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- PDB-7pmo: Ruminococcus gnavus ATC29149 endo-beta-1,4-galactosidase (RgGH98) -

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Basic information

Entry
Database: PDB / ID: 7pmo
TitleRuminococcus gnavus ATC29149 endo-beta-1,4-galactosidase (RgGH98)
ComponentsRuminococcus gnavus endogalactosidase GH98
KeywordsHYDROLASE / endogalactosidase / glycoside hydrolase
Function / homology
Function and homology information


carbohydrate metabolic process
Similarity search - Function
Chitobiase/beta-hexosaminidase C-terminal domain / Glycosyl hydrolase family 98, C-terminal / Glycosyl hydrolase family 98, central domain / Glycosyl hydrolase family 98 / Glycosyl hydrolase family 98 C-terminal domain / Polysaccharide lyase family 8-like, C-terminal / Fibronectin type 3 domain / Fibronectin type-III domain profile. / Galactose-binding-like domain superfamily / Fibronectin type III ...Chitobiase/beta-hexosaminidase C-terminal domain / Glycosyl hydrolase family 98, C-terminal / Glycosyl hydrolase family 98, central domain / Glycosyl hydrolase family 98 / Glycosyl hydrolase family 98 C-terminal domain / Polysaccharide lyase family 8-like, C-terminal / Fibronectin type 3 domain / Fibronectin type-III domain profile. / Galactose-binding-like domain superfamily / Fibronectin type III / Fibronectin type III superfamily / Immunoglobulin-like fold
Similarity search - Domain/homology
DI(HYDROXYETHYL)ETHER / Fibronectin type-III domain-containing protein
Similarity search - Component
Biological speciesRuminococcus gnavus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å
AuthorsOwen, C.D. / Wu, H. / Crost, E.H. / van Bakel, W. / Gascuena, A.M. / Latousakis, D. / Hicks, T. / Walpole, S. / Urbanowicz, P.A. / Ndeh, D. ...Owen, C.D. / Wu, H. / Crost, E.H. / van Bakel, W. / Gascuena, A.M. / Latousakis, D. / Hicks, T. / Walpole, S. / Urbanowicz, P.A. / Ndeh, D. / Monaco, S. / Salom, L.S. / Griffiths, R. / Colvile, A. / Spencer, D.I.R. / Walsh, M.A. / Angulo, J. / Juge, N.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: Plos Biol. / Year: 2021
Title: The human gut symbiont Ruminococcus gnavus shows specificity to blood group A antigen during mucin glycan foraging: Implication for niche colonisation in the gastrointestinal tract.
Authors: Wu, H. / Crost, E.H. / Owen, C.D. / van Bakel, W. / Martinez Gascuena, A. / Latousakis, D. / Hicks, T. / Walpole, S. / Urbanowicz, P.A. / Ndeh, D. / Monaco, S. / Sanchez Salom, L. / ...Authors: Wu, H. / Crost, E.H. / Owen, C.D. / van Bakel, W. / Martinez Gascuena, A. / Latousakis, D. / Hicks, T. / Walpole, S. / Urbanowicz, P.A. / Ndeh, D. / Monaco, S. / Sanchez Salom, L. / Griffiths, R. / Reynolds, R.S. / Colvile, A. / Spencer, D.I.R. / Walsh, M. / Angulo, J. / Juge, N.
History
DepositionSep 2, 2021Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 2, 2022Provider: repository / Type: Initial release
Revision 1.1Jan 31, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model / struct_ncs_dom_lim
Item: _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id ..._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
D: Ruminococcus gnavus endogalactosidase GH98
G: Ruminococcus gnavus endogalactosidase GH98
hetero molecules


Theoretical massNumber of molelcules
Total (without water)191,08718
Polymers190,2452
Non-polymers84216
Water20,3211128
1
D: Ruminococcus gnavus endogalactosidase GH98
hetero molecules


Theoretical massNumber of molelcules
Total (without water)95,59010
Polymers95,1221
Non-polymers4679
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
G: Ruminococcus gnavus endogalactosidase GH98
hetero molecules


Theoretical massNumber of molelcules
Total (without water)95,4978
Polymers95,1221
Non-polymers3757
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)105.313, 85.566, 112.628
Angle α, β, γ (deg.)90.000, 98.940, 90.000
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11D
21G

NCS domain segments:

