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- PDB-6gqd: Structure of human galactose-1-phosphate uridylyltransferase (GAL... -

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Basic information

Entry
Database: PDB / ID: 6gqd
TitleStructure of human galactose-1-phosphate uridylyltransferase (GALT), with crystallization epitope mutations A21Y:A22T:T23P:R25L
ComponentsGalactose-1-phosphate uridylyltransferase
KeywordsTRANSFERASE / crystal epitope / glucose-1-phosphate / uridine monophosphate / Structural Genomics / Structural Genomics Consortium / SGC
Function / homology
Function and homology information


UDP-glucose catabolic process / Defective GALT can cause GALCT / UDP-glucose-hexose-1-phosphate uridylyltransferase / UDP-glucose:hexose-1-phosphate uridylyltransferase activity / galactose catabolic process / Galactose catabolism / UDP-glucose metabolic process / galactose catabolic process via UDP-galactose / galactose metabolic process / Golgi apparatus ...UDP-glucose catabolic process / Defective GALT can cause GALCT / UDP-glucose-hexose-1-phosphate uridylyltransferase / UDP-glucose:hexose-1-phosphate uridylyltransferase activity / galactose catabolic process / Galactose catabolism / UDP-glucose metabolic process / galactose catabolic process via UDP-galactose / galactose metabolic process / Golgi apparatus / zinc ion binding / cytoplasm / cytosol
Similarity search - Function
Galactose-1-phosphate uridyl transferase, class I His-active site / Galactose-1-phosphate uridyl transferase family 1 active site signature. / Galactose-1-phosphate uridyl transferase, N-terminal / Galactose-1-phosphate uridyl transferase, C-terminal / Galactose-1-phosphate uridyl transferase, N-terminal domain / Galactose-1-phosphate uridyl transferase, C-terminal domain / Galactose-1-phosphate uridyl transferase, class I / HIT-like / HIT family, subunit A / HIT-like superfamily ...Galactose-1-phosphate uridyl transferase, class I His-active site / Galactose-1-phosphate uridyl transferase family 1 active site signature. / Galactose-1-phosphate uridyl transferase, N-terminal / Galactose-1-phosphate uridyl transferase, C-terminal / Galactose-1-phosphate uridyl transferase, N-terminal domain / Galactose-1-phosphate uridyl transferase, C-terminal domain / Galactose-1-phosphate uridyl transferase, class I / HIT-like / HIT family, subunit A / HIT-like superfamily / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
5,6-DIHYDROURIDINE-5'-MONOPHOSPHATE / Galactose-1-phosphate uridylyltransferase
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 1.523 Å
AuthorsFairhead, M. / Strain-Damerell, C. / Kopec, J. / Bezerra, G.A. / Zhang, M. / Burgess-Brown, N. / von Delft, F. / Arrowsmith, C. / Edwards, A. / Bountra, C. ...Fairhead, M. / Strain-Damerell, C. / Kopec, J. / Bezerra, G.A. / Zhang, M. / Burgess-Brown, N. / von Delft, F. / Arrowsmith, C. / Edwards, A. / Bountra, C. / Yue, W.W. / Structural Genomics Consortium (SGC)
Funding support United Kingdom, 1items
OrganizationGrant numberCountry
Wellcome Trust106169/ZZ14/Z United Kingdom
CitationJournal: To Be Published
Title: Structure of human galactose-1-phosphate uridylyltransferase (GALT), with crystallization epitope mutations A21Y:A22T:T23P:R25L
Authors: Fairhead, M. / Strain-Damerell, C. / Kopec, J. / Bezerra, G.A. / Zhang, M. / Burgess-Brown, N. / von Delft, F. / Arrowsmith, C. / Edwards, A. / Bountra, C. / Yue, W.W.
History
DepositionJun 7, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 18, 2018Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Galactose-1-phosphate uridylyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)44,0965
Polymers43,5801
Non-polymers5164
Water8,089449
1
A: Galactose-1-phosphate uridylyltransferase
hetero molecules

A: Galactose-1-phosphate uridylyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)88,19210
Polymers87,1602
Non-polymers1,0318
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_775-x+2,-y+2,z1
Buried area9470 Å2
ΔGint-49 kcal/mol
Surface area28030 Å2
MethodPISA
Unit cell
Length a, b, c (Å)72.647, 96.748, 55.426
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP21212

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Components

#1: Protein Galactose-1-phosphate uridylyltransferase / Gal-1-P uridylyltransferase / UDP-glucose--hexose-1-phosphate uridylyltransferase


Mass: 43580.215 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: GALT / Production host: Escherichia coli (E. coli)
References: UniProt: P07902, UDP-glucose-hexose-1-phosphate uridylyltransferase
#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#3: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6O2
#4: Chemical ChemComp-H2U / 5,6-DIHYDROURIDINE-5'-MONOPHOSPHATE


Type: RNA linking / Mass: 326.197 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C9H15N2O9P
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 449 / Source method: isolated from a natural source / Formula: H2O

