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- PDB-1zy9: Crystal structure of Alpha-galactosidase (EC 3.2.1.22) (Melibiase... -

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Basic information

Entry
Database: PDB / ID: 1zy9
TitleCrystal structure of Alpha-galactosidase (EC 3.2.1.22) (Melibiase) (tm1192) from Thermotoga maritima at 2.34 A resolution
Componentsalpha-galactosidase
KeywordsHYDROLASE / tm1192 / Alpha-galactosidase (EC 3.2.1.22) (Melibiase) / Structural Genomics / Joint Center for Structural Genomics / JCSG / Protein Structure Initiative / PSI
Function / homology
Function and homology information


alpha-galactosidase / alpha-galactosidase activity / glycoside catabolic process / carbohydrate binding / carbohydrate metabolic process / protein homodimerization activity
Similarity search - Function
Immunoglobulin-like - #2760 / Alpha-galactosidase, N-terminal / Melibiase / : / Galactose mutarotase-like domain superfamily / Aldolase class I / Aldolase-type TIM barrel / Glycoside hydrolase superfamily / TIM Barrel / Alpha-Beta Barrel ...Immunoglobulin-like - #2760 / Alpha-galactosidase, N-terminal / Melibiase / : / Galactose mutarotase-like domain superfamily / Aldolase class I / Aldolase-type TIM barrel / Glycoside hydrolase superfamily / TIM Barrel / Alpha-Beta Barrel / Immunoglobulin-like / Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
Alpha-galactosidase / Alpha-galactosidase
Similarity search - Component
Biological speciesThermotoga maritima (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.34 Å
AuthorsJoint Center for Structural Genomics (JCSG)
CitationJournal: to be published
Title: Crystal structure of alpha-galactosidase (ec 3.2.1.22) (melibiase) (tm1192) from Thermotoga maritima at 2.34 A resolution
Authors: Joint Center for Structural Genomics (JCSG)
History
DepositionJun 9, 2005Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 12, 2005Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Non-polymer description / Version format compliance
Revision 1.3Jan 25, 2023Group: Database references / Derived calculations
Category: database_2 / struct_conn ...database_2 / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Oct 16, 2024Group: Data collection / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: alpha-galactosidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)66,0086
Polymers65,6681
Non-polymers3405
Water4,396244
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)121.729, 160.533, 88.258
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number20
Space group name H-MC2221

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Components

#1: Protein alpha-galactosidase


Mass: 65667.961 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermotoga maritima (bacteria) / Gene: tm1192 / Production host: Escherichia coli (E. coli)
References: UniProt: O33835, UniProt: G4FEF4*PLUS, alpha-galactosidase
#2: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C2H6O2
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 244 / Source method: isolated from a natural source / Formula: H2O
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: 3.4 Å3/Da / Density % sol: 63.58 %
Crystal growTemperature: 273 K / Method: vapor diffusion, sitting drop, nanodrop / pH: 8.3
Details: 0.2M K3Cirtrate, 20.0% PEG-3350, No Buffer, pH 8.3, VAPOR DIFFUSION, SITTING DROP, NANODROP, temperature 273K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL11-1 / Wavelength: 0.979413, 0.918370, 0.979170
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: May 1, 2005
Details: Flat mirror, Side-defelecting monochromator (Si 111)
RadiationProtocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.9794131
20.918371
30.979171
ReflectionResolution: 2.34→42.88 Å / Num. obs: 35967 / % possible obs: 98 % / Redundancy: 3.7 % / Rmerge(I) obs: 0.129 / Rsym value: 0.129 / Net I/σ(I): 5.7
Reflection shell

Diffraction-ID: 1

Resolution (Å)% possible obs (%)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured obsRsym value
2.34-2.4799.43.70.6031.352880.603
2.47-2.6299.13.70.4721.649660.472
2.62-2.898.93.70.3562.147080.356
2.8-3.0298.63.70.2383.243270.238
3.02-3.3198.23.70.151539910.151
3.31-3.797.73.70.0977.836210.097
3.7-4.2796.63.70.0729.831530.072
4.27-5.23963.70.05812.226700.058
5.23-7.495.53.70.06211.520740.062
7.4-42.8893.93.60.04213.611690.042

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Phasing

PhasingMethod: MAD

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Processing

Software
NameVersionClassificationNB
REFMAC5.2.0005refinement
SCALAdata scaling
PDB_EXTRACT1.601data extraction
XDSdata reduction
CCP4(SCALA)data scaling
SHELXDphasing
autoSHARPphasing
RefinementMethod to determine structure: MAD / Resolution: 2.34→42.504 Å / Cor.coef. Fo:Fc: 0.959 / Cor.coef. Fo:Fc free: 0.931 / SU B: 5.837 / SU ML: 0.136 / Cross valid method: THROUGHOUT / ESU R: 0.207 / ESU R Free: 0.187
Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. THE DENSITY BLOB BETWEEN SIDE CHAINS OF A220,A387 IS TENATIVELY MODELED AS A GLYCEROL.
RfactorNum. reflection% reflectionSelection details
Rfree0.213 1792 5 %RANDOM
Rwork0.162 ---
all0.165 ---
obs-34093 97.41 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 27.55 Å2
Baniso -1Baniso -2Baniso -3
1-0.38 Å20 Å20 Å2
2--1.61 Å20 Å2
3----1.99 Å2
Refinement stepCycle: LAST / Resolution: 2.34→42.504 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4232 0 22 244 4498
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0180.0224397
X-RAY DIFFRACTIONr_bond_other_d0.0010.023954
X-RAY DIFFRACTIONr_angle_refined_deg1.551.9555970
X-RAY DIFFRACTIONr_angle_other_deg0.81239198
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.1025535
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.94824.258209
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.63315732
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.7581524
X-RAY DIFFRACTIONr_chiral_restr0.0890.2638
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.024881
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02919
X-RAY DIFFRACTIONr_nbd_refined0.1930.2839
X-RAY DIFFRACTIONr_nbd_other0.1840.24137
X-RAY DIFFRACTIONr_nbtor_refined0.1830.22130
X-RAY DIFFRACTIONr_nbtor_other0.0890.22672
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1670.2214
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1080.26
X-RAY DIFFRACTIONr_symmetry_vdw_other0.1750.225
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1370.25
X-RAY DIFFRACTIONr_mcbond_it2.58832841
X-RAY DIFFRACTIONr_mcbond_other0.50831066
X-RAY DIFFRACTIONr_mcangle_it3.32454284
X-RAY DIFFRACTIONr_scbond_it5.91781997
X-RAY DIFFRACTIONr_scangle_it7.69111682
LS refinement shellResolution: 2.34→2.401 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.315 123 -
Rwork0.236 2559 -
obs--99.3 %

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