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- PDB-6dms: Endo-fucoidan hydrolase MfFcnA4_H294Q from glycoside hydrolase fa... -

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Basic information

Entry
Database: PDB / ID: 6dms
TitleEndo-fucoidan hydrolase MfFcnA4_H294Q from glycoside hydrolase family 107
ComponentsAlpha-1,4-endofucoidanase
KeywordsHYDROLASE / fucan / fucoidan / glycoside hydrolase / retaining mechanism
Function / homologyPutative Ig domain / Secretion system C-terminal sorting domain / Secretion system C-terminal sorting domain / Cadherin-like superfamily / calcium ion binding / Immunoglobulin-like fold / membrane / Alpha-1,4-endofucoidanase
Function and homology information
Biological speciesMariniflexile fucanivorans (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.85 Å
AuthorsVickers, C. / Abe, K. / Salama-Alber, O. / Boraston, A.B.
CitationJournal: J. Biol. Chem. / Year: 2018
Title: Endo-fucoidan hydrolases from glycoside hydrolase family 107 (GH107) display structural and mechanistic similarities to alpha-l-fucosidases from GH29.
Authors: Vickers, C. / Liu, F. / Abe, K. / Salama-Alber, O. / Jenkins, M. / Springate, C.M.K. / Burke, J.E. / Withers, S.G. / Boraston, A.B.
History
DepositionJun 5, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 3, 2018Provider: repository / Type: Initial release
Revision 1.1Nov 28, 2018Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Dec 5, 2018Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title / _citation_author.name
Revision 1.3Jan 22, 2020Group: Author supporting evidence / Category: pdbx_audit_support
Revision 1.4Mar 13, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / refine
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _refine.pdbx_starting_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Alpha-1,4-endofucoidanase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)81,2784
Polymers81,1351
Non-polymers1423
Water1,06359
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)156.527, 156.527, 84.409
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number152
Space group name H-MP3121

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Components

#1: Protein Alpha-1,4-endofucoidanase


Mass: 81135.328 Da / Num. of mol.: 1 / Mutation: H294Q
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mariniflexile fucanivorans (bacteria) / Gene: fcnA / Production host: Escherichia coli (E. coli) / References: UniProt: Q08I46
#2: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ca
#3: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


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


Mass: 18.015 Da / Num. of mol.: 59 / 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: 3.85 Å3/Da / Density % sol: 68.05 %
Crystal growTemperature: 291.15 K / Method: vapor diffusion, hanging drop
Details: 0.1 M NaCl, 1.4 M (NH4)2SO4, sodium acetate:acetic acid, (pH 4.5)

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.54178 Å
DetectorType: DECTRIS PILATUS3 R 200K-A / Detector: PIXEL / Date: Jan 11, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54178 Å / Relative weight: 1
ReflectionResolution: 2.85→29.581 Å / Num. obs: 27694 / % possible obs: 98.5 % / Redundancy: 6.3 % / Rmerge(I) obs: 0.089 / Rpim(I) all: 0.038 / Rrim(I) all: 0.097 / Χ2: 0.851 / Net I/σ(I): 8.4
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
2.85-2.96.40.71213000.9460.3040.7750.71493.5
2.9-2.956.50.48513150.960.2050.5270.73495.3
2.95-3.016.40.36913360.970.1570.4010.75295.5
3.01-3.076.40.3413760.980.1440.370.71298.2
3.07-3.146.50.25713290.9810.1090.280.71196.3
3.14-3.216.50.19613710.9880.0830.2130.688100
3.21-3.296.50.15313830.9890.0650.1660.71498.5
3.29-3.386.50.12713840.9910.0540.1380.75398.9
3.38-3.486.40.10613890.9920.0450.1160.782100
3.48-3.596.50.08913800.9930.0380.0960.899
3.59-3.726.40.09114010.9910.0390.0991.17999.3
3.72-3.876.40.08313830.9950.0360.091.06499.3
3.87-4.046.20.07914000.9960.0340.0860.93799.5
4.04-4.256.10.07113850.9960.0310.0770.94699.4
4.25-4.526.10.06314050.9960.0270.0691.14699.6
4.52-4.876.10.0613960.9960.0260.0660.90299.4
4.87-5.366.10.05514160.9970.0240.0610.81399.5
5.36-6.126.10.0614250.9960.0260.0650.8299.8
6.12-7.695.90.05614360.9960.0250.0610.87599.7
7.69-305.30.04614840.9970.0210.0510.99999.4

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Processing

Software
NameVersionClassification
HKL-2000data scaling
REFMAC5.8.0189refinement
PDB_EXTRACT3.24data extraction
HKL-2000data reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.85→29.581 Å / Cor.coef. Fo:Fc: 0.906 / Cor.coef. Fo:Fc free: 0.879 / SU B: 16.912 / SU ML: 0.308 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.9 / ESU R Free: 0.397
RfactorNum. reflection% reflectionSelection details
Rfree0.2933 1367 5 %RANDOM
Rwork0.2575 ---
obs0.2592 25716 96.22 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 110.29 Å2 / Biso mean: 58.83 Å2 / Biso min: 19.25 Å2
Baniso -1Baniso -2Baniso -3
1-0.57 Å20.29 Å20 Å2
2--0.57 Å20 Å2
3----1.86 Å2
Refinement stepCycle: final / Resolution: 2.85→29.581 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5400 0 6 59 5465
Biso mean--72.29 34.77 -
Num. residues----703
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.025554
X-RAY DIFFRACTIONr_angle_refined_deg1.1261.9317616
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.1455702
X-RAY DIFFRACTIONr_dihedral_angle_2_deg39.13325.019263
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.63115770
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.0491521
X-RAY DIFFRACTIONr_chiral_restr0.0690.2841
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.0214380
LS refinement shellResolution: 2.849→2.923 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.519 100 -
Rwork0.485 1757 -
all-1857 -
obs--89.75 %

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