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- PDB-4m4u: Structural evaluation D84A mutant of the aspergillus fumigatus kd... -

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Basic information

Entry
Database: PDB / ID: 4m4u
TitleStructural evaluation D84A mutant of the aspergillus fumigatus kdnase (sialidase)
ComponentsExtracellular sialidase/neuraminidase, putative
KeywordsHYDROLASE / KDNase
Function / homology
Function and homology information


ganglioside catabolic process / oligosaccharide catabolic process / exo-alpha-sialidase / exo-alpha-sialidase activity / intracellular membrane-bounded organelle / membrane / cytoplasm
Similarity search - Function
BNR repeat-like domain / Sialidase family / Sialidase / Neuraminidase - #10 / Sialidase superfamily / 6 Propeller / Neuraminidase / Mainly Beta
Similarity search - Domain/homology
NITRITE ION / NITRATE ION / PHOSPHATE ION / Exo-alpha-sialidase
Similarity search - Component
Biological speciesAspergillus fumigatus (mold)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.84 Å
AuthorsTelford, J.C. / Taylor, G.L.
CitationJournal: To be Published
Title: Active site mutants of a fungal KDNase
Authors: Yeung, J.Y. / Telford, J.C. / Shidmoossavee, F.S. / Bennet, A.J. / Taylor, G.L. / Moore, M.M.
History
DepositionAug 7, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 17, 2014Provider: repository / Type: Initial release
Revision 1.1Sep 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / 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 / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _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: Extracellular sialidase/neuraminidase, putative
B: Extracellular sialidase/neuraminidase, putative
hetero molecules


Theoretical massNumber of molelcules
Total (without water)93,52816
Polymers92,4652
Non-polymers1,06314
Water20,9331162
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A: Extracellular sialidase/neuraminidase, putative
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,7548
Polymers46,2331
Non-polymers5227
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Extracellular sialidase/neuraminidase, putative
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,7748
Polymers46,2331
Non-polymers5417
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)75.940, 57.870, 94.610
Angle α, β, γ (deg.)90.000, 99.910, 90.000
Int Tables number4
Space group name H-MP1211

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein Extracellular sialidase/neuraminidase, putative


Mass: 46232.586 Da / Num. of mol.: 2 / Mutation: D84A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Aspergillus fumigatus (mold) / Strain: ATCC MYA-4609 / Af293 / CBS 101355 / FGSC A1100 / Gene: AFUA_4G13800 / Production host: Escherichia coli (E. coli) / References: UniProt: Q4WQS0, exo-alpha-sialidase

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Non-polymers , 7 types, 1176 molecules

#2: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#3: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: C3H8O3
#4: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: PO4
#5: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#6: Chemical ChemComp-NO3 / NITRATE ION


Mass: 62.005 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: NO3
#7: Chemical ChemComp-NO2 / NITRITE ION


Mass: 46.005 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: NO2
#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1162 / 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: 2.21 Å3/Da / Density % sol: 44.46 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7
Details: 20% (w/v) PEG 3350, 0.2M Sodium nitrate, pH 7, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 / Wavelength: 1.54 Å
DetectorType: RIGAKU SATURN 944+ / Detector: CCD / Date: Aug 4, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 1.84→12.393 Å / Num. all: 69554 / Num. obs: 69554 / % possible obs: 98.9 % / Observed criterion σ(I): 2 / Redundancy: 3.9 % / Rsym value: 0.055 / Net I/σ(I): 18.2
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allRsym value% possible all
1.84-1.943.40.1425.43314196540.14294.4
1.94-2.063.90.1126.73778396630.112100
2.06-2.240.0898.43598390720.089100
2.2-2.3840.0759.83394284780.075100
2.38-2.640.06123137578130.06100
2.6-2.914.10.05113.72903571020.051100
2.91-3.364.10.04216.12534162360.042100
3.36-4.124.10.03617.42173453250.036100
4.12-5.824.10.03218.61692341360.032100
5.82-12.39340.03515.9837620750.03589.8

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Processing

Software
NameVersionClassificationNB
MOSFLMdata reduction
SCALA3.3.16data scaling
REFMAC5.5.0109refinement
PDB_EXTRACT3.11data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: pdb entry 2XCY

2xcy


Resolution: 1.84→12.39 Å / Cor.coef. Fo:Fc: 0.96 / Cor.coef. Fo:Fc free: 0.941 / Occupancy max: 1 / Occupancy min: 0.3 / SU B: 2.024 / SU ML: 0.063 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.118 / ESU R Free: 0.111 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.1789 3499 5 %RANDOM
Rwork0.1428 ---
obs0.1446 69499 99.11 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso max: 70.77 Å2 / Biso mean: 9.9534 Å2 / Biso min: 2 Å2
Baniso -1Baniso -2Baniso -3
1-0.21 Å20 Å2-0.14 Å2
2---0.02 Å20 Å2
3----0.23 Å2
Refinement stepCycle: LAST / Resolution: 1.84→12.39 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5904 0 65 1162 7131
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0216190
X-RAY DIFFRACTIONr_angle_refined_deg1.1441.9488410
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.3515796
X-RAY DIFFRACTIONr_dihedral_angle_2_deg29.03722.897290
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.55415959
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.1081561
X-RAY DIFFRACTIONr_chiral_restr0.0770.2875
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0214857
X-RAY DIFFRACTIONr_mcbond_it0.4281.53845
X-RAY DIFFRACTIONr_mcangle_it0.78826156
X-RAY DIFFRACTIONr_scbond_it1.36232345
X-RAY DIFFRACTIONr_scangle_it2.2154.52239
LS refinement shellResolution: 1.841→1.888 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.211 245 -
Rwork0.175 4256 -
all-4501 -
obs--89.02 %

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