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- PDB-3pt5: Crystal structure of NanS -

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Basic information

Entry
Database: PDB / ID: 3pt5
TitleCrystal structure of NanS
ComponentsNANS (YJHS), A 9-O-acetyl N-acetylneuraminic acid esterase
KeywordsHYDROLASE / SGNH hydrolase / 9-O-acetyl N-acetylneuraminic acid esterase / Structural genomics / Montreal-Kingston Bacterial Structural Genomics Initiative / BSGI
Function / homology: / Sialate O-acetylesterase domain / Carbohydrate esterase, sialic acid-specific acetylesterase / SGNH hydrolase superfamily / hydrolase activity, acting on ester bonds / hydrolase activity / Sialate O-acetylesterase domain-containing protein / Sialate O-acetylesterase
Function and homology information
Biological speciesEscherichia coli O157:H7 EDL933 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.6 Å
AuthorsRuane, K.M. / Rangarajan, E.S. / Proteau, A. / Schrag, J.D. / Cygler, M. / Montreal-Kingston Bacterial Structural Genomics Initiative (BSGI)
CitationJournal: Protein Sci. / Year: 2011
Title: Structural and enzymatic characterization of NanS (YjhS), a 9-O-Acetyl N-acetylneuraminic acid esterase from Escherichia coli O157:H7.
Authors: Rangarajan, E.S. / Ruane, K.M. / Proteau, A. / Schrag, J.D. / Valladares, R. / Gonzalez, C.F. / Gilbert, M. / Yakunin, A.F. / Cygler, M.
History
DepositionDec 2, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 18, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 8, 2017Group: Refinement description / Category: software
Revision 1.3Feb 21, 2024Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: NANS (YJHS), A 9-O-acetyl N-acetylneuraminic acid esterase


Theoretical massNumber of molelcules
Total (without water)38,1271
Polymers38,1271
Non-polymers00
Water4,594255
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)41.080, 57.919, 135.392
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein NANS (YJHS), A 9-O-acetyl N-acetylneuraminic acid esterase


Mass: 38127.176 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli O157:H7 EDL933 (bacteria)
Strain: O157:H7 EDL933 / Gene: ECs5268, YjhS / Plasmid: pET / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q7A8N3, UniProt: A0A0H3JKI3*PLUS
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 255 / 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: 2.11 Å3/Da / Density % sol: 41.77 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop / pH: 5.5
Details: 0.2 M NaCl, 0.1 M Bis-Tris pH 5.5, 30% (w/v) PEG 3350, vapor diffusion, sitting drop, temperature 295K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: CLSI / Beamline: 08ID-1 / Wavelength: 0.97923 Å
DetectorType: Mar225 / Detector: CCD / Date: May 15, 2010
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97923 Å / Relative weight: 1
ReflectionResolution: 1.6→50 Å / Num. obs: 40446 / % possible obs: 92.8 % / Redundancy: 7.2 % / Rmerge(I) obs: 0.075 / Net I/σ(I): 13.8
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsDiffraction-ID% possible all
1.6-1.667.30.4231100
1.66-1.727.30.3181100
1.72-1.87.30.2351100
1.8-1.97.20.189192.6
1.9-2.0270.152175.9
2.02-2.177.30.1121100
2.17-2.3970.087166.2
2.39-2.747.30.0741100
2.74-3.457.30.0611100
3.45-506.70.042193.1

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
REFMAC5.4.0065refinement
PDB_EXTRACT3.1data extraction
HKL-2000data collection
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.6→33.84 Å / Cor.coef. Fo:Fc: 0.949 / Cor.coef. Fo:Fc free: 0.928 / Occupancy max: 1 / Occupancy min: 0.5 / SU B: 2.098 / SU ML: 0.074 / Cross valid method: THROUGHOUT / ESU R: 0.109 / ESU R Free: 0.11 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.24272 2045 5.1 %RANDOM
Rwork0.2013 ---
obs0.20335 38168 92.3 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 16.489 Å2
Baniso -1Baniso -2Baniso -3
1--0.74 Å20 Å20 Å2
2--0.63 Å20 Å2
3---0.11 Å2
Refinement stepCycle: LAST / Resolution: 1.6→33.84 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2556 0 0 255 2811
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0212646
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.4341.9163608
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.9795320
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.64723.333141
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.21615381
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.2321519
X-RAY DIFFRACTIONr_chiral_restr0.1010.2366
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.0212136
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.8011.51602
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.40822575
X-RAY DIFFRACTIONr_scbond_it2.16131044
X-RAY DIFFRACTIONr_scangle_it3.2544.51033
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.6→1.642 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.262 146 -
Rwork0.223 2993 -
obs--98.28 %

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