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- PDB-8znm: CRYSTAL STRUCTURE OF DI-C-GLYCOSYLTRANSFERASE GGCGT MUTANT IN COM... -

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Basic information

Entry
Database: PDB / ID: 8znm
TitleCRYSTAL STRUCTURE OF DI-C-GLYCOSYLTRANSFERASE GGCGT MUTANT IN COMPLEX WITH UDP-GLC
ComponentsGgCGT
KeywordsTRANSFERASE / Thermostable di-C-glycosyltransferase / mutant
Function / homology: / UDP-glucosyltransferase activity / UDP-glucoronosyl and UDP-glucosyl transferase / UDP-glucuronosyl/UDP-glucosyltransferase / URIDINE-5'-DIPHOSPHATE-GLUCOSE / GgCGT
Function and homology information
Biological speciesGlycyrrhiza glabra (plant)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.21 Å
AuthorsFeng, X.D. / Liu, X.H.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)2018YFA0901800 China
CitationJournal: To Be Published
Title: CRYSTAL STRUCTURE OF DI-C-GLYCOSYLTRANSFERASE GGCGT MUTANT IN COMPLEX WITH UDP-GLC
Authors: Feng, X.D. / Liu, X.H.
History
DepositionMay 27, 2024Deposition site: PDBJ / Processing site: PDBC
Revision 1.0Jun 4, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)210,6978
Polymers208,4324
Non-polymers2,2654
Water9,512528
1
A: GgCGT
hetero molecules

B: GgCGT
hetero molecules


Theoretical massNumber of molelcules
Total (without water)105,3494
Polymers104,2162
Non-polymers1,1332
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation1_655x+1,y,z1
Buried area3770 Å2
ΔGint-26 kcal/mol
Surface area35690 Å2
MethodPISA
2
C: GgCGT
D: GgCGT
hetero molecules


Theoretical massNumber of molelcules
Total (without water)105,3494
Polymers104,2162
Non-polymers1,1332
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3700 Å2
ΔGint-27 kcal/mol
Surface area35120 Å2
MethodPISA
Unit cell
Length a, b, c (Å)75.618, 81.849, 94.141
Angle α, β, γ (deg.)64.760, 88.280, 88.240
Int Tables number1
Space group name H-MP1
Space group name HallP1
Symmetry operation#1: x,y,z

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Components

#1: Protein
GgCGT


Mass: 52107.977 Da / Num. of mol.: 4
Mutation: S155A/G424A/L227E/G200Y/D411G/V194D/V437R/K381P/G456S/C457Q
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Glycyrrhiza glabra (plant) / Production host: Escherichia coli (E. coli) / References: UniProt: A0A6I8WFN2
#2: Chemical
ChemComp-UPG / URIDINE-5'-DIPHOSPHATE-GLUCOSE / URIDINE-5'-MONOPHOSPHATE GLUCOPYRANOSYL-MONOPHOSPHATE ESTER


Mass: 566.302 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C15H24N2O17P2 / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 528 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationN

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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: 2.53 Å3/Da / Density % sol: 51.32 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 0.2 M Sodium chloride, 0.1 M Tris pH7.5, 22.5% w/v Polyethylene glycol 3,350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL02U1 / Wavelength: 0.97915 Å
DetectorType: DECTRIS EIGER2 S 9M / Detector: PIXEL / Date: Jan 5, 2024
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97915 Å / Relative weight: 1
ReflectionResolution: 2.21→29.64 Å / Num. obs: 98869 / % possible obs: 96.75 % / Redundancy: 3.5 % / Biso Wilson estimate: 39.53 Å2 / CC1/2: 0.997 / CC star: 0.999 / Rmerge(I) obs: 0.05923 / Rpim(I) all: 0.03748 / Rrim(I) all: 0.07038 / Net I/σ(I): 7.54
Reflection shellResolution: 2.21→2.289 Å / Redundancy: 3.4 % / Rmerge(I) obs: 0.4958 / Num. unique obs: 9933 / CC1/2: 0.79 / CC star: 0.94 / Rpim(I) all: 0.32 / Rrim(I) all: 0.5928 / % possible all: 97.15

