PDB-6zmz: UDPG-bound Trehalose transferase from Thermoproteus uzoniensis

ID or keywords:

Entry

Database: PDB / ID: 6zmz

Title

UDPG-bound Trehalose transferase from Thermoproteus uzoniensis

Components

Trehalose phosphorylase/synthase

Keywords

TRANSFERASE / trehalose transferase / retaining glycosyltransferase / glycosidic bond formation

Function / homology

Function and homology information

glycosyltransferase activity / glucose metabolic process
Similarity search - Function

Biological species

Thermoproteus uzoniensis (archaea)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 1.9 Å

Authors

Bento, I. / Mestrom, L. / Marsden, S.R. / van der Eijk, H. / Laustsen, J.U. / Jeffries, C.M. / Svergun, D.I. / Hagedoorn, P.-H. / Hanefeld, U.

Funding support

Germany, 1items

Citation

Journal: Acs Catalysis / Year: 2020
Title: Anomeric Selectivity of Trehalose Transferase with Rare l-Sugars.
Authors: Mestrom, L. / Marsden, S.R. / van der Eijk, H. / Laustsen, J.U. / Jeffries, C.M. / Svergun, D.I. / Hagedoorn, P.L. / Bento, I. / Hanefeld, U.

History

Deposition	Jul 5, 2020	Deposition site: PDBE / Processing site: PDBE
Revision 1.0	Sep 30, 2020	Provider: repository / Type: Initial release
Revision 1.1	May 1, 2024	Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description Category: atom_type / chem_comp_atom ...atom_type / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model Item: _atom_type.pdbx_N_electrons / _atom_type.pdbx_scat_Z ..._atom_type.pdbx_N_electrons / _atom_type.pdbx_scat_Z / _database_2.pdbx_DOI / _database_2.pdbx_database_accession

Structure viewer	Molecule: MolmilJmol/JSmol

-
Download

PDBx/mmCIF format	6zmz.cif.gz	100.6 KB	Display	PDBx/mmCIF format
PDB format	pdb6zmz.ent.gz		Display	PDB format
PDBx/mmJSON format	6zmz.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

-
Validation report

Summary document	6zmz_validation.pdf.gz	758 KB	Display	wwPDB validaton report
Full document	6zmz_full_validation.pdf.gz	760 KB	Display
Data in XML	6zmz_validation.xml.gz	16.8 KB	Display
Data in CIF	6zmz_validation.cif.gz	23.2 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/zm/6zmz ftp://data.pdbj.org/pub/pdb/validation_reports/zm/6zmz	HTTPS FTP

-
Related structure data

Related structure data	6zj4C 6zj7C 6zjhC 6zn1C C: citing same article (ref.)
Similar structure data	6zj4-d 6zjh-d 2yhg-d 5ysf-1 5t4k-d 4pfd-2 7c6n-1 7c6k-d 7c6t-d 6a8z-2 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	SASBDB: SASDHK9associated SAS data

-
Links

PDB pages	PDBj / wwPDB / NCBI
Related items in Molecule of the Month	#254 - Feb 2021 Cellulose Synthase similarity (3)

Deposited unit

AAA: Trehalose phosphorylase/synthase

hetero molecules

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

1

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

Unit cell

Length a, b, c (Å)	53.045, 69.327, 98.912
Angle α, β, γ (deg.)	90.000, 90.000, 90.000
Int Tables number	19
Space group name H-M	P2₁2₁2₁

#1: Protein	Trehalose phosphorylase/synthase Mass: 45503.316 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Details: TreT soaked with UDPG / Source: (gene. exp.) Thermoproteus uzoniensis (archaea) / Gene: TUZN_0976 / Production host: Escherichia coli (E. coli) / References: UniProt: F2L613
#2: Chemical	ChemComp-UPG / URIDINE-5'-DIPHOSPHATE-GLUCOSE / URIDINE-5'-MONOPHOSPHATE GLUCOPYRANOSYL-MONOPHOSPHATE ESTER Mass: 566.302 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C₁₅H₂₄N₂O₁₇P₂ / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical	ChemComp-PEG / DI(HYDROXYETHYL)ETHER Mass: 106.120 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Formula: C₄H₁₀O₃
#4: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 98 / Source method: isolated from a natural source / Formula: H₂O
Has ligand of interest	Y

-
Experiment

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

-
Sample preparation

Crystal	Density Matthews: 2.02 Å³/Da / Density % sol: 39.17 %
Crystal grow	Temperature: 292 K / Method: vapor diffusion / pH: 6.5 Details: Bis-Tris Propane, PEG 3350, potassium thiocyanate, PEG 400

-
Data collection

Diffraction	Mean temperature: 100 K / Serial crystal experiment: N
Diffraction source	Source: SYNCHROTRON / Site: PETRA III, EMBL c/o DESY / Beamline: P13 (MX1) / Wavelength: 0.9762 Å
Detector	Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Nov 25, 2019
Radiation	Monochromator: double-crystal monochromator (DCM) FMB-OXFORD (Oxford, UK) Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.9762 Å / Relative weight: 1
Reflection	Resolution: 1.9→98.9 Å / Num. obs: 29213 / % possible obs: 99.3 % / Redundancy: 6.5 % / B_iso Wilson estimate: 39.056 Å² / CC_1/2: 0.999 / R_merge(I) obs: 0.065 / R_pim(I) all: 0.041 / R_rim(I) all: 0.077 / Net I/σ(I): 14.6
Reflection shell	Resolution: 1.9→1.94 Å / Redundancy: 6.7 % / R_merge(I) obs: 1.337 / Mean I/σ(I) obs: 1.3 / Num. unique obs: 1838 / CC_1/2: 0.508 / R_pim(I) all: 0.836 / R_rim(I) all: 1.58 / % possible all: 98.5

