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- PDB-9nhf: The structure of a family 168 glycoside hydrolase from the marine... -

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Basic information

Entry
Database: PDB / ID: 9nhf
TitleThe structure of a family 168 glycoside hydrolase from the marine bacterium Muricauda eckloniae.
ComponentsGlycosyl hydrolase-like family 15 (GHL15) protein
KeywordsHYDROLASE / Glycoside Hydrolase / GH168 / fucoidan / Muricauda / fucoidanase
Function / homologyHypothetical glycosyl hydrolase family 15 / Hypothetical glycosyl hydrolase family 15 / Glycoside hydrolase superfamily / Glycosyl hydrolase-like family 15 (GHL15) protein
Function and homology information
Biological speciesFlagellimonas eckloniae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsKnudson-Goerner, E.J. / Boraston, A.B.
Funding support Canada, 1items
OrganizationGrant numberCountry
Natural Sciences and Engineering Research Council (NSERC, Canada) Canada
CitationJournal: Acta Crystallogr.,Sect.F / Year: 2025
Title: The structure of a family 168 glycoside hydrolase from the marine bacterium Muricauda eckloniae.
Authors: Knudson-Goerner, E. / Boraston, A.B.
History
DepositionFeb 24, 2025Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 11, 2025Provider: repository / Type: Initial release
Revision 1.1Jul 9, 2025Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Glycosyl hydrolase-like family 15 (GHL15) protein
B: Glycosyl hydrolase-like family 15 (GHL15) protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)88,4503
Polymers88,3882
Non-polymers621
Water15,169842
1
A: Glycosyl hydrolase-like family 15 (GHL15) protein


Theoretical massNumber of molelcules
Total (without water)44,1941
Polymers44,1941
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Glycosyl hydrolase-like family 15 (GHL15) protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)44,2562
Polymers44,1941
Non-polymers621
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)47.274, 120.934, 163.845
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP22121
Space group name HallP22ab(z,x,y)
Symmetry operation#1: x,y,z
#2: x,-y,-z
#3: -x,y+1/2,-z+1/2
#4: -x,-y+1/2,z+1/2

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Components

#1: Protein Glycosyl hydrolase-like family 15 (GHL15) protein


Mass: 44194.117 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Flagellimonas eckloniae (bacteria) / Strain: DOKDO 007T / Gene: AAY42_01205 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0A0Q0XIY0
#2: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 842 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN
Has protein modificationN

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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: 2.65 Å3/Da / Density % sol: 53.67 % / Description: rod
Crystal growTemperature: 291.15 K / Method: vapor diffusion, sitting drop / pH: 7 / Details: 20% w/v PEG 3350, 8% v/v Tacsimate pH 7.0

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: CLSI / Beamline: 08ID-1 / Wavelength: 0.954 Å
DetectorType: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Aug 15, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.954 Å / Relative weight: 1
ReflectionResolution: 2→97.31 Å / Num. obs: 64544 / % possible obs: 100 % / Redundancy: 7.6 % / Biso Wilson estimate: 23.59 Å2 / CC1/2: 0.997 / Rmerge(I) obs: 0.132 / Rpim(I) all: 0.051 / Rrim(I) all: 0.142 / Net I/σ(I): 12.8
Reflection shellResolution: 2→2.05 Å / Redundancy: 8 % / Rmerge(I) obs: 0.978 / Mean I/σ(I) obs: 2.4 / Num. unique obs: 4512 / CC1/2: 0.764 / Rpim(I) all: 0.364 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMACrefinement
PHENIX1.19.2_4158refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2→48.65 Å / SU ML: 0.2234 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 23.7983
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2327 3186 4.94 %
Rwork0.1989 61332 -
obs0.2006 64518 99.97 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 27.73 Å2
Refinement stepCycle: LAST / Resolution: 2→48.65 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5904 0 4 842 6750
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00186081
X-RAY DIFFRACTIONf_angle_d0.46288218
X-RAY DIFFRACTIONf_chiral_restr0.0408822
X-RAY DIFFRACTIONf_plane_restr0.00291050
X-RAY DIFFRACTIONf_dihedral_angle_d4.8346771
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2-2.030.32641230.26612634X-RAY DIFFRACTION99.96
2.03-2.060.26871290.25172652X-RAY DIFFRACTION99.96
2.06-2.10.28221580.24582572X-RAY DIFFRACTION100
2.1-2.130.28861300.25062659X-RAY DIFFRACTION100
2.13-2.170.27161410.24782609X-RAY DIFFRACTION100
2.17-2.210.28391530.26292605X-RAY DIFFRACTION99.96
2.21-2.260.29261180.24052677X-RAY DIFFRACTION99.96
2.26-2.310.28471460.23912597X-RAY DIFFRACTION99.96
2.31-2.360.27711410.22582679X-RAY DIFFRACTION100
2.36-2.420.27181370.23722596X-RAY DIFFRACTION100
2.42-2.480.26221460.22062678X-RAY DIFFRACTION100
2.48-2.560.30611290.22562635X-RAY DIFFRACTION99.96
2.56-2.640.27561440.22282656X-RAY DIFFRACTION99.96
2.64-2.730.23541370.22172626X-RAY DIFFRACTION100
2.73-2.840.23081280.20572678X-RAY DIFFRACTION100
2.84-2.970.24591320.20292667X-RAY DIFFRACTION99.96
2.97-3.130.25061380.19922673X-RAY DIFFRACTION100
3.13-3.330.23211570.19072663X-RAY DIFFRACTION100
3.33-3.580.20061430.17442680X-RAY DIFFRACTION100
3.58-3.940.16811300.14912741X-RAY DIFFRACTION99.97
3.94-4.510.1671730.14842657X-RAY DIFFRACTION100
4.51-5.680.18181250.16062779X-RAY DIFFRACTION99.9
5.68-48.650.2251280.19592919X-RAY DIFFRACTION99.8

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