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- PDB-4nzj: Crystal structure of a putative alpha-galactosidase (BF1418) from... -

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Basic information

Entry
Database: PDB / ID: 4nzj
TitleCrystal structure of a putative alpha-galactosidase (BF1418) from Bacteroides fragilis NCTC 9343 at 1.57 A resolution
ComponentsPutative alpha-galactosidase
KeywordsHYDROLASE / The catalytic TIM beta/alpha barrel domain accompanied by N-terminal Ig-like domain and C-terminal beta-sheet domain / Structural Genomics / Joint Center for Structural Genomics / JCSG / Protein Structure Initiative / PSI-BIOLOGY
Function / homology
Function and homology information


raffinose alpha-galactosidase activity / alpha-galactosidase / carbohydrate metabolic process / calcium ion binding / membrane
Similarity search - Function
Alpha galactosidase, C-terminal beta sandwich domain / Alpha galactosidase C-terminal beta sandwich domain / Alpha galactosidase A / Glycoside hydrolase, family 27 / Cadherin-like superfamily / Golgi alpha-mannosidase II / Glycosyl hydrolase, all-beta / Aldolase class I / Aldolase-type TIM barrel / Glycoside hydrolase superfamily ...Alpha galactosidase, C-terminal beta sandwich domain / Alpha galactosidase C-terminal beta sandwich domain / Alpha galactosidase A / Glycoside hydrolase, family 27 / Cadherin-like superfamily / Golgi alpha-mannosidase II / Glycosyl hydrolase, all-beta / Aldolase class I / Aldolase-type TIM barrel / Glycoside hydrolase superfamily / Immunoglobulins / TIM Barrel / Alpha-Beta Barrel / Immunoglobulin-like fold / Immunoglobulin-like / Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
Biological speciesBacteroides fragilis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.57 Å
AuthorsJoint Center for Structural Genomics (JCSG)
CitationJournal: To be published
Title: Crystal structure of a putative alpha-galactosidase (BF1418) from Bacteroides fragilis NCTC 9343 at 1.57 A resolution
Authors: Joint Center for Structural Genomics (JCSG)
History
DepositionDec 12, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 25, 2013Provider: repository / Type: Initial release
Revision 1.1Nov 22, 2017Group: Refinement description / Category: software / Item: _software.classification / _software.name
Revision 1.2Jan 24, 2018Group: Database references / Category: citation_author / Item: _citation_author.name
Revision 1.3Feb 1, 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Putative alpha-galactosidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)53,9732
Polymers53,8811
Non-polymers921
Water8,647480
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: Putative alpha-galactosidase
hetero molecules

A: Putative alpha-galactosidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)107,9464
Polymers107,7622
Non-polymers1842
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_556y,x,-z+11
Buried area3320 Å2
ΔGint-3 kcal/mol
Surface area34170 Å2
MethodPISA
Unit cell
Length a, b, c (Å)114.614, 114.614, 77.051
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number94
Space group name H-MP42212
Components on special symmetry positions
IDModelComponents
11A-983-

HOH

21A-1002-

HOH

DetailsCRYSTAL PACKING ANALYSIS SUGGESTS THE ASSIGNMENT OF A MONOMER AS THE SIGNIFICANT OLIGOMERIZATION STATE.

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Components

#1: Protein Putative alpha-galactosidase


Mass: 53880.934 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacteroides fragilis (bacteria) / Strain: NCTC 9343 / Gene: BF9343_1347, YP_211072.1 / Plasmid: SpeedET / Production host: Escherichia Coli (E. coli) / Strain (production host): PB1 / References: UniProt: Q5LFG6, alpha-galactosidase
#2: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


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


Mass: 18.015 Da / Num. of mol.: 480 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsTHIS CONSTRUCT WAS EXPRESSED WITH AN N-TERMINAL PURIFICATION TAG MGSDKIHHHHHHENLYFQG. THE TAG WAS ...THIS CONSTRUCT WAS EXPRESSED WITH AN N-TERMINAL PURIFICATION TAG MGSDKIHHHHHHENLYFQG. THE TAG WAS REMOVED WITH TEV PROTEASE WITH TEV PROTEASE LEAVING ONLY A GLYCINE (0) FOLLOWED BY RESIDUES 25-500 OF THE TARGET SEQUENCE.

