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- PDB-8bpd: Structural and Functional Characterization of the Novel Endo-alph... -

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Basic information

Entry
Database: PDB / ID: 8bpd
TitleStructural and Functional Characterization of the Novel Endo-alpha(1,4)-Fucoidanase Mef1 from the Marine Bacterium Muricauda eckloniae
ComponentsGlycosyl hydrolase
KeywordsHYDROLASE / Fucoidanase / Fucoidan / GH107 / glycosyl hydrolase / Fucanase / calcium binding / polysaccharide / sulfated.
Function / homologymetal ion binding / Chem-3CX / Uncharacterized protein
Function and homology information
Biological speciesMuricauda eckloniae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsMikkelsen, M.D. / Meyer, A.S. / Morth, J.P.
Funding support Denmark, 1items
OrganizationGrant numberCountry
Techical University of Denmark (DTU)9082-00021B Denmark
CitationJournal: Acta Crystallogr D Struct Biol / Year: 2023
Title: Structural and functional characterization of the novel endo-alpha (1,4)-fucoidanase Mef1 from the marine bacterium Muricauda eckloniae.
Authors: Mikkelsen, M.D. / Tran, V.H.N. / Meier, S. / Nguyen, T.T. / Holck, J. / Cao, H.T.T. / Van, T.T.T. / Thinh, P.D. / Meyer, A.S. / Morth, J.P.
History
DepositionNov 16, 2022Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 8, 2023Provider: repository / Type: Initial release
Revision 1.1Nov 15, 2023Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Glycosyl hydrolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,0058
Polymers45,0891
Non-polymers9167
Water6,395355
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area610 Å2
ΔGint-16 kcal/mol
Surface area15450 Å2
Unit cell
Length a, b, c (Å)105.416, 105.416, 78.247
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number173
Space group name H-MP63
Space group name HallP6c
Symmetry operation#1: x,y,z
#2: x-y,x,z+1/2
#3: y,-x+y,z+1/2
#4: -y,x-y,z
#5: -x+y,-x,z
#6: -x,-y,z+1/2

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Components

#1: Protein Glycosyl hydrolase


Mass: 45088.668 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Muricauda eckloniae (bacteria) / Gene: AAY42_01290 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A0N8WFH1, EC: 3.2.1.212
#2: Chemical ChemComp-3CX / (2S)-3-(cyclohexylamino)-2-hydroxypropane-1-sulfonic acid


Mass: 237.316 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C9H19NO4S / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6O2
#4: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ca
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 355 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 2.78 Å3/Da / Density % sol: 55.81 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 9
Details: 24 % PEG 3350, 0.1 M CAPSO pH 9, 3 % isopropanol, 4 % PEG 400

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: MAX IV / Beamline: BioMAX / Wavelength: 0.9786 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Oct 24, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9786 Å / Relative weight: 1
ReflectionResolution: 1.8→43.72 Å / Num. obs: 45842 / % possible obs: 99.87 % / Redundancy: 6.8 % / Biso Wilson estimate: 25.27 Å2 / CC1/2: 0.996 / CC star: 0.999 / Rmerge(I) obs: 0.1267 / Rpim(I) all: 0.05163 / Rrim(I) all: 0.1369 / Net I/σ(I): 6.8
Reflection shellResolution: 1.8→1.864 Å / Rmerge(I) obs: 1 / Mean I/σ(I) obs: 0.48 / Num. unique obs: 4540 / CC1/2: 0.833 / CC star: 0.953 / Rpim(I) all: 0.4176 / Rrim(I) all: 1 / % possible all: 99.6

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Processing

Software
NameVersionClassification
PHENIX1.19.2_4158refinement
xia2data reduction
DIALSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6M8N

6m8n


Resolution: 1.8→43.72 Å / SU ML: 0.2742 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 22.7185
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2016 2259 4.93 %
Rwork0.1648 43536 -
obs0.1667 45795 99.88 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 29.58 Å2
Refinement stepCycle: LAST / Resolution: 1.8→43.72 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2954 0 55 355 3364
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01033115
X-RAY DIFFRACTIONf_angle_d1.07174224
X-RAY DIFFRACTIONf_chiral_restr0.0582434
X-RAY DIFFRACTIONf_plane_restr0.0087544
X-RAY DIFFRACTIONf_dihedral_angle_d15.64361145
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.8-1.840.37271370.37272686X-RAY DIFFRACTION99.44
1.84-1.880.39731360.33892721X-RAY DIFFRACTION99.93
1.88-1.930.29451270.27742711X-RAY DIFFRACTION99.86
1.93-1.980.25231410.23392702X-RAY DIFFRACTION99.96
1.98-2.040.26281450.21282709X-RAY DIFFRACTION99.93
2.04-2.110.26241260.19152727X-RAY DIFFRACTION99.86
2.11-2.180.20551340.19422730X-RAY DIFFRACTION99.97
2.18-2.270.20721630.17272693X-RAY DIFFRACTION99.93
2.27-2.370.22611370.15932703X-RAY DIFFRACTION99.86
2.37-2.50.20141270.15342734X-RAY DIFFRACTION99.9
2.5-2.650.22211340.15992722X-RAY DIFFRACTION99.96
2.65-2.860.19821350.15952761X-RAY DIFFRACTION99.97
2.86-3.140.19911410.15532714X-RAY DIFFRACTION99.96
3.15-3.60.20951540.13882706X-RAY DIFFRACTION100
3.6-4.530.13331500.12052754X-RAY DIFFRACTION100
4.54-43.720.16771720.14242763X-RAY DIFFRACTION99.73
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.524343321347-0.273631243489-0.01972206678261.94826388292-0.5680792864631.17493452531-0.02083047703560.0175779306433-0.0147212649778-0.01107275641810.03742950929630.1327764900990.00270374015021-0.198142709652-5.36144798015E-50.210926413743-0.0106451995732-0.01418812612460.220940152388-0.006506394925380.25066931996636.9766916755-11.9674891997-2.79959745117
20.187965889506-0.130849532201-0.002366987469910.0991410003544-0.02180572280930.1387500216070.0655554752493-0.10015607061-0.1020202573780.1072652487-0.138829459557-0.07789286218230.2293908115390.1078416489420.0001154096384210.4143079079310.0410191075448-0.02871664193780.3136094703620.02505794191450.35032996466966.313132502-5.85213943784-18.1975984906
30.98770203011-0.2370827440280.0245192132181.2731496718-0.2343456270171.22489849527-0.0525559080316-0.02649329022140.05547321479560.05701359922860.0270244895438-0.0500069566736-0.04461018012810.09329067095432.88311446098E-50.2933071205410.0113572188673-0.01162001495920.1994705913660.01074154421290.23008400239151.79860175183.79254347382-13.4688508705
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION / Auth asym-ID: A / Label asym-ID: A

IDRefine TLS-IDSelection detailsAuth seq-IDLabel seq-ID
11chain 'A' and (resid 27 through 224 )27 - 2243 - 200
22chain 'A' and (resid 225 through 244 )225 - 244201 - 220
33chain 'A' and (resid 245 through 394 )245 - 394221 - 370

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