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- PDB-4lks: Structure of CBM32-3 from a family 31 glycoside hydrolase from Cl... -

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Basic information

Entry
Database: PDB / ID: 4lks
TitleStructure of CBM32-3 from a family 31 glycoside hydrolase from Clostridium perfringens in complex with galactose
ComponentsGlycosyl hydrolase, family 31/fibronectin type III domain protein
KeywordsSUGAR BINDING PROTEIN / B-sandwich / carbohydrate-binding / galactose
Function / homology
Function and homology information


polysaccharide catabolic process / hydrolase activity, hydrolyzing O-glycosyl compounds / carbohydrate binding / metal ion binding
Similarity search - Function
Alpha-glucosidase, N-terminal / : / : / Domain of unknown function DUF5110 / Domain of unknown function (DUF5110) / Glycoside hydrolase family 31, N-terminal domain / Bacterial Ig-like domain (group 2) / Glycosyl hydrolase 31 N-terminal galactose mutarotase-like domain / Invasin/intimin cell-adhesion fragments / Bacterial Ig-like domain 2 ...Alpha-glucosidase, N-terminal / : / : / Domain of unknown function DUF5110 / Domain of unknown function (DUF5110) / Glycoside hydrolase family 31, N-terminal domain / Bacterial Ig-like domain (group 2) / Glycosyl hydrolase 31 N-terminal galactose mutarotase-like domain / Invasin/intimin cell-adhesion fragments / Bacterial Ig-like domain 2 / Bacterial Ig-like domain, group 2 / : / Glycosyl hydrolase family 31 C-terminal domain / Glycoside hydrolase family 31 / Glycosyl hydrolases family 31 TIM-barrel domain / Dockerin type I domain / Dockerin type I repeat / Dockerin domain superfamily / CBM2/CBM3, carbohydrate-binding domain superfamily / Coagulation factors 5/8 type C domain (FA58C) profile. / F5/8 type C domain / Coagulation factor 5/8 C-terminal domain / Galactose mutarotase-like domain superfamily / Galactose-binding domain-like / Glycosyl hydrolase, all-beta / Fibronectin type III domain / Fibronectin type 3 domain / Fibronectin type-III domain profile. / Galactose-binding-like domain superfamily / Fibronectin type III / Fibronectin type III superfamily / EF-Hand 1, calcium-binding site / EF-hand calcium-binding domain. / Glycoside hydrolase superfamily / Jelly Rolls / Immunoglobulin-like fold / Sandwich / Mainly Beta
Similarity search - Domain/homology
beta-D-galactopyranose / Glycosyl hydrolase, family 31/fibronectin type III domain protein / Glycosyl hydrolase, family 31/fibronectin type III domain protein
Similarity search - Component
Biological speciesClostridium perfringens (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.5 Å
AuthorsGrondin, J.M. / Duan, D. / Kirlin, A.C. / Furness, H.S. / Allingham, J.S. / Smith, S.P.
CitationJournal: Plos One / Year: 2017
Title: Diverse modes of galacto-specific carbohydrate recognition by a family 31 glycoside hydrolase from Clostridium perfringens.
Authors: Grondin, J.M. / Duan, D. / Kirlin, A.C. / Abe, K.T. / Chitayat, S. / Spencer, H.L. / Spencer, C. / Campigotto, A. / Houliston, S. / Arrowsmith, C.H. / Allingham, J.S. / Boraston, A.B. / Smith, S.P.
History
DepositionJul 8, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 24, 2014Provider: repository / Type: Initial release
Revision 1.1Mar 8, 2017Group: Database references
Revision 1.2Nov 15, 2017Group: Refinement description / Category: software
Revision 1.3Jul 29, 2020Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp / entity ...chem_comp / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / pdbx_struct_conn_angle / struct_conn / struct_ref_seq_dif / struct_site / struct_site_gen
Item: _chem_comp.name / _chem_comp.type ..._chem_comp.name / _chem_comp.type / _entity.pdbx_description / _pdbx_entity_nonpoly.name / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_label_asym_id / _struct_ref_seq_dif.details
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.4Sep 20, 2023Group: Data collection / Database references ...Data collection / Database references / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Glycosyl hydrolase, family 31/fibronectin type III domain protein
C: Glycosyl hydrolase, family 31/fibronectin type III domain protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,4286
Polymers37,9882
Non-polymers4404
Water9,278515
1
A: Glycosyl hydrolase, family 31/fibronectin type III domain protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,2143
Polymers18,9941
Non-polymers2202
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
C: Glycosyl hydrolase, family 31/fibronectin type III domain protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,2143
Polymers18,9941
Non-polymers2202
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)62.338, 62.325, 85.350
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Glycosyl hydrolase, family 31/fibronectin type III domain protein


