PDB-8f03: Thaumatin Anomalous Dataset at 293 K and 12 keV

ID or keywords:

Entry

Database: PDB / ID: 8f03

Title

Thaumatin Anomalous Dataset at 293 K and 12 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: 1.39 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	Oct 9, 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

-
Download

PDBx/mmCIF format	8f03.cif.gz	131.5 KB	Display	PDBx/mmCIF format
PDB format	pdb8f03.ent.gz	78.5 KB	Display	PDB format
PDBx/mmJSON format	8f03.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

-
Validation report

Summary document	8f03_validation.pdf.gz	441.5 KB	Display	wwPDB validaton report
Full document	8f03_full_validation.pdf.gz	443 KB	Display
Data in XML	8f03_validation.xml.gz	11.9 KB	Display
Data in CIF	8f03_validation.cif.gz	17 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/f0/8f03 ftp://data.pdbj.org/pub/pdb/validation_reports/f0/8f03	HTTPS FTP

-
Related structure data

Related structure data	8ezoC 8ezpC 8ezuC 8ezxC 8f00C 8f01C 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

-
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)	58.937, 58.937, 151.298
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.: 157 / Source method: isolated from a natural source / Formula: H₂O
Has ligand of interest	N
Has protein modification	Y

-
Experiment

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

-
Sample preparation

Crystal	Density Matthews: 2.95 Å³/Da / Density % sol: 56.3 %
Crystal grow	Temperature: 293 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

-
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: 1.0332 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: 1.0332 Å / Relative weight: 1
Reflection	Resolution: 1.39→38.323 Å / Num. obs: 54660 / % possible obs: 99.8 % / Redundancy: 52.4 % / B_iso Wilson estimate: 27.4 Å² / CC_1/2: 1 / R_merge(I) obs: 0.093 / R_pim(I) all: 0.013 / Net I/σ(I): 29.7
Reflection shell	Resolution: 1.39→1.41 Å / Redundancy: 52.3 % / R_merge(I) obs: 5.181 / Mean I/σ(I) obs: 1.3 / Num. unique obs: 2617 / CC_1/2: 0.686 / R_pim(I) all: 0.713 / % possible all: 98.7

-
Processing

Software

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

Refinement

Method to determine structure:

SAD / Resolution: 1.39→38.323 Å / Cor.coef. F_o:F_c: 0.986 / Cor.coef. F_o:F_c free: 0.983 / SU B: 1.541 / SU ML: 0.025 / Cross valid method: FREE R-VALUE / ESU R: 0.035 / ESU R Free: 0.036
Details: Hydrogens have been added in their riding positions

	R_factor	Num. reflection	% reflection
R_free	0.1374	2737	5.022 %
R_work	0.1113	51768	-
all	0.113	-	-
obs	-	54505	99.769 %

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: 22.772 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	0.145 Å²	-0 Å²	-0 Å²
2-	-	0.145 Å²	-0 Å²
3-	-	-	-0.29 Å²

Refinement step

Cycle: LAST / Resolution: 1.39→38.323 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	1552	0	11	157	1720

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.011	0.011	1680
X-RAY DIFFRACTION	r_bond_other_d	0.001	0.016	1483
X-RAY DIFFRACTION	r_angle_refined_deg	1.618	1.66	2296
X-RAY DIFFRACTION	r_angle_other_deg	0.628	1.561	3490
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	7	5	224
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	9.51	5	14
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	13.643	10	269
X-RAY DIFFRACTION	r_dihedral_angle_6_deg	17.08	10	70
X-RAY DIFFRACTION	r_chiral_restr	0.096	0.2	246
X-RAY DIFFRACTION	r_gen_planes_refined	0.009	0.02	1964
X-RAY DIFFRACTION	r_gen_planes_other	0.001	0.02	348
X-RAY DIFFRACTION	r_nbd_refined	0.249	0.2	280
X-RAY DIFFRACTION	r_symmetry_nbd_other	0.216	0.2	1288
X-RAY DIFFRACTION	r_nbtor_refined	0.191	0.2	819
X-RAY DIFFRACTION	r_symmetry_nbtor_other	0.09	0.2	885
X-RAY DIFFRACTION	r_xyhbond_nbd_refined	0.324	0.2	96
X-RAY DIFFRACTION	r_metal_ion_refined	0.175	0.2	1
X-RAY DIFFRACTION	r_symmetry_nbd_refined	0.126	0.2	5
X-RAY DIFFRACTION	r_nbd_other	0.154	0.2	33
X-RAY DIFFRACTION	r_symmetry_xyhbond_nbd_refined	0.377	0.2	14
X-RAY DIFFRACTION	r_mcbond_it	2.536	1.982	845
X-RAY DIFFRACTION	r_mcbond_other	2.539	1.978	845
X-RAY DIFFRACTION	r_mcangle_it	2.8	2.983	1059
X-RAY DIFFRACTION	r_mcangle_other	2.8	2.988	1060
X-RAY DIFFRACTION	r_scbond_it	5.715	2.571	835
X-RAY DIFFRACTION	r_scbond_other	5.716	2.569	834
X-RAY DIFFRACTION	r_scangle_it	5.33	3.597	1228
X-RAY DIFFRACTION	r_scangle_other	5.33	3.596	1228
X-RAY DIFFRACTION	r_lrange_it	5.362	33.548	1846
X-RAY DIFFRACTION	r_lrange_other	4.552	29.656	1815
X-RAY DIFFRACTION	r_rigid_bond_restr	5.231	3	3163

