Related structure data

Related structure data	8ezoC 8ezpC 8ezuC 8ezxC 8f00C 8f03C 8f05C 8f06C 8f07C 8f0bC C: citing same article (ref.)
Similar structure data	Similarity search - Function & homologyF&H Search Similarity search - FunctionF&H Search Similarity search - HomologyF&H Search

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Links

PDB pages	PDBj / wwPDB / NCBI
Related items in Molecule of the Month	#199 - Jul 2016 Monellin similarity (8) #228 - Dec 2018 Directed Evolution of Enzymes similarity (1)

Deposited unit

A: Thaumatin I

hetero molecules

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

1

Idetical with deposited unit
defined by author&software
Evidence: homology

Unit cell

Length a, b, c (Å)	58.960, 58.960, 151.243
Angle α, β, γ (deg.)	90.000, 90.000, 90.000
Int Tables number	92
Space group name H-M	P4₁2₁2

#1: Protein	Thaumatin I / Thaumatin-1 Mass: 22243.119 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Thaumatococcus daniellii (katemfe) / Production host: Thaumatococcus daniellii (katemfe) / References: UniProt: P02883
#2: Chemical	ChemComp-TLA / L(+)-TARTARIC ACID Mass: 150.087 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C₄H₆O₆
#3: Chemical	ChemComp-K / POTASSIUM ION Mass: 39.098 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: K
#4: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 122 / Source method: isolated from a natural source / Formula: H₂O
Has ligand of interest	N
Has protein modification	Y

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Experiment

Experiment	Method: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

Crystal	Density Matthews: 2.95 Å³/Da / Density % sol: 0.563 %
Crystal grow	Temperature: 298 K / Method: vapor diffusion, sitting drop / pH: 6.6 Details: 5 uL 24% potassium/sodium phosphate, 15% ethylene glycol, 0.1 M Bis-Tris, pH 6.6 + 5 uL 20mg/mL thaumatin in distilled water

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Data collection

Diffraction	Mean temperature: 293 K / Ambient temp details: Oxford Cryo / Serial crystal experiment: N
Diffraction source	Source: SYNCHROTRON / Site: SSRL / Beamline: BL14-1 / Wavelength: 1.7462 Å
Detector	Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jan 19, 2020
Radiation	Monochromator: Si 111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 1.7462 Å / Relative weight: 1
Reflection	Resolution: 1.8→38.346 Å / Num. obs: 25629 / % possible obs: 99.5 % / Redundancy: 7.3 % / B_iso Wilson estimate: 30.9 Å² / CC_1/2: 0.999 / R_merge(I) obs: 0.046 / R_pim(I) all: 0.019 / Net I/σ(I): 20.6
Reflection shell	Resolution: 1.8→1.84 Å / Redundancy: 2.7 % / R_merge(I) obs: 0.481 / Num. unique obs: 1386 / CC_1/2: 0.742 / R_pim(I) all: 0.044 / % possible all: 93.8

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Processing

Software

Name	Version	Classification
REFMAC	5.8.0352	refinement
XDS		data reduction
Aimless		data scaling
SHELXCD		phasing

Refinement

Method to determine structure:

SAD / Resolution: 1.8→38.346 Å / Cor.coef. F_o:F_c: 0.976 / Cor.coef. F_o:F_c free: 0.969 / SU B: 3.56 / SU ML: 0.052 / Cross valid method: FREE R-VALUE / ESU R: 0.081 / ESU R Free: 0.078
Details: Hydrogens have been added in their riding positions

	R_factor	Num. reflection	% reflection
R_free	0.1607	1266	4.967 %
R_work	0.1406	24223	-
all	0.142	-	-
obs	-	25489	99.427 %

Solvent computation

Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT

Displacement parameters

B_iso mean: 29.795 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	0.51 Å²	-0 Å²	-0 Å²
2-	-	0.51 Å²	-0 Å²
3-	-	-	-1.02 Å²

Refinement step

Cycle: LAST / Resolution: 1.8→38.346 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	1552	0	11	122	1685