-
Processing

Software

Name	Version	Classification
REFMAC	5.8.0258	refinement
XDS		data reduction
Aimless		data scaling
MOLREP		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: Apo-Tret

Resolution: 1.9→56.771 Å / Cor.coef. F_o:F_c: 0.968 / Cor.coef. F_o:F_c free: 0.953 / WR_factor R_free: 0.203 / WR_factor R_work: 0.169 / SU B: 4.375 / SU ML: 0.122 / Average fsc free: 0.9015 / Average fsc work: 0.9121 / Cross valid method: FREE R-VALUE / ESU R: 0.172 / ESU R Free: 0.15
Details: Hydrogens have been added in their riding positions

	R_factor	Num. reflection	% reflection
R_free	0.2227	1445	4.953 %
R_work	0.1847	27727	-
all	0.187	-	-
obs	-	29172	99.036 %

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: 39.5 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	1.214 Å²	0 Å²	-0 Å²
2-	-	-1.036 Å²	0 Å²
3-	-	-	-0.178 Å²

Refinement step

Cycle: LAST / Resolution: 1.9→56.771 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	3184	0	43	98	3325

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.006	0.013	3317
X-RAY DIFFRACTION	r_bond_other_d	0.002	0.017	3147
X-RAY DIFFRACTION	r_angle_refined_deg	1.351	1.648	4501
X-RAY DIFFRACTION	r_angle_other_deg	1.267	1.578	7289
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	6.501	5	398
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	32.086	21.285	179
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	13.001	15	572
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	17.693	15	27
X-RAY DIFFRACTION	r_chiral_restr	0.063	0.2	427
X-RAY DIFFRACTION	r_gen_planes_refined	0.005	0.02	3648
X-RAY DIFFRACTION	r_gen_planes_other	0.001	0.02	709
X-RAY DIFFRACTION	r_nbd_refined	0.202	0.2	600
X-RAY DIFFRACTION	r_symmetry_nbd_other	0.189	0.2	2868
X-RAY DIFFRACTION	r_nbtor_refined	0.158	0.2	1605
X-RAY DIFFRACTION	r_symmetry_nbtor_other	0.078	0.2	1334
X-RAY DIFFRACTION	r_xyhbond_nbd_refined	0.169	0.2	115
X-RAY DIFFRACTION	r_symmetry_xyhbond_nbd_other	0.032	0.2	2
X-RAY DIFFRACTION	r_symmetry_nbd_refined	0.164	0.2	14
X-RAY DIFFRACTION	r_nbd_other	0.212	0.2	55
X-RAY DIFFRACTION	r_symmetry_xyhbond_nbd_refined	0.247	0.2	9
X-RAY DIFFRACTION	r_mcbond_it	2.35	3.942	1592
X-RAY DIFFRACTION	r_mcbond_other	2.347	3.94	1591
X-RAY DIFFRACTION	r_mcangle_it	3.418	5.903	1990
X-RAY DIFFRACTION	r_mcangle_other	3.417	5.905	1991
X-RAY DIFFRACTION	r_scbond_it	3.098	4.402	1725
X-RAY DIFFRACTION	r_scbond_other	3.097	4.403	1726
X-RAY DIFFRACTION	r_scangle_it	4.97	6.422	2511
X-RAY DIFFRACTION	r_scangle_other	4.969	6.423	2512
X-RAY DIFFRACTION	r_lrange_it	6.53	45.794	3594
X-RAY DIFFRACTION	r_lrange_other	6.519	45.735	3582

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
1.9-1.949	0.335	96	0.301	2006	0.303	2139	0.75	0.741	98.2702	0.29
1.949-2.003	0.326	100	0.273	1958	0.276	2086	0.763	0.804	98.6577	0.255
2.003-2.061	0.257	86	0.258	1922	0.258	2035	0.862	0.854	98.6732	0.237
2.061-2.124	0.279	71	0.227	1891	0.229	1986	0.871	0.903	98.7915	0.202
2.124-2.194	0.245	99	0.213	1786	0.215	1908	0.905	0.916	98.7945	0.187
2.194-2.27	0.245	84	0.205	1743	0.206	1843	0.91	0.922	99.1319	0.175
2.27-2.356	0.3	79	0.195	1716	0.199	1809	0.882	0.929	99.2261	0.166
2.356-2.452	0.249	97	0.19	1607	0.193	1717	0.925	0.937	99.2429	0.161
2.452-2.561	0.225	78	0.188	1579	0.19	1670	0.935	0.945	99.2216	0.157
2.561-2.686	0.216	90	0.18	1496	0.182	1599	0.936	0.953	99.187	0.152
2.686-2.83	0.249	77	0.185	1413	0.188	1506	0.924	0.948	98.9376	0.159
2.83-3.002	0.222	84	0.179	1357	0.182	1449	0.946	0.952	99.4479	0.157
3.002-3.208	0.223	73	0.173	1270	0.176	1352	0.943	0.957	99.3343	0.153
3.208-3.464	0.202	80	0.17	1193	0.172	1282	0.951	0.959	99.298	0.159
3.464-3.794	0.187	60	0.156	1114	0.158	1181	0.961	0.966	99.4073	0.15
3.794-4.239	0.222	60	0.152	998	0.155	1060	0.95	0.972	99.8113	0.149
4.239-4.89	0.137	43	0.15	915	0.149	966	0.976	0.974	99.1718	0.15
4.89-5.978	0.298	36	0.187	773	0.192	814	0.93	0.958	99.3857	0.186
5.978-8.408	0.203	37	0.209	609	0.209	649	0.967	0.954	99.5378	0.211
8.408-56.771	0.222	15	0.196	381	0.197	405	0.964	0.968	97.7778	0.207

-
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