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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: 2.23 Å3/Da / Density % sol: 44.96 %
Crystal growTemperature: 277.15 K / Method: vapor diffusion, sitting drop / Details: 0.2M ammonium sulphate, 30% PEG4000

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04-1 / Wavelength: 0.92818 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Jun 21, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.92818 Å / Relative weight: 1
ReflectionResolution: 1.52→72.65 Å / Num. obs: 60414 / % possible obs: 99.9 % / Redundancy: 6.5 % / Biso Wilson estimate: 15.29 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.087 / Rpim(I) all: 0.037 / Rrim(I) all: 0.095 / Net I/σ(I): 12.6
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. measured allNum. unique obsCC1/2Rpim(I) allRrim(I) allNet I/σ(I) obs% possible all
1.52-1.616.80.8365909487050.8880.3440.9052.3100
4.82-72.655.90.0321241520990.9990.0140.03640.399.5

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Processing

Software
NameVersionClassification
Aimless0.5.26data scaling
PHENIX1.13_2998refinement
PDB_EXTRACT3.24data extraction
xia2data reduction
PHASERphasing
RefinementResolution: 1.523→58.093 Å / SU ML: 0.17 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 21.73
RfactorNum. reflection% reflection
Rfree0.1877 2963 4.91 %
Rwork0.1624 --
obs0.1636 60315 99.73 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 94.33 Å2 / Biso mean: 26.019 Å2 / Biso min: 7.38 Å2
Refinement stepCycle: final / Resolution: 1.523→58.093 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2783 0 52 449 3284
Biso mean--32.17 32.57 -
Num. residues----344
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 21

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.5232-1.54820.36321340.30727152849100
1.5482-1.57490.2851420.280326832825100
1.5749-1.60350.26781570.258726702827100
1.6035-1.63440.251330.239227062839100
1.6344-1.66770.23121450.213526902835100
1.6677-1.7040.23361390.200526872826100
1.704-1.74360.26391270.194927292856100
1.7436-1.78720.20711300.179327252855100
1.7872-1.83560.20981310.166727142845100
1.8356-1.88960.1641300.161227222852100
1.8896-1.95060.24361430.197127122855100
1.9506-2.02030.17711320.162227402872100
2.0203-2.10120.1891510.142527052856100
2.1012-2.19680.19181570.145127092866100
2.1968-2.31260.2041400.17192710285099
2.3126-2.45750.16791590.146827262885100
2.4575-2.64730.16771470.143227562903100
2.6473-2.91370.17171280.147227752903100
2.9137-3.33530.17331410.14672734287599
3.3353-4.20190.17331480.136528112959100
4.2019-58.13510.14881490.15262933308299
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)
12.1233-0.9189-0.96125.03121.51462.22260.0388-0.0559-0.0950.1707-0.0491-0.27020.09230.1730.05640.19990.0075-0.02670.17580.01510.199785.767285.465118.167
20.06180.13310.00050.32640.04580.0119-0.03270.0823-0.0968-0.54710.07310.13490.26780.0448-0.01770.3113-0.0181-0.02730.273-0.00740.341680.796292.2969-6.6794
32.17160.3334-0.0842.1733-0.14232.0579-0.00610.08710.21880.08590.08450.1606-0.1441-0.1102-0.12920.14810.0128-0.00710.12020.0080.241374.4726123.42881.4103
41.02090.4055-0.19031.0238-0.13490.370.0104-0.0250.14290.07110.00440.0101-0.02470.0207-0.02120.13390.0008-0.01690.12620.00450.175880.3879114.70037.7887
51.3957-0.14330.28871.2488-0.50911.2869-0.038-0.2546-0.05590.24750.00540.03650.0013-0.0631-0.03960.1693-0.00880.00050.1322-0.01870.131679.7799106.499722.2822
60.89420.2055-0.09440.9748-0.04610.3579-0.0077-0.072-0.03890.0916-0.0113-0.1258-0.020.03610.0230.14120.001-0.01450.14670.0080.175389.4476101.244512.5589
72.42120.4024-0.05174.4724-2.98243.136-0.07250.317-0.1064-0.31830.0307-0.1670.16390.13760.01670.175-0.00830.01830.1963-0.01970.214196.512794.7806-0.3659
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 21 through 44 )A21 - 44
2X-RAY DIFFRACTION2chain 'A' and (resid 45 through 68 )A45 - 68
3X-RAY DIFFRACTION3chain 'A' and (resid 69 through 111 )A69 - 111
4X-RAY DIFFRACTION4chain 'A' and (resid 112 through 185 )A112 - 185
5X-RAY DIFFRACTION5chain 'A' and (resid 186 through 213 )A186 - 213
6X-RAY DIFFRACTION6chain 'A' and (resid 214 through 350 )A214 - 350
7X-RAY DIFFRACTION7chain 'A' and (resid 351 through 368 )A351 - 368

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