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.008	0.011	1637
X-RAY DIFFRACTION	r_bond_other_d	0.001	0.016	1424
X-RAY DIFFRACTION	r_angle_refined_deg	1.423	1.658	2225
X-RAY DIFFRACTION	r_angle_other_deg	0.519	1.562	3345
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	7.21	5	210
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	17.977	10	13
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	13.812	10	258
X-RAY DIFFRACTION	r_dihedral_angle_6_deg	16.784	10	69
X-RAY DIFFRACTION	r_chiral_restr	0.077	0.2	237
X-RAY DIFFRACTION	r_gen_planes_refined	0.008	0.02	1904
X-RAY DIFFRACTION	r_gen_planes_other	0.001	0.02	340
X-RAY DIFFRACTION	r_nbd_refined	0.245	0.2	254
X-RAY DIFFRACTION	r_symmetry_nbd_other	0.211	0.2	1247
X-RAY DIFFRACTION	r_nbtor_refined	0.187	0.2	808
X-RAY DIFFRACTION	r_symmetry_nbtor_other	0.085	0.2	864
X-RAY DIFFRACTION	r_xyhbond_nbd_refined	0.306	0.2	72
X-RAY DIFFRACTION	r_symmetry_xyhbond_nbd_other	0.077	0.2	1
X-RAY DIFFRACTION	r_symmetry_nbd_refined	0.119	0.2	7
X-RAY DIFFRACTION	r_nbd_other	0.149	0.2	26
X-RAY DIFFRACTION	r_symmetry_xyhbond_nbd_refined	0.235	0.2	12
X-RAY DIFFRACTION	r_mcbond_it	3.159	3.897	831
X-RAY DIFFRACTION	r_mcbond_other	3.162	3.895	831
X-RAY DIFFRACTION	r_mcangle_it	4.204	7.264	1038
X-RAY DIFFRACTION	r_mcangle_other	4.216	7.277	1039
X-RAY DIFFRACTION	r_scbond_it	5.377	4.94	806
X-RAY DIFFRACTION	r_scbond_other	5.372	4.936	805
X-RAY DIFFRACTION	r_scangle_it	7.613	8.639	1185
X-RAY DIFFRACTION	r_scangle_other	7.619	8.639	1185
X-RAY DIFFRACTION	r_lrange_it	10.016	32.729	1753
X-RAY DIFFRACTION	r_lrange_other	9.927	32.044	1740

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	R_factor all	Num. reflection all	Fsc free	Fsc work	% reflection obs (%)	WR_factor R_work
1.8-1.847	0.274	85	0.28	1670	0.28	1867	0.95	0.958	94.0011	0.266
1.847-1.897	0.281	80	0.243	1684	0.245	1791	0.953	0.969	98.4925	0.225
1.897-1.952	0.174	80	0.173	1653	0.173	1733	0.981	0.983	100	0.152
1.952-2.012	0.158	94	0.136	1624	0.137	1718	0.982	0.988	100	0.12
2.012-2.078	0.193	85	0.14	1568	0.142	1653	0.978	0.987	100	0.123
2.078-2.15	0.196	70	0.137	1539	0.14	1609	0.977	0.988	100	0.122
2.15-2.231	0.15	79	0.128	1474	0.129	1555	0.985	0.99	99.8714	0.115
2.231-2.322	0.148	80	0.127	1424	0.128	1504	0.988	0.99	100	0.114
2.322-2.425	0.157	74	0.124	1362	0.126	1436	0.986	0.991	100	0.112
2.425-2.543	0.161	71	0.121	1311	0.123	1382	0.984	0.991	100	0.111
2.543-2.68	0.149	75	0.123	1260	0.124	1335	0.988	0.991	100	0.114
2.68-2.841	0.148	67	0.123	1172	0.124	1239	0.985	0.991	100	0.114
2.841-3.036	0.158	66	0.122	1119	0.124	1185	0.985	0.99	100	0.115
3.036-3.278	0.135	55	0.117	1069	0.118	1124	0.987	0.992	100	0.113
3.278-3.588	0.133	46	0.122	970	0.122	1016	0.99	0.992	100	0.121
3.588-4.007	0.124	47	0.121	900	0.121	948	0.991	0.992	99.8945	0.125
4.007-4.619	0.122	34	0.119	805	0.119	839	0.992	0.992	100	0.126
4.619-5.636	0.179	39	0.153	688	0.155	727	0.986	0.989	100	0.163
5.636-7.886	0.203	28	0.208	556	0.207	584	0.984	0.982	100	0.211
7.886-38.346	0.254	11	0.233	369	0.234	380	0.942	0.957	100	0.25

Refinement TLS params.

Method: refined / Origin x: 4.8945 Å / Origin y: 17.0362 Å / Origin z: 42.6868 Å

	11	12	13	21	22	23	31	32	33
T	0.015 Å²	0.012 Å²	0 Å²	-	0.0308 Å²	-0.0089 Å²	-	-	0.0089 Å²
L	1.5183 °²	0.0994 °²	1.1559 °²	-	0.6995 °²	-0.0137 °²	-	-	3.3938 °²
S	-0.025 Å °	0.0897 Å °	-0.0176 Å °	-0.0294 Å °	0.046 Å °	-0.0753 Å °	0.0588 Å °	0.2615 Å °	-0.021 Å °

Refinement TLS group

Selection: ALL

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