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- PDB-8k7j: Crystal structure of human lysosomal alpha-galactosidase A in com... -

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Basic information

Entry
Database: PDB / ID: 8k7j
TitleCrystal structure of human lysosomal alpha-galactosidase A in complex with (2R,3R,4S,5R)-2-((dimethylamino)methyl)-5-(hydroxymethyl)pyrrolidine-3,4-diol
ComponentsAlpha-galactosidase A
KeywordsHYDROLASE / alpha-galactosidase / glycosidase / iminosugar
Function / homology
Function and homology information


negative regulation of nitric-oxide synthase activity / glycosylceramide catabolic process / alpha-galactosidase / glycosphingolipid catabolic process / alpha-galactosidase activity / oligosaccharide metabolic process / glycoside catabolic process / Glycosphingolipid catabolism / negative regulation of nitric oxide biosynthetic process / catalytic activity ...negative regulation of nitric-oxide synthase activity / glycosylceramide catabolic process / alpha-galactosidase / glycosphingolipid catabolic process / alpha-galactosidase activity / oligosaccharide metabolic process / glycoside catabolic process / Glycosphingolipid catabolism / negative regulation of nitric oxide biosynthetic process / catalytic activity / lysosomal lumen / azurophil granule lumen / lysosome / hydrolase activity / signaling receptor binding / Neutrophil degranulation / Golgi apparatus / protein homodimerization activity / extracellular exosome / extracellular region / membrane / cytoplasm
Similarity search - Function
Alpha galactosidase A, C-terminal beta-sandwich domain / Alpha galactosidase A C-terminal beta sandwich domain / Alpha galactosidase A / Glycoside hydrolase, family 27 / Glycoside hydrolase family 27/36, conserved site / Alpha-galactosidase signature. / Glycosyl hydrolase, all-beta / Aldolase-type TIM barrel / Glycoside hydrolase superfamily
Similarity search - Domain/homology
: / Alpha-galactosidase A
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.01 Å
AuthorsLi, H.Y. / Huang, K.F. / Ko, T.P. / Cheng, W.C.
Funding support Taiwan, 2items
OrganizationGrant numberCountry
Ministry of Science and Technology (MoST, Taiwan) Taiwan
Academia Sinica (Taiwan) Taiwan
CitationJournal: Jacs Au / Year: 2024
Title: Mechanistic Insights into Dibasic Iminosugars as pH-Selective Pharmacological Chaperones to Stabilize Human alpha-Galactosidase.
Authors: Li, H.Y. / Lin, H.Y. / Chang, S.K. / Chiu, Y.T. / Hou, C.C. / Ko, T.P. / Huang, K.F. / Niu, D.M. / Cheng, W.C.
History
DepositionJul 26, 2023Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Apr 10, 2024Provider: repository / Type: Initial release
Revision 1.1Oct 23, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Alpha-galactosidase A
B: Alpha-galactosidase A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)94,92416
Polymers90,7892
Non-polymers4,13514
Water13,043724
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7250 Å2
ΔGint-29 kcal/mol
Surface area30920 Å2
MethodPISA
Unit cell
Length a, b, c (Å)90.677, 90.677, 216.331
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number154
Space group name H-MP3221
Space group name HallP322"
Symmetry operation#1: x,y,z
#2: -y,x-y,z+2/3
#3: -x+y,-x,z+1/3
#4: x-y,-y,-z+1/3
#5: -x,-x+y,-z+2/3
#6: y,x,-z
Components on special symmetry positions
IDModelComponents
11B-921-

HOH

Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
d_1ens_1(chain "A" and (resid 32 through 50 or resid 52...
d_2ens_1(chain "B" and (resid 32 through 50 or resid 52...

NCS domain segments:

