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- PDB-3h72: Crystal structure of Streptococcus pneumoniae D39 neuraminidase A... -

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Basic information

Entry
Database: PDB / ID: 3h72
TitleCrystal structure of Streptococcus pneumoniae D39 neuraminidase A precursor (NanA) in complex with NANA
ComponentsSialidase A
KeywordsHYDROLASE / six-bladed beta-propeller / Cell wall / Glycosidase / Peptidoglycan-anchor / Secreted
Function / homology
Function and homology information


ganglioside catabolic process / oligosaccharide catabolic process / exo-alpha-sialidase activity / exo-alpha-(2->3)-sialidase activity / exo-alpha-(2->6)-sialidase activity / exo-alpha-(2->8)-sialidase activity / exo-alpha-sialidase / intracellular membrane-bounded organelle / extracellular region / membrane / cytoplasm
Similarity search - Function
BNR/Asp-box repeat / Intramolecular trans-sialidase; domain 3 / Intramolecular Trans-sialidase; Domain 3 / Trans-sialidase, domain 3 / Glycoside hydrolase, family 33, N-terminal / Sialidase, N-terminal domain / BNR repeat-like domain / Laminin G domain / Laminin G domain / Sialidase family ...BNR/Asp-box repeat / Intramolecular trans-sialidase; domain 3 / Intramolecular Trans-sialidase; Domain 3 / Trans-sialidase, domain 3 / Glycoside hydrolase, family 33, N-terminal / Sialidase, N-terminal domain / BNR repeat-like domain / Laminin G domain / Laminin G domain / Sialidase family / Sialidase / YSIRK type signal peptide / YSIRK Gram-positive signal peptide / Neuraminidase - #10 / Gram-positive cocci surface proteins LPxTG motif profile. / LPXTG cell wall anchor domain / Sialidase superfamily / 6 Propeller / Neuraminidase / Concanavalin A-like lectin/glucanase domain superfamily / Beta Barrel / Mainly Beta
Similarity search - Domain/homology
N-acetyl-alpha-neuraminic acid / Sialidase A
Similarity search - Component
Biological speciesStreptococcus pneumoniae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.7 Å
AuthorsHsiao, Y.-S. / Tong, L.
CitationJournal: Biochem.Biophys.Res.Commun. / Year: 2009
Title: Crystal structures of respiratory pathogen neuraminidases
Authors: Hsiao, Y.-S. / Parker, D. / Ratner, A.J. / Prince, A. / Tong, L.
History
DepositionApr 24, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 12, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 1, 2017Group: Refinement description / Category: software / Item: _software.classification / _software.name
Revision 1.3Jul 29, 2020Group: Data collection / Derived calculations / Structure summary
Category: chem_comp / entity ...chem_comp / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / struct_site / struct_site_gen
Item: _chem_comp.name / _chem_comp.type ..._chem_comp.name / _chem_comp.type / _entity.pdbx_description / _pdbx_entity_nonpoly.name
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.4Feb 21, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Sialidase A
B: Sialidase A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)107,7624
Polymers107,1442
Non-polymers6192
Water26,0501446
1
A: Sialidase A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)53,8812
Polymers53,5721
Non-polymers3091
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Sialidase A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)53,8812
Polymers53,5721
Non-polymers3091
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)158.630, 47.370, 137.060
Angle α, β, γ (deg.)90.00, 116.41, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein Sialidase A / Neuraminidase A


Mass: 53571.906 Da / Num. of mol.: 2 / Fragment: UNP residues 317-793
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptococcus pneumoniae (bacteria) / Strain: R6 / Gene: nanA, spr1536 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)Star / References: UniProt: P62576, exo-alpha-sialidase
#2: Sugar ChemComp-SIA / N-acetyl-alpha-neuraminic acid / N-acetylneuraminic acid / sialic acid / alpha-sialic acid / O-SIALIC ACID / Sialic acid


Type: D-saccharide, alpha linking / Mass: 309.270 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Formula: C11H19NO9
IdentifierTypeProgram
DNeup5AcaCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
N-acetyl-a-D-neuraminic acidCOMMON NAMEGMML 1.0
a-D-Neup5AcIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
Neu5AcSNFG CARBOHYDRATE SYMBOLGMML 1.0
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 1446 / 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: 2.15 Å3/Da / Density % sol: 42.85 %
Crystal growTemperature: 294 K / Method: vapor diffusion, sitting drop / pH: 7
Details: 100 mM Hepes, 30% Jeffamine ED-2001, pH 7.0, VAPOR DIFFUSION, SITTING DROP, temperature 294K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X4C / Wavelength: 0.9798 / Wavelength: 0.981 Å
DetectorType: MAR CCD 165 mm / Detector: CCD / Date: Apr 18, 2008 / Details: MIRRORS
RadiationMonochromator: SI(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.97981
20.9811
ReflectionResolution: 1.7→30 Å / Num. obs: 86773 / % possible obs: 89.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 2.8 % / Biso Wilson estimate: 12.4 Å2 / Rmerge(I) obs: 0.06 / Net I/σ(I): 13.0437
Reflection shellResolution: 1.7→1.76 Å / Redundancy: 2.5 % / Rmerge(I) obs: 0.142 / Mean I/σ(I) obs: 6.862 / Num. unique all: 8124 / % possible all: 82.9

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Processing

Software
NameVersionClassification
ADSCQuantumdata collection
SnBTHEN SOLVE/RESOLVEphasing
CNS1.2refinement
DENZOdata reduction
SCALEPACKdata scaling
COMOphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.7→28.34 Å / Rfactor Rfree error: 0.003 / Data cutoff high absF: 662438.23 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber / Details: BULK SOLVENT MODEL USED
RfactorNum. reflection% reflectionSelection details
Rfree0.209 6556 7.6 %RANDOM
Rwork0.175 ---
all0.175 ---
obs0.175 86772 87.2 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 68.6741 Å2 / ksol: 0.4 e/Å3
Displacement parametersBiso mean: 17.7 Å2
Baniso -1Baniso -2Baniso -3
1--2.45 Å20 Å20.82 Å2
2--0.5 Å20 Å2
3---1.96 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.2 Å0.17 Å
Luzzati d res low-5 Å
Luzzati sigma a0.15 Å0.09 Å
Refinement stepCycle: LAST / Resolution: 1.7→28.34 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7518 0 42 1446 9006
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.005
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.4
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d25.9
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.8
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it1.161.5
X-RAY DIFFRACTIONc_mcangle_it1.762
X-RAY DIFFRACTIONc_scbond_it1.912
X-RAY DIFFRACTIONc_scangle_it2.822.5
LS refinement shellResolution: 1.7→1.81 Å / Rfactor Rfree error: 0.008 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.248 889 7.6 %
Rwork0.208 10793 -
obs-10793 69.9 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2dna-rna_rep.paramdna-rna.top
X-RAY DIFFRACTION3water_rep.paramwater.top
X-RAY DIFFRACTION4ion.paramion.top
X-RAY DIFFRACTION5sib.parsib.top

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