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- PDB-6yp6: Structural annotation of the conserved carbohydrate esterase vb_2... -

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Basic information

Entry
Database: PDB / ID: 6yp6
TitleStructural annotation of the conserved carbohydrate esterase vb_24B_21 from Shiga toxin-encoding bacteriophage phi24B
ComponentsNanS-p
KeywordsSUGAR BINDING PROTEIN / Carbohydrate binding protein
Function / homology
Function and homology information


Domain of unknown function DUF1737 / Domain of unknown function DUF6645 / Domain of unknown function (DUF1737) / Family of unknown function (DUF6645) / : / Sialate O-acetylesterase domain / Carbohydrate esterase, sialic acid-specific acetylesterase / SGNH hydrolase superfamily
Similarity search - Domain/homology
DUF1737 domain-containing protein
Similarity search - Component
Biological speciesEscherichia phage vB_EcoP_24B (virus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 0.97 Å
AuthorsMayans, O. / Franke, B.
CitationJournal: J.Struct.Biol. / Year: 2020
Title: Structural annotation of the conserved carbohydrate esterase vb_24B_21 from Shiga toxin-encoding bacteriophage Phi 24 B .
Authors: Franke, B. / Veses-Garcia, M. / Diederichs, K. / Allison, H. / Rigden, D.J. / Mayans, O.
History
DepositionApr 15, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 16, 2020Provider: repository / Type: Initial release
Revision 1.1Oct 7, 2020Group: Database references / Category: citation / Item: _citation.journal_volume / _citation.title
Revision 1.2May 15, 2024Group: Advisory / Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_unobs_or_zero_occ_atoms
Item: _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: NanS-p
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,9942
Polymers22,9021
Non-polymers921
Water7,764431
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area210 Å2
ΔGint-0 kcal/mol
Surface area9670 Å2
Unit cell
Length a, b, c (Å)54.522, 54.824, 72.770
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Space group name HallP2ac2ab
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x,y+1/2,-z+1/2
#4: -x+1/2,-y,z+1/2

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Components

#1: Protein NanS-p / 933Wp42 / vb_24B_21


Mass: 22901.604 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia phage vB_EcoP_24B (virus) / Gene: vb_24B_21 / Production host: Escherichia coli (E. coli) / References: UniProt: G3CFL3
#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.: 431 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 2.37 Å3/Da / Density % sol: 48.2 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: 0.9 M LiSO4, 10% [v/v] glycerol, 0.1 M Hepes pH 7.0

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.7514 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Apr 10, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.7514 Å / Relative weight: 1
ReflectionResolution: 0.97→25 Å / Num. obs: 128671 / % possible obs: 99.5 % / Redundancy: 7.1 % / CC1/2: 0.99 / Rsym value: 0.079 / Net I/σ(I): 14.64
Reflection shellResolution: 0.97→0.98 Å / Mean I/σ(I) obs: 1 / Num. unique obs: 3878 / CC1/2: 0.4 / Rsym value: 1.55

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Processing

Software
NameVersionClassification
XDSVERSION Mar 15, 2019data processing
PHENIX1.17.1_3660refinement
XDSVERSION Mar 15, 2019data reduction
XDSVERSION Mar 15, 2019data scaling
SHELXDEphasing
RefinementMethod to determine structure: SAD / Resolution: 0.97→24.49 Å / SU ML: 0.0824 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 15.737
RfactorNum. reflection% reflection
Rfree0.1719 6441 5.01 %
Rwork0.1501 --
obs0.1512 128655 99.5 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 15.71 Å2
Refinement stepCycle: LAST / Resolution: 0.97→24.49 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1615 0 6 431 2052
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00661703
X-RAY DIFFRACTIONf_angle_d0.98342323
X-RAY DIFFRACTIONf_chiral_restr0.0833264
X-RAY DIFFRACTIONf_plane_restr0.0055303
X-RAY DIFFRACTIONf_dihedral_angle_d14.0221593
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
0.97-0.980.28782510.30273997X-RAY DIFFRACTION99.46
0.98-0.990.28982120.2754041X-RAY DIFFRACTION99.91
0.99-10.24472160.24974042X-RAY DIFFRACTION99.95
1-1.020.24152380.22964039X-RAY DIFFRACTION99.91
1.02-1.030.2292180.20774040X-RAY DIFFRACTION99.95
1.03-1.040.23191930.19884072X-RAY DIFFRACTION99.98
1.04-1.060.20772180.19094038X-RAY DIFFRACTION99.95
1.06-1.080.32112090.30554004X-RAY DIFFRACTION98.87
1.08-1.090.29452260.23874016X-RAY DIFFRACTION98.77
1.09-1.110.16532350.15334038X-RAY DIFFRACTION99.91
1.11-1.130.21312190.17944017X-RAY DIFFRACTION99.93
1.13-1.150.14522370.14234036X-RAY DIFFRACTION99.84
1.15-1.170.14862060.12564082X-RAY DIFFRACTION99.98
1.17-1.20.14872030.12684108X-RAY DIFFRACTION100
1.2-1.220.17862190.15964009X-RAY DIFFRACTION99.37
1.22-1.250.19182150.17434083X-RAY DIFFRACTION99.49
1.25-1.280.13591820.12784077X-RAY DIFFRACTION99.93
1.28-1.320.20932400.18734010X-RAY DIFFRACTION98.7
1.32-1.360.16071950.12674092X-RAY DIFFRACTION99.93
1.36-1.40.14422060.11824117X-RAY DIFFRACTION100
1.4-1.450.14372120.12714078X-RAY DIFFRACTION99.88
1.45-1.510.14922000.13374080X-RAY DIFFRACTION99.72
1.51-1.580.13851780.11364143X-RAY DIFFRACTION99.93
1.58-1.660.14532210.11614128X-RAY DIFFRACTION99.98
1.66-1.760.15142310.12454100X-RAY DIFFRACTION100
1.76-1.90.15762010.12964154X-RAY DIFFRACTION99.93
1.9-2.090.16192130.14884101X-RAY DIFFRACTION99.01
2.09-2.390.15271870.14844130X-RAY DIFFRACTION98.56
2.39-3.010.15812500.13754176X-RAY DIFFRACTION99.98
3.01-24.490.18292100.15194166X-RAY DIFFRACTION94.72

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