Ens-ID: ens_1

Dom-IDComponent-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
d_11LEULEUPHEPHEAA32 - 501 - 19
d_12CYSCYSTYRTYRAA52 - 8621 - 55
d_13TYRTYRILEILEAA88 - 11757 - 86
d_14GLNGLNASNASNAA119 - 22888 - 197
d_15ALAALALYSLYSAA230 - 237199 - 206
d_16ILEILELYSLYSAA239 - 240208 - 209
d_17ILEILEASPASPAA242 - 244211 - 213
d_18THRTHRLEULEUAA246 - 344215 - 313
d_19GLYGLYARGARGAA346 - 404315 - 373
d_110HISHISMETMETAA406 - 423375 - 392
d_111NAGNAGNAGNAGAH501
d_112NAGNAGNAGNAGCC1
d_113NAGNAGNAGNAGCC2
d_114NAGNAGNAGNAGDD2
d_21LEULEUPHEPHEBB32 - 501 - 19
d_22CYSCYSTYRTYRBB52 - 8621 - 55
d_23TYRTYRILEILEBB88 - 11757 - 86
d_24GLNGLNASNASNBB119 - 22888 - 197
d_25ALAALALYSLYSBB230 - 237199 - 206
d_26ILEILELYSLYSBB239 - 240208 - 209
d_27ILEILEASPASPBB242 - 244211 - 213
d_28THRTHRLEULEUBB246 - 344215 - 313
d_29GLYGLYARGARGBB346 - 404315 - 373
d_210HISHISMETMETBB406 - 423375 - 392
d_211NAGNAGNAGNAGEE1
d_212NAGNAGNAGNAGEE2
d_213NAGNAGNAGNAGFF1
d_214NAGNAGNAGNAGGG1

NCS oper: (Code: givenMatrix: (-0.975321766276, -0.217697467662, 0.0368139213121), (-0.215404021649, 0.901618438836, -0.375080388995), (0.048461940593, -0.373753934193, -0.926260998309)Vector: -89. ...NCS oper: (Code: given
Matrix: (-0.975321766276, -0.217697467662, 0.0368139213121), (-0.215404021649, 0.901618438836, -0.375080388995), (0.048461940593, -0.373753934193, -0.926260998309)
Vector: -89.2607696234, -13.4271016034, -16.4177716202)

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein Alpha-galactosidase A / Alpha-D-galactosidase A / Alpha-D-galactoside galactohydrolase / ...Alpha-D-galactosidase A / Alpha-D-galactoside galactohydrolase / Galactosylgalactosylglucosylceramidase GLA / Melibiase


Mass: 45394.543 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: GLA / Production host: Homo sapiens (human) / References: UniProt: P06280, alpha-galactosidase

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Sugars , 3 types, 6 molecules

#2: Polysaccharide alpha-D-mannopyranose-(1-3)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1- ...alpha-D-mannopyranose-(1-3)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 748.682 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpa1-3DManpb1-4DGlcpNAcb1-4DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/3,4,3/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1b_1-5][a1122h-1a_1-5]/1-1-2-3/a4-b1_b4-c1_c3-d1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{[(3+1)][a-D-Manp]{}}}}}LINUCSPDB-CARE
#3: Polysaccharide 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 424.401 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGlcpNAcb1-4DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/1,2,1/[a2122h-1b_1-5_2*NCC/3=O]/1-1/a4-b1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{}}}LINUCSPDB-CARE
#4: Sugar ChemComp-NAG / 2-acetamido-2-deoxy-beta-D-glucopyranose / N-acetyl-beta-D-glucosamine / 2-acetamido-2-deoxy-beta-D-glucose / 2-acetamido-2-deoxy-D-glucose / 2-acetamido-2-deoxy-glucose / N-ACETYL-D-GLUCOSAMINE


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H15NO6
IdentifierTypeProgram
DGlcpNAcbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
N-acetyl-b-D-glucopyranosamineCOMMON NAMEGMML 1.0
b-D-GlcpNAcIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcNAcSNFG CARBOHYDRATE SYMBOLGMML 1.0

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Non-polymers , 4 types, 732 molecules

#5: Chemical ChemComp-VNB / (2~{R},3~{R},4~{S},5~{R})-2-[(dimethylamino)methyl]-5-(hydroxymethyl)pyrrolidine-3,4-diol


Mass: 190.240 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C8H18N2O3 / Feature type: SUBJECT OF INVESTIGATION
#6: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: SO4
#7: Chemical ChemComp-P6G / HEXAETHYLENE GLYCOL / POLYETHYLENE GLYCOL PEG400


Mass: 282.331 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C12H26O7 / Comment: precipitant*YM
#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 724 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY
Has protein modificationY

