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- PDB-4fj6: Crystal structure of a glycoside hydrolase family 33, candidate s... -

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Entry
Database: PDB / ID: 4fj6
TitleCrystal structure of a glycoside hydrolase family 33, candidate sialidase (BDI_2946) from Parabacteroides distasonis ATCC 8503 at 1.90 A resolution
Componentsglycoside hydrolase family 33, candidate sialidase
KeywordsHYDROLASE / bacterial neuraminidase repeat / intramolecular trans-sialidase / a carbohydrate binding domain / Structural Genomics / Joint Center for Structural Genomics / JCSG / Protein Structure Initiative / PSI-BIOLOGY
Function / homology
Function and homology information


exo-alpha-sialidase activity / :
Similarity search - Function
Sialidase, N-terminal / N-terminal domain of BNR-repeat neuraminidase / Immunoglobulin-like - #1290 / Trypanosome sialidase / BNR repeat-like domain / Sialidase family / Sialidase / Neuraminidase - #10 / Sialidase superfamily / 6 Propeller ...Sialidase, N-terminal / N-terminal domain of BNR-repeat neuraminidase / Immunoglobulin-like - #1290 / Trypanosome sialidase / BNR repeat-like domain / Sialidase family / Sialidase / Neuraminidase - #10 / Sialidase superfamily / 6 Propeller / Neuraminidase / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
PHOSPHATE ION / Glycoside hydrolase family 33, candidate sialidase
Similarity search - Component
Biological speciesParabacteroides distasonis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.9 Å
AuthorsJoint Center for Structural Genomics (JCSG)
CitationJournal: To be published
Title: Crystal structure of a glycoside hydrolase family 33, candidate sialidase (BDI_2946) from Parabacteroides distasonis ATCC 8503 at 1.90 A resolution
Authors: Joint Center for Structural Genomics (JCSG)
History
DepositionJun 11, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 25, 2012Provider: repository / Type: Initial release
Revision 1.1Aug 1, 2012Group: Structure summary
Revision 1.2Nov 15, 2017Group: Refinement description / Category: software / Item: _software.classification / _software.name
Revision 1.3Jan 24, 2018Group: Database references / Category: citation_author / Item: _citation_author.name
Revision 1.4Feb 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: glycoside hydrolase family 33, candidate sialidase
B: glycoside hydrolase family 33, candidate sialidase
C: glycoside hydrolase family 33, candidate sialidase
D: glycoside hydrolase family 33, candidate sialidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)238,47339
Polymers235,3714
Non-polymers3,10235
Water36,0302000
1
A: glycoside hydrolase family 33, candidate sialidase
B: glycoside hydrolase family 33, candidate sialidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)119,16119
Polymers117,6852
Non-polymers1,47517
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6340 Å2
ΔGint-57 kcal/mol
Surface area36130 Å2
MethodPISA
2
C: glycoside hydrolase family 33, candidate sialidase
D: glycoside hydrolase family 33, candidate sialidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)119,31220
Polymers117,6852
Non-polymers1,62718
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6850 Å2
ΔGint-60 kcal/mol
Surface area35940 Å2
MethodPISA
Unit cell
Length a, b, c (Å)171.738, 171.738, 243.786
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number146
Space group name H-MH3
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
31C
41D

NCS domain segments:
Dom-IDComponent-IDEns-IDRefine codeAuth asym-IDAuth seq-ID
1116A22 - 539
2116B22 - 539
3116C22 - 539
4116D22 - 539
DetailsCRYSTAL PACKING ANALYSIS SUGGESTS THE ASSIGNMENT OF A DIMER AS THE SIGNIFICANT OLIGOMERIZATION STATE.

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Components

#1: Protein
glycoside hydrolase family 33, candidate sialidase


Mass: 58842.746 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Parabacteroides distasonis (bacteria) / Strain: ATCC 8503 / Gene: BDI_2946 / Plasmid: SpeedET / Production host: Escherichia Coli (E. coli) / Strain (production host): PB1 / References: UniProt: A6LG40
#2: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 15 / Source method: obtained synthetically / Formula: C3H8O3
#3: Chemical
ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 17 / Source method: obtained synthetically / Formula: PO4
#4: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Cl
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 2000 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsTHIS CONSTRUCT WAS EXPRESSED WITH A PURIFICATION TAG MGSDKIHHHHHHENLYFQG. THE TAG WAS REMOVED WITH ...THIS CONSTRUCT WAS EXPRESSED WITH A PURIFICATION TAG MGSDKIHHHHHHENLYFQG. THE TAG WAS REMOVED WITH TEV PROTEASE LEAVING ONLY A GLYCINE (0) FOLLOWED BY RESIDUES 20-541 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: 2.94 Å3/Da / Density % sol: 58.16 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 10.5
Details: 0.2M lithium sulfate, 1.2M sodium dihydrogen phosphate, 0.8M di-potassium hydrogen phosphate, 0.1M Glycine pH 10.5, VAPOR DIFFUSION,SITTING DROP,NANODROP, temperature 277K, VAPOR DIFFUSION, SITTING DROP

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL11-1 / Wavelength: 0.97922,0.91837,0.97871
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Apr 4, 2012
Details: Flat mirror (vertical focusing); single crystal Si(111) bent monochromator (horizontal focusing)
RadiationMonochromator: single crystal Si(111) bent / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.979221
20.918371
30.978711
ReflectionResolution: 1.9→29.773 Å / Num. obs: 209534 / % possible obs: 95.9 % / Observed criterion σ(I): -3 / Biso Wilson estimate: 19.77 Å2 / Rmerge F obs: 0.269 / Rmerge(I) obs: 0.105 / Rrim(I) all: 0.143 / Net I/σ(I): 6.44 / Num. measured all: 741693
Reflection shell

