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- PDB-6tr4: Ruminococcus gnavus GH29 fucosidase E1_10125 D221A mutant in comp... -

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Basic information

Entry
Database: PDB / ID: 6tr4
TitleRuminococcus gnavus GH29 fucosidase E1_10125 D221A mutant in complex with fucose
ComponentsF5/8 type C domain-containing protein
KeywordsHYDROLASE / fucosidase / fucose / ruminococcus gnavus / GH29
Function / homology
Function and homology information


(Ara-f)3-Hyp beta-L-arabinobiosidase / alpha-L-fucosidase activity / fucose metabolic process / glycoside catabolic process / lysosome / membrane / metal ion binding
Similarity search - Function
FIVAR domain / CalX-like domain superfamily / Glycoside hydrolase, family 29 / Alpha-L-fucosidase / Alpha-L-fucosidase / Coagulation factors 5/8 type C domain (FA58C) profile. / F5/8 type C domain / Coagulation factor 5/8 C-terminal domain / Galactose-binding-like domain superfamily / Glycoside hydrolase superfamily
Similarity search - Domain/homology
alpha-L-fucopyranose / beta-L-fucopyranose / F5/8 type C domain-containing protein / Beta-L-arabinobiosidase
Similarity search - Component
Biological species[Ruminococcus] gnavus E1 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.45 Å
AuthorsOwen, C.D. / Wu, H. / Crost, E. / Colvile, A. / Juge, N. / Walsh, M.A.
Funding support United Kingdom, 2items
OrganizationGrant numberCountry
Biotechnology and Biological Sciences Research Council (BBSRC)BB/M029042 United Kingdom
Biotechnology and Biological Sciences Research Council (BBSRC)BB/J004529/1 United Kingdom
CitationJournal: Cell.Mol.Life Sci. / Year: 2021
Title: Fucosidases from the human gut symbiont Ruminococcus gnavus.
Authors: Wu, H. / Rebello, O. / Crost, E.H. / Owen, C.D. / Walpole, S. / Bennati-Granier, C. / Ndeh, D. / Monaco, S. / Hicks, T. / Colvile, A. / Urbanowicz, P.A. / Walsh, M.A. / Angulo, J. / Spencer, D.I.R. / Juge, N.
History
DepositionDec 17, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 28, 2020Provider: repository / Type: Initial release
Revision 1.1Feb 17, 2021Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.year / _citation_author.identifier_ORCID
Revision 1.2Jan 24, 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 / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: F5/8 type C domain-containing protein
B: F5/8 type C domain-containing protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)124,32620
Polymers123,3302
Non-polymers99618
Water27,1491507
1
A: F5/8 type C domain-containing protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)62,25711
Polymers61,6651
Non-polymers59210
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: F5/8 type C domain-containing protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)62,0699
Polymers61,6651
Non-polymers4048
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)49.780, 74.060, 76.509
Angle α, β, γ (deg.)82.470, 80.430, 70.410
Int Tables number1
Space group name H-MP1
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B

NCS domain segments:

Component-ID: _ / Ens-ID: 1 / Beg auth comp-ID: ASN / Beg label comp-ID: ASN / End auth comp-ID: PRO / End label comp-ID: PRO / Refine code: _ / Auth seq-ID: 7 - 512 / Label seq-ID: 7 - 512

Dom-IDAuth asym-IDLabel asym-ID
1AA
2BB

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein F5/8 type C domain-containing protein


Mass: 61664.961 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) [Ruminococcus] gnavus E1 (bacteria) / Gene: CDL26_02305 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A2N5PIE7, UniProt: A0A6N3BKT0*PLUS

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Sugars , 2 types, 3 molecules

#2: Sugar ChemComp-FUL / beta-L-fucopyranose / beta-L-fucose / 6-deoxy-beta-L-galactopyranose / L-fucose / fucose / 6-DEOXY-BETA-L-GALACTOSE