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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: 2.83 Å3/Da / Density % sol: 56.5 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.2
Details: 100 mM Tris-HCl buffer 7.2, 25% PEG4000 and 200 mM ammonium sulfate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: NSRRC / Beamline: TPS 05A / Wavelength: 1 Å
DetectorType: RAYONIX MX300HE / Detector: CCD / Date: Mar 25, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.01→30 Å / Num. obs: 68290 / % possible obs: 98.6 % / Redundancy: 10.2 % / Biso Wilson estimate: 25.99 Å2 / Rmerge(I) obs: 0.105 / Net I/σ(I): 21.1
Reflection shellResolution: 2.01→2.08 Å / Rmerge(I) obs: 0.657 / Num. unique obs: 6025

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Processing

Software
NameVersionClassification
PHENIX1.19.2_4158refinement
HKL-2000data reduction
HKL-2000data scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1R47

1r47


Resolution: 2.01→29.68 Å / SU ML: 0.1936 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 19.2649
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.1907 2005 3.15 %
Rwork0.1571 61559 -
obs0.1582 63564 91.92 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 33.02 Å2
Refinement stepCycle: LAST / Resolution: 2.01→29.68 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6278 0 262 728 7268
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0076746
X-RAY DIFFRACTIONf_angle_d0.90659154
X-RAY DIFFRACTIONf_chiral_restr0.0556986
X-RAY DIFFRACTIONf_plane_restr0.00691155
X-RAY DIFFRACTIONf_dihedral_angle_d13.72022476
Refine LS restraints NCSType: Torsion NCS / Rms dev position: 2.44107927104 Å
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.01-2.060.3013630.21612225X-RAY DIFFRACTION47.1
2.06-2.120.24551040.20292981X-RAY DIFFRACTION63.41
2.12-2.180.23781260.19713842X-RAY DIFFRACTION81.36
2.18-2.250.25181480.18634448X-RAY DIFFRACTION94.35
2.25-2.330.21781460.17794704X-RAY DIFFRACTION99.26
2.33-2.430.22011550.16654723X-RAY DIFFRACTION99.88
2.43-2.540.2061590.15794742X-RAY DIFFRACTION99.92
2.54-2.670.19861530.16244785X-RAY DIFFRACTION100
2.67-2.840.20431540.15364745X-RAY DIFFRACTION100
2.84-3.060.1991560.15384753X-RAY DIFFRACTION100
3.06-3.360.17061570.14944821X-RAY DIFFRACTION100
3.36-3.850.14781590.13324825X-RAY DIFFRACTION100
3.85-4.840.14551610.12554873X-RAY DIFFRACTION99.98
4.84-29.680.22111640.18375092X-RAY DIFFRACTION99.92
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)
10.0597398211364-0.007836284892660.0117000353660.0235199438503-0.0085200106590.008831919193130.035999555320.00990008402240.0465185159880.04805542295940.00825500601873-0.101432194198-0.09620544222650.1314474842230.002025665374150.162005427215-0.0652869953102-0.0005314450984540.198022228857-0.01517645142660.180054915414-27.058967391931.3344222173-6.44913006972
20.009776795810410.0129526510475-0.001738850855030.0102369168411-0.005911394247070.01775851630120.03708219386840.06748115666440.0530780730147-0.0164039079204-0.0435635923188-0.00622342505331-0.02698778243640.1347713430972.46383244413E-50.18689467921-0.02170159514650.009714542682020.201800302598-0.01767042679740.184630721665-25.581844453431.5303136461-2.12103875908
30.05732063366790.0195377808561-0.01222521413350.0325415048696-0.05378237834530.1488939079390.042346670360.00324911930293-0.0227586179189-0.00714331420222-0.041205976359-0.1663434381520.02084986375430.36614798205-0.00254126543150.15281485383-0.0308732308111-0.03069764192390.279958553622-0.003102086692630.251968758984-16.526507216125.74996298170.861657842194
40.01977892236610.00179153625116-0.01811244881290.00683922495675-0.005858320128120.01848260778770.0229750230479-0.148259229474-0.06574329670730.0301948645341-0.0499059469764-0.02777177082930.07269380549890.235577512499-0.01913419056160.213218873019-0.00522133255498-0.06694560388630.2627924105260.04362802534140.235628186737-25.111079797416.294043537910.9998817453
50.01477930709350.000465384944703-0.008616941443620.003686425973280.0002181015206040.00458923857033-0.0312532760057-0.0432763651954-0.08722160057530.0494073568573-0.031852118218-0.0596062869127-0.01199087380630.0452571345935-3.87302393E-60.217739380396-0.0153061032833-0.04098841037280.1944913493630.03642730612590.177846564118-33.850932443418.46439935227.60803007115