Diffraction-ID: 1

Resolution (Å)Highest resolution (Å)Rmerge F obsRmerge(I) obsMean I/σ(I) obsNum. measured obsNum. possibleNum. unique obsRrim(I) all% possible all
1.9-1.971.1750.6191.47554143476411700.8594.7
1.97-2.050.8920.4711.97526542808412150.64696.3
2.05-2.140.6620.3612.36956640832388710.49595.2
2.14-2.250.4990.2782.96945641368391710.3894.7
2.25-2.390.4140.2393.57635042158408520.32796.9
2.39-2.580.3180.1884.47831943678424470.25797.2
2.58-2.840.2270.1395.87060242332402310.18995
2.84-3.250.1270.0839.67795342200410730.11497.3
3.25-4.080.0680.04914.87232741806399550.06795.6
4.080.0520.03617.87631442828409490.04995.6

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Phasing

PhasingMethod: MAD

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Processing

Software
NameVersionClassificationNB
MolProbity3beta29model building
PDB_EXTRACT3.1data extraction
SHELXphasing
SHARPphasing
XSCALEDecember 29, 2011data scaling
REFMAC5.6.0117refinement
XDSdata reduction
SHELXDphasing
RefinementMethod to determine structure: MAD / Resolution: 1.9→29.773 Å / Cor.coef. Fo:Fc: 0.931 / Cor.coef. Fo:Fc free: 0.902 / Occupancy max: 1 / Occupancy min: 0.23 / SU B: 7.394 / SU ML: 0.116 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.155 / ESU R Free: 0.144
Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES
Details: 1. HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. 2. ATOM RECORD CONTAINS SUM OF TLS AND RESIDUAL B FACTORS. 3. ANISOU RECORD CONTAINS SUM OF TLS AND RESIDUAL U FACTORS. 4. WATERS WERE ...Details: 1. HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. 2. ATOM RECORD CONTAINS SUM OF TLS AND RESIDUAL B FACTORS. 3. ANISOU RECORD CONTAINS 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. PHOSPHATE IONS (PO4) AND GLYCEROL (GOL) MOLECULES FROM THE CRYSTALLIZATION/CRYOPROTECTION SOLUTION ARE MODELED. 7. CHLORIDE (CL) IONS FROM PROTEIN BUFFER HAVE BEEN MODELED.
RfactorNum. reflection% reflectionSelection details
Rfree0.2426 10526 5 %RANDOM
Rwork0.207 198969 --
obs0.2088 209495 99.09 %-
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: 85.84 Å2 / Biso mean: 27.3971 Å2 / Biso min: 13.32 Å2
Baniso -1Baniso -2Baniso -3
1-0.21 Å20.1 Å20 Å2
2--0.21 Å20 Å2
3----0.31 Å2
Refinement stepCycle: LAST / Resolution: 1.9→29.773 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms16160 0 178 2000 18338
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0216905
X-RAY DIFFRACTIONr_bond_other_d0.0020.0211325
X-RAY DIFFRACTIONr_angle_refined_deg1.5311.95623016
X-RAY DIFFRACTIONr_angle_other_deg0.999327804
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.87352155
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.34924.748733
X-RAY DIFFRACTIONr_dihedral_angle_3_deg10.521152928
X-RAY DIFFRACTIONr_dihedral_angle_4_deg10.8731596
X-RAY DIFFRACTIONr_chiral_restr0.0780.22612
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.02118667
X-RAY DIFFRACTIONr_gen_planes_other0.0010.023221
Refine LS restraints NCS

Ens-ID: 1 / Number: 6506 / Refine-ID: X-RAY DIFFRACTION

Dom-IDAuth asym-IDTypeRms dev position (Å)Weight position
1ALOOSE POSITIONAL0.25
2BLOOSE POSITIONAL0.225
3CLOOSE POSITIONAL0.245
4DLOOSE POSITIONAL0.25
1ALOOSE THERMAL1.7210
2BLOOSE THERMAL1.8510
3CLOOSE THERMAL1.810
4DLOOSE THERMAL2.0710
LS refinement shellResolution: 1.9→1.949 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.311 785 -
Rwork0.265 14788 -
all-15573 -
obs--99.55 %
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)
10.4293-0.08650.17860.1685-0.09810.3873-0.0269-0.06220.00090.02920.06370.02240.0156-0.0427-0.03680.10730.0349-0.03880.0458-0.00770.066499.66424.208275.783
20.19870.1244-0.08760.1324-0.00240.4798-0.0309-0.01230.0329-0.0730.01890.0040.03740.10910.0120.10920.026-0.01970.0705-0.030.0651120.50927.803238.1
30.12420.15160.23520.56150.06340.67110.03210.0111-0.0462-0.08680.0096-0.05550.0843-0.0019-0.04160.08330.0272-0.02050.0447-0.01380.0971135.493-20.591277.887
40.16390.19510.06570.45490.02560.37120.0473-0.0553-0.01680.0047-0.0617-0.0108-0.0041-0.00780.01430.0442-0.0101-0.00050.10370.00630.0676142.818-0.855315.658
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A22 - 540
2X-RAY DIFFRACTION2B21 - 540
3X-RAY DIFFRACTION3C21 - 539
4X-RAY DIFFRACTION4D20 - 540

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