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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: 2.35 Å3/Da / Density % sol: 47.62 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 0.16M magnesium acetate, 20.0% Glycerol, 16.0% polyethylene glycol 8000, 0.1M sodium cacodylate pH 6.5, NANODROP, VAPOR DIFFUSION, SITTING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.2.1 / Wavelength: 0.918401,0.979261,0.979152
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Oct 17, 2013 / Details: KOHZU: Double Crystal Si(111)
RadiationMonochromator: Double Crystal Si(111) / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.9184011
20.9792611
30.9791521
ReflectionResolution: 1.57→29.386 Å / Num. obs: 71815 / % possible obs: 99.1 % / Observed criterion σ(I): -3 / Biso Wilson estimate: 22.74 Å2 / Rmerge(I) obs: 0.076 / Net I/σ(I): 9.28
Reflection shell

Diffraction-ID: 1

Resolution (Å)Highest resolution (Å)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. unique obs% possible all
1.57-1.630.9471.5514781387894.7
1.63-1.690.7412.1478451258299.6
1.69-1.770.5622.8543841426699.8
1.77-1.860.3874506061325399.8
1.86-1.980.2585.8541801415599.8
1.98-2.130.1688.3515431344599.8
2.13-2.340.11511.2518741356099.8
2.34-2.680.08514.2527811384399.7
2.68-3.380.0618.6515031381099.4
3.380.04423.9507341373499.3

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Phasing

PhasingMethod: MAD

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Processing

Software
NameVersionClassificationNB
MolProbity3beta29model building
PDB_EXTRACT3.1data extraction
SHELXphasing
SHARPphasing
XSCALEdata scaling
REFMAC5.7.0032refinement
XDSdata reduction
SHELXDphasing
RefinementMethod to determine structure: MAD / Resolution: 1.57→29.386 Å / Cor.coef. Fo:Fc: 0.975 / Cor.coef. Fo:Fc free: 0.973 / Occupancy max: 1 / Occupancy min: 0.1 / SU B: 2.612 / SU ML: 0.046 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.072 / ESU R Free: 0.068
Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES
Details: 1. HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. 2. ATOM RECORDS CONTAIN SUM OF TLS AND RESIDUAL B FACTORS. 3. ANISOU RECORDS CONTAIN SUM OF TLS AND RESIDUAL U FACTORS. 4. WATERS WERE ...Details: 1. HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. 2. ATOM RECORDS CONTAIN SUM OF TLS AND RESIDUAL B FACTORS. 3. ANISOU RECORDS CONTAIN SUM OF TLS AND RESIDUAL U FACTORS. 4. WATERS WERE EXCLUDED FROM AUTOMATIC TLS ASSIGNMENT. 5. A MET-INHIBITION PROTOCOL WAS USED FOR SELENOMETHIONINE INCORPORATION DURING PROTEIN EXPRESSION. THE OCCUPANCY OF THE SE ATOMS IN THE MSE RESIDUES WAS REDUCED TO 0.75 FOR THE REDUCED SCATTERING POWER DUE TO PARTIAL S-MET INCORPORATION. 6. GLYCEROL (GOL) FROM THE CRYSTALLIZATION SOLUTION IS MODELED.
RfactorNum. reflection% reflectionSelection details
Rfree0.1685 3628 5.1 %RANDOM
Rwork0.1541 ---
obs0.1549 71742 99.75 %-
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 max: 95.61 Å2 / Biso mean: 27.1649 Å2 / Biso min: 15.05 Å2
Baniso -1Baniso -2Baniso -3
1--0.41 Å2-0 Å2-0 Å2
2---0.41 Å20 Å2
3---0.82 Å2
Refinement stepCycle: LAST / Resolution: 1.57→29.386 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3656 0 6 480 4142
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0050.0193994
X-RAY DIFFRACTIONr_bond_other_d0.0010.023771
X-RAY DIFFRACTIONr_angle_refined_deg1.0991.9715473
X-RAY DIFFRACTIONr_angle_other_deg0.69538732
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.4585541
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.48724.355186
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.52715650
X-RAY DIFFRACTIONr_dihedral_angle_4_deg12.631525
X-RAY DIFFRACTIONr_chiral_restr0.0650.2595
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.0214623
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02924
X-RAY DIFFRACTIONr_mcbond_it1.2243.3571948
X-RAY DIFFRACTIONr_mcbond_other1.2233.3531947
X-RAY DIFFRACTIONr_mcangle_it2.0156.2742451
LS refinement shellResolution: 1.57→1.611 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.287 236 -
Rwork0.279 4916 -
all-5152 -
obs--98.77 %
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)
11.0202-0.3905-0.13760.9009-0.03350.73910.03090.028-0.0348-0.0526-0.00710.0342-0.023-0.0367-0.02390.00520.0044-0.00020.02680.0120.0083-0.73533.46429.062
22.2289-0.861-0.20522.0787-0.62741.12180.14040.2284-0.2109-0.3119-0.1191-0.04440.14510.0568-0.02130.05420.0208-0.00260.0515-0.01960.041817.13120.90517.867
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A27 - 353
2X-RAY DIFFRACTION2A360 - 500

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