PDB-8ie4: Crystal structure of GcCGT

ID or keywords:

Entry

Database: PDB / ID: 8ie4

Title

Crystal structure of GcCGT

Components

GcCGT

Keywords

TRANSFERASE / Glycosyltransferases

Biological species

Gentiana crassicaulis (plant)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 2.1 Å

Authors

Zhang, M. / Bao, Y. / He, C. / Ye, M.

Funding support

China, 1items

Citation

Journal: To Be Published
Title: Crystal structure of GcCGT
Authors: Zhang, M. / Bao, Y. / He, C. / Ye, M.

History

Deposition	Feb 15, 2023	Deposition site: PDBJ / Processing site: PDBC
Revision 1.0	Feb 28, 2024	Provider: repository / Type: Initial release

Structure viewer	Molecule: MolmilJmol/JSmol

-
Download

PDBx/mmCIF format	8ie4.cif.gz	706.9 KB	Display	PDBx/mmCIF format
PDB format	pdb8ie4.ent.gz	589.3 KB	Display	PDB format
PDBx/mmJSON format	8ie4.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

-
Validation report

Summary document	8ie4_validation.pdf.gz	477.2 KB	Display	wwPDB validaton report
Full document	8ie4_full_validation.pdf.gz	502 KB	Display
Data in XML	8ie4_validation.xml.gz	65.4 KB	Display
Data in CIF	8ie4_validation.cif.gz	92 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/ie/8ie4 ftp://data.pdbj.org/pub/pdb/validation_reports/ie/8ie4	HTTPS FTP

-
Related structure data

Related structure data	8w7yC C: citing same article (ref.)

-
Links

PDB pages	PDBj / wwPDB / NCBI

Deposited unit

A: GcCGT

B: GcCGT

C: GcCGT

D: GcCGT

hetero molecules

217 kDa, 4 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

A: GcCGT

hetero molecules

defined by author
Evidence: gel filtration
54.4 kDa, 1 polymers
Search similar-shape structures of this assembly by Omokage search (details)

2

B: GcCGT

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

3

C: GcCGT

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

4

D: GcCGT

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

Unit cell

Length a, b, c (Å)	79.180, 95.930, 132.220
Angle α, β, γ (deg.)	90.00, 103.54, 90.00
Int Tables number	4
Space group name H-M	P12₁1

#1: Protein	GcCGT Mass: 54202.691 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Gentiana crassicaulis (plant) / Production host: Escherichia coli (E. coli)
#2: Chemical	ChemComp-MES / 2-(N-MORPHOLINO)-ETHANESULFONIC ACID Mass: 195.237 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C₆H₁₃NO₄S / Comment: pH buffer*YM
#3: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 524 / Source method: isolated from a natural source / Formula: H₂O
Has ligand of interest	N

-
Experiment

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

-
Sample preparation

Crystal	Density Matthews: 2.25 Å³/Da / Density % sol: 45.38 %
Crystal grow	Temperature: 289 K / Method: vapor diffusion, sitting drop / Details: 0.1 M MES, 0.2 M Li2SO4, pH 6.25, 25% w/v PEG 3000

-
Data collection

Diffraction	Mean temperature: 100 K / Serial crystal experiment: N
Diffraction source	Source: SYNCHROTRON / Site: SSRF / Beamline: BL02U1 / Wavelength: 0.9792 Å
Detector	Type: DECTRIS EIGER2 S 9M / Detector: PIXEL / Date: May 5, 2021
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.9792 Å / Relative weight: 1
Reflection	Resolution: 2.1→39.5 Å / Num. obs: 112015 / % possible obs: 99.8 % / Redundancy: 4.9 % / CC_1/2: 0.996 / R_merge(I) obs: 0.109 / R_pim(I) all: 0.054 / R_rim(I) all: 0.122 / Χ²: 0.99 / Net I/σ(I): 7.2 / Num. measured all: 548820
Reflection shell	Resolution: 2.1→2.14 Å / % possible obs: 99.8 % / Redundancy: 5.1 % / R_merge(I) obs: 0.82 / Num. measured all: 28344 / Num. unique obs: 5544 / CC_1/2: 0.869 / R_pim(I) all: 0.398 / R_rim(I) all: 0.913 / Χ²: 0.88 / Net I/σ(I) obs: 1.7

-
Processing

Software

Name	Version	Classification
Aimless		data scaling
PHENIX	1.20.1	refinement
XDS		data reduction
PHASER		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT / Resolution: 2.1→39.5 Å / SU ML: 0.28 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 31 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection
R_free	0.2498	5770	5.16 %
R_work	0.2016	-	-
obs	0.2041	111754	99.61 %

Solvent computation

Shrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL

Refinement step

Cycle: LAST / Resolution: 2.1→39.5 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	13995	0	12	524	14531