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
1.39-1.426	0.342	191	0.306	3661	0.307	3950	0.91	0.931	97.519	0.299
1.426-1.465	0.297	177	0.259	3703	0.26	3883	0.936	0.951	99.9227	0.247
1.465-1.508	0.194	201	0.209	3542	0.208	3745	0.975	0.968	99.9466	0.191
1.508-1.554	0.249	169	0.169	3496	0.173	3665	0.958	0.979	100	0.147
1.554-1.605	0.165	194	0.146	3336	0.147	3530	0.981	0.985	100	0.121
1.605-1.661	0.161	165	0.127	3276	0.129	3441	0.984	0.989	100	0.103
1.661-1.724	0.129	172	0.107	3148	0.108	3320	0.99	0.993	100	0.084
1.724-1.794	0.131	174	0.092	3036	0.094	3210	0.99	0.995	100	0.073
1.794-1.873	0.119	157	0.078	2909	0.08	3066	0.991	0.996	100	0.062
1.873-1.965	0.116	152	0.073	2832	0.075	2984	0.992	0.997	100	0.059
1.965-2.071	0.108	153	0.067	2642	0.069	2796	0.993	0.997	99.9642	0.056
2.071-2.196	0.095	143	0.068	2541	0.07	2684	0.994	0.997	100	0.059
2.196-2.347	0.114	143	0.078	2373	0.079	2517	0.992	0.997	99.9603	0.07
2.347-2.534	0.109	105	0.077	2256	0.079	2361	0.993	0.996	100	0.069
2.534-2.775	0.101	96	0.081	2084	0.082	2180	0.994	0.996	100	0.075
2.775-3.1	0.117	98	0.095	1898	0.096	1997	0.991	0.994	99.9499	0.093
3.1-3.576	0.121	76	0.105	1702	0.105	1778	0.991	0.994	100	0.107
3.576-4.37	0.139	65	0.111	1460	0.113	1525	0.988	0.992	100	0.122
4.37-6.141	0.147	62	0.137	1159	0.138	1221	0.992	0.991	100	0.157
6.141-38.323	0.211	44	0.207	715	0.208	759	0.978	0.974	100	0.225

Refinement TLS params.

Method: refined / Origin x: 12.402 Å / Origin y: -24.623 Å / Origin z: 4.883 Å

	11	12	13	21	22	23	31	32	33
T	0.039 Å²	-0.0137 Å²	0.005 Å²	-	0.0231 Å²	-0.0065 Å²	-	-	0.0036 Å²
L	0.1404 °²	-0.1511 °²	-0.0509 °²	-	0.2841 °²	0.3692 °²	-	-	0.9683 °²
S	0.0299 Å °	0.0132 Å °	0.0099 Å °	-0.034 Å °	-0.0234 Å °	-0.0082 Å °	-0.0809 Å °	0.0123 Å °	-0.0065 Å °

Refinement TLS group

Selection: ALL

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

Version 3 of the EMDB header file is now the official format.
The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

+
Jul 12, 2017. Major update of PDB

-
Yorodumi

Thousand views of thousand structures

Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

-
Movie

-
Structure viewers

+
Viewer log

-
This page

-
This web site

-
Options

+
Open data

-
Basic information

-
Structure visualization

-
Downloads & links

-
Download

-
Validation report

-
Related structure data

-
Links

-
Assembly

-
Components

-
Experimental details

-
Experiment

-
Sample preparation

-
Data collection

-
Processing

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

-
Aug 12, 2020. Covid-19 info

+
Mar 5, 2020. Novel coronavirus structure data

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

+
Jul 12, 2017. Major update of PDB

-
Yorodumi

-Movie

-Structure viewers

+Viewer log

-This page

-This web site

-Options

+Open data

-Basic information

-Structure visualization

-Downloads & links

-Download

-Validation report

-Related structure data

-Links

-Assembly

-Components

-Experimental details

-Experiment

-Sample preparation

-Data collection

-Processing

+About Yorodumi

-News

-Feb 9, 2022. New format data for meta-information of EMDB entries

-Aug 12, 2020. Covid-19 info

+Mar 5, 2020. Novel coronavirus structure data

+Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

+Jul 12, 2017. Major update of PDB

-Yorodumi

-
Movie

-
Structure viewers

+
Viewer log

-
This page

-
This web site

-
Options

+
Open data

-
Basic information

-
Structure visualization

-
Downloads & links

-
Download

-
Validation report

-
Related structure data

-
Links

-
Assembly

-
Components

-
Experimental details

-
Experiment

-
Sample preparation

-
Data collection

-
Processing

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

-
Aug 12, 2020. Covid-19 info

+
Mar 5, 2020. Novel coronavirus structure data

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

+
Jul 12, 2017. Major update of PDB

-
Yorodumi