Type: L-saccharide, beta linking / Mass: 164.156 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Formula: C6H12O5 / Feature type: SUBJECT OF INVESTIGATION
IdentifierTypeProgram
LFucpbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
b-L-fucopyranoseCOMMON NAMEGMML 1.0
b-L-FucpIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
FucSNFG CARBOHYDRATE SYMBOLGMML 1.0
#3: Sugar ChemComp-FUC / alpha-L-fucopyranose / alpha-L-fucose / 6-deoxy-alpha-L-galactopyranose / L-fucose / fucose


Type: L-saccharide, alpha linking / Mass: 164.156 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Formula: C6H12O5 / Feature type: SUBJECT OF INVESTIGATION
IdentifierTypeProgram
LFucpaCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
a-L-fucopyranoseCOMMON NAMEGMML 1.0
a-L-FucpIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
FucSNFG CARBOHYDRATE SYMBOLGMML 1.0

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Non-polymers , 4 types, 1522 molecules

#4: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: Mg
#5: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Ca
#6: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Cl
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1507 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 2.12 Å3/Da / Density % sol: 41.88 %
Crystal growTemperature: 273 K / Method: vapor diffusion, sitting drop
Details: 2 M magnesium chloride, 25% PEG 3350, 0.1 M bis-tris pH 5.5, 10mM 2FL

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.9763 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Sep 10, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9763 Å / Relative weight: 1
ReflectionResolution: 1.45→69.64 Å / Num. obs: 166349 / % possible obs: 92.7 % / Redundancy: 2 % / CC1/2: 0.995 / Rmerge(I) obs: 0.043 / Rpim(I) all: 0.043 / Rrim(I) all: 0.06 / Net I/σ(I): 12.7
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. measured allNum. unique obsCC1/2Rpim(I) allRrim(I) allNet I/σ(I) obs% possible all
1.45-1.471.80.111930450660.9550.1110.1573.456.9
7.94-69.5420.029218311010.9950.0290.04128.999.6

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Processing

Software
NameVersionClassification
Aimless0.7.2data scaling
REFMAC5.8.0258refinement
PDB_EXTRACT3.25data extraction
xia2data reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4OUE

4oue


Resolution: 1.45→69.64 Å / Cor.coef. Fo:Fc: 0.971 / Cor.coef. Fo:Fc free: 0.962 / SU B: 1.687 / SU ML: 0.035 / SU R Cruickshank DPI: 0.0606 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.061 / ESU R Free: 0.06
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.1605 8116 4.9 %RANDOM
Rwork0.1406 ---
obs0.1416 158233 92.66 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 52.09 Å2 / Biso mean: 11.7 Å2 / Biso min: 1.62 Å2
Baniso -1Baniso -2Baniso -3
1-0.33 Å2-0.02 Å20.07 Å2
2---0.51 Å2-0.04 Å2
3---0.3 Å2
Refinement stepCycle: final / Resolution: 1.45→69.64 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7962 0 48 1507 9517
Biso mean--7.79 23.65 -
Num. residues----1012
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0138363
X-RAY DIFFRACTIONr_bond_other_d0.0190.0187353
X-RAY DIFFRACTIONr_angle_refined_deg1.4321.65211335
X-RAY DIFFRACTIONr_angle_other_deg1.7121.59517257
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.29551050
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.725.475442
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.687151453
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.341520
X-RAY DIFFRACTIONr_chiral_restr0.0690.21085
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.029568
X-RAY DIFFRACTIONr_gen_planes_other0.0060.021652
Refine LS restraints NCS

Ens-ID: 1 / Number: 17888 / Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Rms dev position: 0.05 Å / Weight position: 0.05

Dom-IDAuth asym-ID
1A
2B
LS refinement shellResolution: 1.45→1.488 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.179 381 -
Rwork0.165 7556 -
all-7937 -
obs--59.55 %
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)
10.09950.08310.03590.52540.13480.2563-0.00030.00440.0129-0.0051-0.0026-0.0075-0.02280.00050.00290.00380.006-0.00250.0214-0.00780.00590.0490.0510.004
20.0496-0.0041-0.00670.45970.11190.25020.0093-0.004-0.008-0.0074-0.0062-0.01010.0160.0057-0.00310.00580.0076-0.00430.0249-0.00820.004812.78937.52136.462
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A7 - 701
2X-RAY DIFFRACTION2B7 - 701

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