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.007	14371
X-RAY DIFFRACTION	f_angle_d	0.843	19537
X-RAY DIFFRACTION	f_dihedral_angle_d	16.342	5291
X-RAY DIFFRACTION	f_chiral_restr	0.052	2162
X-RAY DIFFRACTION	f_plane_restr	0.007	2521

LS refinement shell

Resolution (Å)	R_factor R_free	Num. reflection R_free	R_factor R_work	Num. reflection R_work	Refine-ID	% reflection obs (%)
2.1-2.12	0.3562	210	0.326	3478	X-RAY DIFFRACTION	99
2.12-2.15	0.3655	189	0.3207	3542	X-RAY DIFFRACTION	99
2.15-2.18	0.3362	198	0.3055	3486	X-RAY DIFFRACTION	99
2.18-2.2	0.3559	209	0.3021	3525	X-RAY DIFFRACTION	99
2.2-2.23	0.3807	195	0.2947	3487	X-RAY DIFFRACTION	100
2.23-2.26	0.3445	202	0.2832	3518	X-RAY DIFFRACTION	100
2.26-2.29	0.3596	158	0.2727	3520	X-RAY DIFFRACTION	100
2.29-2.33	0.3109	196	0.265	3571	X-RAY DIFFRACTION	100
2.33-2.37	0.3419	171	0.2533	3483	X-RAY DIFFRACTION	100
2.37-2.4	0.295	170	0.2539	3601	X-RAY DIFFRACTION	100
2.4-2.45	0.3161	184	0.261	3487	X-RAY DIFFRACTION	100
2.45-2.49	0.3052	201	0.2495	3536	X-RAY DIFFRACTION	100
2.49-2.54	0.289	180	0.2275	3546	X-RAY DIFFRACTION	100
2.54-2.59	0.2847	220	0.238	3503	X-RAY DIFFRACTION	100
2.59-2.65	0.2948	210	0.2359	3497	X-RAY DIFFRACTION	99
2.65-2.71	0.2819	190	0.2357	3497	X-RAY DIFFRACTION	100
2.71-2.77	0.2885	201	0.2369	3519	X-RAY DIFFRACTION	100
2.77-2.85	0.296	212	0.238	3518	X-RAY DIFFRACTION	100
2.85-2.93	0.2926	169	0.2286	3579	X-RAY DIFFRACTION	100
2.93-3.03	0.3017	201	0.2202	3514	X-RAY DIFFRACTION	100
3.03-3.14	0.276	199	0.2167	3520	X-RAY DIFFRACTION	100
3.14-3.26	0.2901	180	0.2161	3554	X-RAY DIFFRACTION	100
3.26-3.41	0.2755	171	0.2073	3564	X-RAY DIFFRACTION	100
3.41-3.59	0.2479	192	0.1935	3542	X-RAY DIFFRACTION	100
3.59-3.81	0.2292	184	0.1848	3556	X-RAY DIFFRACTION	100
3.82-4.11	0.2333	200	0.168	3522	X-RAY DIFFRACTION	99
4.11-4.52	0.1814	193	0.1536	3544	X-RAY DIFFRACTION	99
4.52-5.18	0.1847	175	0.1516	3571	X-RAY DIFFRACTION	99
5.18-6.52	0.2239	208	0.1819	3579	X-RAY DIFFRACTION	100
6.52-39.5	0.1729	202	0.1559	3625	X-RAY DIFFRACTION	99

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	1.8188	0.3084	0.8075	0.7452	0.0745	1.3223	0.0206	-0.0372	0.0102	0.0771	-0.0186	0.0164	-0.1518	-0.0175	-0.017	0.3945	-0.0013	-0.0595	0.2168	0.0164	0.2198	35.2476	0.3038	11.962
2	2.2948	0.0422	0.7675	0.6079	0.0866	0.8988	-0.2607	0.2932	0.3008	-0.0923	0.0571	0.1039	-0.2486	0.1051	0.1327	0.4959	0.0683	-0.1561	0.3783	0.0169	0.3652	8.1976	2.2869	-19.9546
3	0.9618	0.1927	0.6207	0.7718	0.4676	3.1965	-0.0709	-0.1823	0.0156	-0.0115	0.0229	0.0589	-0.1811	-0.1954	0.0596	0.3898	0.0002	-0.0776	0.5864	0.0945	0.3156	-11.2722	5.3869	49.5877
4	2.1357	0.0113	0.7506	0.8621	0.3654	2.3636	-0.2302	-0.3238	0.0352	-0.1578	0.1045	0.3371	-0.148	-0.2318	0.1156	0.4596	-0.0069	-0.1888	0.4614	0.0553	0.5267	26.9889	-41.4851	53.2794

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	(chain 'A' and resid 7 through 476)
2	X-RAY DIFFRACTION	2	(chain 'B' and resid 7 through 476)
3	X-RAY DIFFRACTION	3	(chain 'C' and resid 7 through 476)
4	X-RAY DIFFRACTION	4	(chain 'D' and resid 7 through 476)

-
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