Component-ID: 0 / Ens-ID: 1 / Beg auth comp-ID: LYS / Beg label comp-ID: LYS / End auth comp-ID: GLU / End label comp-ID: GLU / Refine code: 0 / Auth seq-ID: 48 - 892 / Label seq-ID: 1 - 845

Dom-IDAuth asym-IDLabel asym-ID
1DA
2GB

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Components

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Protein , 1 types, 2 molecules DG

#1: Protein Ruminococcus gnavus endogalactosidase GH98


Mass: 95122.430 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Ruminococcus gnavus (strain ATCC 29149 / VPI C7-9) (bacteria)
Strain: ATCC 29149 / VPI C7-9 / Gene: RUMGNA_03119 / Production host: Escherichia coli (E. coli) / References: UniProt: A7B6A6

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Non-polymers , 5 types, 1144 molecules

#2: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: C2H6O2
#3: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER / Diethylene glycol


Mass: 106.120 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O3
#4: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Mg
#5: Chemical ChemComp-CA / CALCIUM ION


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


Mass: 18.015 Da / Num. of mol.: 1128 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 2.65 Å3/Da / Density % sol: 53.62 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 0% PEG 500 MME, 10% PEG20K, 0.1M Sodium HEPES/MOPS pH 7.5

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.97628 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: May 23, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97628 Å / Relative weight: 1
ReflectionResolution: 2.1→104.25 Å / Num. obs: 115358 / % possible obs: 99.9 % / Redundancy: 3.5 % / CC1/2: 0.988 / Rmerge(I) obs: 0.135 / Rpim(I) all: 0.083 / Rrim(I) all: 0.159 / Net I/σ(I): 5.4
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
2.1-2.143.50.8581982556940.3420.5381.0161.4100
11.5-104.033.20.05924247680.9820.0390.07112.899.9

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Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
Aimless0.7.7data scaling
PDB_EXTRACT3.27data extraction
xia2data reduction
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4D6C

4d6c


Resolution: 2.1→104.03 Å / Cor.coef. Fo:Fc: 0.966 / Cor.coef. Fo:Fc free: 0.951 / SU B: 11.448 / SU ML: 0.147 / SU R Cruickshank DPI: 0.1997 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.2 / ESU R Free: 0.161 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.2063 5601 4.9 %RANDOM
Rwork0.1749 ---
obs0.1765 109735 99.89 %-
Solvent computationIon probe radii: 0.7 Å / Shrinkage radii: 0.7 Å / VDW probe radii: 1.1 Å / Solvent model: MASK
Displacement parametersBiso max: 105 Å2 / Biso mean: 38.933 Å2 / Biso min: 19.63 Å2
Baniso -1Baniso -2Baniso -3
1--0.65 Å20 Å20.18 Å2
2---1.41 Å2-0 Å2
3---1.91 Å2
Refinement stepCycle: final / Resolution: 2.1→104.03 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms13381 0 49 1128 14558
Biso mean--47.01 42.3 -
Num. residues----1695
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0050.01313817
X-RAY DIFFRACTIONr_bond_other_d0.0010.01712557
X-RAY DIFFRACTIONr_angle_refined_deg1.3131.64918753
X-RAY DIFFRACTIONr_angle_other_deg1.211.58229041
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.99951710
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.63825.288730
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.256152287
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.0841534
X-RAY DIFFRACTIONr_chiral_restr0.0590.21739
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0216095
X-RAY DIFFRACTIONr_gen_planes_other0.0010.023129
Refine LS restraints NCS

Ens-ID: 1 / Number: 28352 / Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Rms dev position: 0.07 Å / Weight position: 0.05

Dom-IDAuth asym-ID
1D
2G
LS refinement shellResolution: 2.1→2.155 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.335 441 -
Rwork0.314 8083 -
all-8524 -
obs--99.96 %
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)
10.54980.1467-0.24230.6666-0.36141.22260.00290.04770.01530.12410.05060.0697-0.1545-0.1302-0.05350.320.048-0.04090.161-0.00080.018342.866-0.76733.634
20.3501-0.0572-0.00470.74680.02562.0190.03680.09950.0238-0.22060.0109-0.0870.1268-0.0377-0.04780.3154-0.0104-0.01910.18210.02340.0215-0.118-37.81535.605
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1D48 - 893
2X-RAY DIFFRACTION2G48 - 896

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