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- PDB-8ie4: Crystal structure of GcCGT -

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Basic information

Entry
Database: PDB / ID: 8ie4
TitleCrystal structure of GcCGT
ComponentsGcCGT
KeywordsTRANSFERASE / Glycosyltransferases
Biological speciesGentiana crassicaulis (plant)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å
AuthorsZhang, M. / Bao, Y. / He, C. / Ye, M.
Funding support China, 1items
OrganizationGrant numberCountry
National Science Foundation (NSF, China) China
CitationJournal: To Be Published
Title: Crystal structure of GcCGT
Authors: Zhang, M. / Bao, Y. / He, C. / Ye, M.
History
DepositionFeb 15, 2023Deposition site: PDBJ / Processing site: PDBC
Revision 1.0Feb 28, 2024Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: GcCGT
B: GcCGT
C: GcCGT
D: GcCGT
hetero molecules


Theoretical massNumber of molelcules
Total (without water)217,0065
Polymers216,8114
Non-polymers1951
Water9,440524
1
A: GcCGT
hetero molecules


Theoretical massNumber of molelcules
Total (without water)54,3982
Polymers54,2031
Non-polymers1951
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: GcCGT


Theoretical massNumber of molelcules
Total (without water)54,2031
Polymers54,2031
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: GcCGT


Theoretical massNumber of molelcules
Total (without water)54,2031
Polymers54,2031
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: GcCGT


Theoretical massNumber of molelcules
Total (without water)54,2031
Polymers54,2031
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
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 number4
Space group name H-MP1211

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Components

#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 interestN

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

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

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL02U1 / Wavelength: 0.9792 Å
DetectorType: DECTRIS EIGER2 S 9M / Detector: PIXEL / Date: May 5, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 2.1→39.5 Å / Num. obs: 112015 / % possible obs: 99.8 % / Redundancy: 4.9 % / CC1/2: 0.996 / Rmerge(I) obs: 0.109 / Rpim(I) all: 0.054 / Rrim(I) all: 0.122 / Χ2: 0.99 / Net I/σ(I): 7.2 / Num. measured all: 548820
Reflection shellResolution: 2.1→2.14 Å / % possible obs: 99.8 % / Redundancy: 5.1 % / Rmerge(I) obs: 0.82 / Num. measured all: 28344 / Num. unique obs: 5544 / CC1/2: 0.869 / Rpim(I) all: 0.398 / Rrim(I) all: 0.913 / Χ2: 0.88 / Net I/σ(I) obs: 1.7

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Processing

Software
NameVersionClassification
Aimlessdata scaling
PHENIX1.20.1refinement
XDSdata reduction
PHASERphasing
RefinementMethod 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
RfactorNum. reflection% reflection
Rfree0.2498 5770 5.16 %
Rwork0.2016 --
obs0.2041 111754 99.61 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.1→39.5 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms13995 0 12 524 14531
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00714371
X-RAY DIFFRACTIONf_angle_d0.84319537
X-RAY DIFFRACTIONf_dihedral_angle_d16.3425291
X-RAY DIFFRACTIONf_chiral_restr0.0522162
X-RAY DIFFRACTIONf_plane_restr0.0072521
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.1-2.120.35622100.3263478X-RAY DIFFRACTION99
2.12-2.150.36551890.32073542X-RAY DIFFRACTION99
2.15-2.180.33621980.30553486X-RAY DIFFRACTION99
2.18-2.20.35592090.30213525X-RAY DIFFRACTION99
2.2-2.230.38071950.29473487X-RAY DIFFRACTION100
2.23-2.260.34452020.28323518X-RAY DIFFRACTION100
2.26-2.290.35961580.27273520X-RAY DIFFRACTION100
2.29-2.330.31091960.2653571X-RAY DIFFRACTION100
2.33-2.370.34191710.25333483X-RAY DIFFRACTION100
2.37-2.40.2951700.25393601X-RAY DIFFRACTION100
2.4-2.450.31611840.2613487X-RAY DIFFRACTION100
2.45-2.490.30522010.24953536X-RAY DIFFRACTION100
2.49-2.540.2891800.22753546X-RAY DIFFRACTION100
2.54-2.590.28472200.2383503X-RAY DIFFRACTION100
2.59-2.650.29482100.23593497X-RAY DIFFRACTION99
2.65-2.710.28191900.23573497X-RAY DIFFRACTION100
2.71-2.770.28852010.23693519X-RAY DIFFRACTION100
2.77-2.850.2962120.2383518X-RAY DIFFRACTION100
2.85-2.930.29261690.22863579X-RAY DIFFRACTION100
2.93-3.030.30172010.22023514X-RAY DIFFRACTION100
3.03-3.140.2761990.21673520X-RAY DIFFRACTION100
3.14-3.260.29011800.21613554X-RAY DIFFRACTION100
3.26-3.410.27551710.20733564X-RAY DIFFRACTION100
3.41-3.590.24791920.19353542X-RAY DIFFRACTION100
3.59-3.810.22921840.18483556X-RAY DIFFRACTION100
3.82-4.110.23332000.1683522X-RAY DIFFRACTION99
4.11-4.520.18141930.15363544X-RAY DIFFRACTION99
4.52-5.180.18471750.15163571X-RAY DIFFRACTION99
5.18-6.520.22392080.18193579X-RAY DIFFRACTION100
6.52-39.50.17292020.15593625X-RAY DIFFRACTION99
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°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)
11.81880.30840.80750.74520.07451.32230.0206-0.03720.01020.0771-0.01860.0164-0.1518-0.0175-0.0170.3945-0.0013-0.05950.21680.01640.219835.24760.303811.962
22.29480.04220.76750.60790.08660.8988-0.26070.29320.3008-0.09230.05710.1039-0.24860.10510.13270.49590.0683-0.15610.37830.01690.36528.19762.2869-19.9546
30.96180.19270.62070.77180.46763.1965-0.0709-0.18230.0156-0.01150.02290.0589-0.1811-0.19540.05960.38980.0002-0.07760.58640.09450.3156-11.27225.386949.5877
42.13570.01130.75060.86210.36542.3636-0.2302-0.32380.0352-0.15780.10450.3371-0.148-0.23180.11560.4596-0.0069-0.18880.46140.05530.526726.9889-41.485153.2794
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(chain 'A' and resid 7 through 476)
2X-RAY DIFFRACTION2(chain 'B' and resid 7 through 476)
3X-RAY DIFFRACTION3(chain 'C' and resid 7 through 476)
4X-RAY DIFFRACTION4(chain 'D' and resid 7 through 476)

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