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.21→29.64 Å / SU ML: 0.2534 / Cross valid method: FREE R-VALUE / σ(F): 1.96 / Phase error: 23.0134
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2174 5169 5.23 %
Rwork0.1764 93689 -
obs0.1785 98858 96.79 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 52.7 Å2
Refinement stepCycle: LAST / Resolution: 2.21→29.64 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms14025 0 144 528 14697
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.002414587
X-RAY DIFFRACTIONf_angle_d0.570919833
X-RAY DIFFRACTIONf_chiral_restr0.04322217
X-RAY DIFFRACTIONf_plane_restr0.00452479
X-RAY DIFFRACTIONf_dihedral_angle_d15.83025330
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.21-2.240.28651760.28783116X-RAY DIFFRACTION97.48
2.24-2.260.42321620.35343153X-RAY DIFFRACTION96.87
2.26-2.290.3241700.29183156X-RAY DIFFRACTION97.14
2.29-2.320.27861830.24373114X-RAY DIFFRACTION97.69
2.32-2.350.26671740.2193137X-RAY DIFFRACTION97.41
2.35-2.380.24381900.213147X-RAY DIFFRACTION97.37
2.38-2.410.27332020.20553123X-RAY DIFFRACTION97.91
2.41-2.450.26151710.20113122X-RAY DIFFRACTION97.86
2.45-2.490.2631790.20993183X-RAY DIFFRACTION97.73
2.49-2.530.25851600.20843160X-RAY DIFFRACTION97.82
2.53-2.570.25211600.2023202X-RAY DIFFRACTION98.3
2.57-2.620.25031700.20693172X-RAY DIFFRACTION98.03
2.62-2.670.25491650.20323122X-RAY DIFFRACTION97.97
2.67-2.720.26221690.20153224X-RAY DIFFRACTION98.12
2.72-2.780.23891680.20093174X-RAY DIFFRACTION98.18
2.78-2.850.24721920.20483124X-RAY DIFFRACTION98.34
2.85-2.920.27951950.20293180X-RAY DIFFRACTION98.28
2.92-30.22432020.19583108X-RAY DIFFRACTION98.34
3-3.090.24061730.1983174X-RAY DIFFRACTION98.35
3.09-3.190.26471490.20023222X-RAY DIFFRACTION98.31
3.19-3.30.22131800.19163176X-RAY DIFFRACTION98.13
3.3-3.430.22131570.1863184X-RAY DIFFRACTION98.18
3.43-3.590.22681970.17613101X-RAY DIFFRACTION97.11
3.59-3.780.22442300.16973062X-RAY DIFFRACTION95.73
3.78-4.010.16941450.15513062X-RAY DIFFRACTION95.56
4.01-4.320.18331800.14063030X-RAY DIFFRACTION93.83
4.32-4.760.16381660.13433042X-RAY DIFFRACTION93.99
4.76-5.440.19091450.14272995X-RAY DIFFRACTION92.24
5.44-6.840.16751220.15162977X-RAY DIFFRACTION90.8
6.84-29.640.14751370.1342947X-RAY DIFFRACTION90.84
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)
10.6652313406860.01518273950270.1479684143420.8454894813620.4894247073661.35642633205-0.00812620973302-0.1360620002990.02949953219340.2080606637010.00566622477979-0.114979405234-0.0574816813540.0677688647087-4.87019239129E-60.39016676063-0.000601437357481-0.01671604372950.307706803752-0.01275021837270.3231361077299.8611530993537.69184427973.38873763636
20.9903661788350.0728136363198-0.441805619320.95949533277-0.02048640319721.23472018521-0.01952437225320.0167890022509-0.04044820945370.0393126724331-0.00285044554252-0.03729870796220.0133145026920.058044291947-1.40979402172E-60.2395450551570.0119146948114-0.02136302174790.2557438940940.005512317692160.23049816238410.441379116824.629766697-13.6473016435
30.7139700305850.1004127894150.1772728678231.34156495393-0.1196567817671.098900033910.0706011320376-0.0394619703174-0.104563024083-0.0454948827696-0.113342557542-0.06397354979670.2222053184130.07830308901231.22847997544E-50.3340430934320.0454703266395-0.01927921669650.2584289329930.009333914659060.323287022198-13.2221707494-14.9483513748-21.5219247204
40.96556271247-0.07482706334150.06805297117241.09661185185-0.3941157360591.093806440560.05470233231640.01509241951810.1030314828780.0120242888041-0.0532709036740.113119101758-0.00658270999274-0.10644763525-6.16807148593E-70.2513006165930.02075074907450.002493662421310.3045562233680.01136729895880.281269088655-23.05390326536.7004190296-24.3607836203
50.669156369139-0.305123446275-0.3332363043510.8227865473140.4774766483581.17751680347-0.0798662679370.143075057855-0.140543380831-0.0785217220673-0.0737684851823-0.0060362080120.217157289538-0.103769203391-3.23832457678E-50.390713211774-0.0308288169110.01547725861180.355787252912-0.06133746195950.380810278574-26.22653811784.51375639804-75.6953881929
61.1297781637-0.0386434359347-0.01129123911490.7549639660830.3314383352151.37379033486-0.05649754410020.0298914707204-0.04267030918920.0450550195377-0.001687304013330.034187375409-0.0481854078257-0.0664206630931-2.06357904084E-60.250849323549-0.006961931458850.0200696548790.2950558389260.004336200859650.284087371766-27.985077271719.8426186093-59.6629208126
70.366971337834-0.2140379075380.08586778972941.45361878679-0.5554555195831.316123152810.07538397331860.08815488738620.2758539168470.108331979094-0.116158717936-0.0932355389516-0.4083689411160.1317196528358.67911028217E-60.491997292572-0.07019308174540.0006831639450370.3574303426520.02301177763570.54556256759824.556252993458.9366622499-51.5628689788
80.09744894943780.013667111098-0.05908184028-0.0105929025577-0.008431517601020.03804768158760.132252803542-0.186945778340.1691834998260.3303889373170.1457373719640.154364736601-0.174187439314-0.3911874979820.0001098984654110.3662246349250.0555790834840.07601353727290.4291116910370.0490408124090.3901126314545.7841951697637.8096893543-39.4929535729
90.8596761034170.0280575658174-0.2422033660861.32026963812-0.6103472473471.030553453760.03150657972080.121901506090.05684656515740.000536434832866-0.02688915601790.0430842410680.01788445222430.023783142319-7.84372114071E-70.281369848191-0.0208938132579-0.02045532880970.359709330630.02011062132180.33260480070516.794190509137.0557617133-49.5599254537
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION

IDRefine TLS-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11chain 'A' and (resid 13 through 171 )AA13 - 1711 - 159
22chain 'A' and (resid 172 through 469 )AA172 - 469160 - 447
33chain 'B' and (resid 14 through 253 )BC14 - 2531 - 240
44chain 'B' and (resid 254 through 469 )BC254 - 469241 - 456
55chain 'C' and (resid 14 through 161 )CE14 - 1611 - 148
66chain 'C' and (resid 162 through 469 )CE162 - 469149 - 445
77chain 'D' and (resid 14 through 253 )DG14 - 2531 - 240
88chain 'D' and (resid 254 through 281 )DG254 - 281241 - 268
99chain 'D' and (resid 282 through 469 )DG282 - 469269 - 451

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