60.0086768734506-0.000930433791767-0.01119796991230.00137321412203-0.002387999322840.01713963315590.012492592961-0.0272824080807-0.06323091548290.0561752015836-0.02139037312410.03225955265650.04177594881960.0575634707276-0.002669257162660.20869856621-0.0317009948678-0.008231430693090.1285741859950.0003818456552370.153590052774-43.200204807917.20555411685.94117366613
70.0944044377554-0.03425020544270.01170525803430.0351750738823-0.023005316580.06030399270870.03636786104520.02931005772480.02447401414230.0459733518752-0.0219159698456-0.00118699377245-0.0614934760653-0.0319897812718-8.00275799385E-50.156630323091-0.02116934483150.01397669984560.111645099797-0.01578055100080.120296749524-50.307463413327.94225313612.00483704833
80.00985293732465-0.00604239596003-0.0100278665250.004003443729630.001655913163120.00606392572654-0.006279568520410.01600231794370.04377875128110.1481095396850.05121676838780.080746990845-0.0843851073173-0.08253334155744.7395789165E-50.2346133537560.03538361463470.04608250181380.162875249119-0.01825776495740.153704407061-61.795923247332.45961469186.35288544903
90.05371365856280.006111962105780.02989398479450.0216147589307-0.005292293527550.04503017639190.01306901739870.1409846778320.00152686172255-0.0383234988661-0.1323823109490.280119666601-0.0685607246736-0.285441128707-0.02586582878780.1068196740720.0397297288885-0.06018151169510.299752356269-0.1148104923730.274446805185-73.917593817821.5302564697-25.6300298255
100.01388959233450.00337258963396-0.0131464263710.0007373107920440.0003985365717940.0131437708018-0.050787707160.087486414478-0.05736367055760.023186765141-0.05503119666060.09122865478760.0588082541879-0.104794740131-0.08490164741920.143483937131-0.191744068317-0.1084482048880.295171104395-0.2827738336670.392023477219-76.77490425197.00737162379-28.4470500538
110.04338739141390.00541001675145-0.01050621073230.02736611241810.02004044437140.0185604786632-0.1063599386030.113353305548-0.06763418214740.000737479860877-0.09647389705280.07718159625330.0447489189792-0.175210408142-0.207315492940.334867116961-0.128458954602-0.1005227947990.258307175254-0.321907846720.437766115208-68.19589011192.66381696543-34.1077109806
120.1673888606790.00887500111622-0.07470876809620.1455633730540.02058195965340.1481493887540.003271874643040.0736730160055-0.0546357208649-0.0677046340937-0.04543598616820.04675836982910.0105936947509-0.0191642816144-0.09749016756490.1813383961060.0195486657985-0.01142099927170.144957770008-0.04846637843280.122379295035-48.733661615717.7333581347-31.1865520463
130.005544043183480.00362692874704-0.002803772859910.00256554702823-0.003695546830620.00304140267890.06984310366870.08953296001610.0333598902092-0.0746869466073-0.000937500313791-0.0998380727227-0.00112921424430.0886997628029-1.32703216399E-50.207193553117-0.003490371851940.0384569417270.227336511994-0.02545838249560.151642324461-35.141039736927.2850509533-37.4998956167
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION

IDRefine TLS-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11chain 'A' and (resid 32 through 78 )AA32 - 781 - 47
22chain 'A' and (resid 79 through 100 )AA79 - 10048 - 69
33chain 'A' and (resid 101 through 176 )AA101 - 17670 - 145
44chain 'A' and (resid 177 through 215 )AA177 - 215146 - 184
55chain 'A' and (resid 216 through 235 )AA216 - 235185 - 204
66chain 'A' and (resid 236 through 264 )AA236 - 264205 - 233
77chain 'A' and (resid 265 through 388 )AA265 - 388234 - 357
88chain 'A' and (resid 389 through 423 )AA389 - 423358 - 392
99chain 'B' and (resid 32 through 136 )BJ32 - 1361 - 105
1010chain 'B' and (resid 137 through 176 )BJ137 - 176106 - 145
1111chain 'B' and (resid 177 through 215 )BJ177 - 215146 - 184
1212chain 'B' and (resid 216 through 388 )BJ216 - 388185 - 357
1313chain 'B' and (resid 389 through 423 )BJ389 - 423358 - 392

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  • 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

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