Mass: 18993.844 Da / Num. of mol.: 2 / Fragment: CBM32-3, UNP residues 1640-1785
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Clostridium perfringens (bacteria) / Strain: ATCC 13124 / NCTC 8237 / Type A / Gene: CPF_1301 / Production host: Escherichia coli (E. coli) / References: UniProt: Q0TRJ3, UniProt: A0A0H2YST8*PLUS
#2: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ca
#3: Sugar ChemComp-GAL / beta-D-galactopyranose / beta-D-galactose / D-galactose / galactose


Type: D-saccharide, beta linking / Mass: 180.156 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Formula: C6H12O6
IdentifierTypeProgram
DGalpbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
b-D-galactopyranoseCOMMON NAMEGMML 1.0
b-D-GalpIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GalSNFG CARBOHYDRATE SYMBOLGMML 1.0
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 515 / 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: 1.95 Å3/Da / Density % sol: 36.3 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 8
Details: 1.6M ammonium citrate, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 93.15 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X6A / Wavelength: 0.98 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Jul 13, 2011
RadiationMonochromator: Si (III) channel cut / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 1.5→40 Å / Num. obs: 53421 / % possible obs: 98.9 % / Redundancy: 4.2 % / Rmerge(I) obs: 0.051 / Χ2: 1.236 / Net I/σ(I): 16.4
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
1.5-1.554.10.3253391.357199.9
1.55-1.624.20.25152891.385199.8
1.62-1.694.20.18953031.409199.7
1.69-1.784.20.13953641.408199.7
1.78-1.894.20.10453011.402199.3
1.89-2.044.30.07253311.367199.5
2.04-2.244.30.05753221.246199.1
2.24-2.564.40.04953511.137198.9
2.56-3.234.40.03853690.933198.1
3.23-404.30.03354520.76195.6

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
PHENIX1.7.3_928refinement
PDB_EXTRACT3.11data extraction
Blu-Icelikedata collection
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2J1A

2j1a


Resolution: 1.5→30.659 Å / Occupancy max: 1 / Occupancy min: 0.31 / FOM work R set: 0.8808 / SU ML: 0.19 / σ(F): 1.34 / Phase error: 18.55 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2012 2717 5.09 %
Rwork0.175 --
obs0.1764 53360 98.93 %
Solvent computationShrinkage radii: 0.73 Å / VDW probe radii: 1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 39.324 Å2 / ksol: 0.394 e/Å3
Displacement parametersBiso max: 69.66 Å2 / Biso mean: 16.3428 Å2 / Biso min: 5.62 Å2
Baniso -1Baniso -2Baniso -3
1-1.1766 Å20 Å2-0 Å2
2--0.5532 Å20 Å2
3----1.7297 Å2
Refinement stepCycle: LAST / Resolution: 1.5→30.659 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2483 0 26 515 3024
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0072590
X-RAY DIFFRACTIONf_angle_d1.123528
X-RAY DIFFRACTIONf_chiral_restr0.076396
X-RAY DIFFRACTIONf_plane_restr0.004462
X-RAY DIFFRACTIONf_dihedral_angle_d13.176958
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 19

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.5001-1.52730.26941290.236326822811100
1.5273-1.55670.27831520.230426352787100
1.5567-1.58850.27661440.218226292773100
1.5885-1.6230.22431340.214426462780100
1.623-1.66080.24591370.197226872824100
1.6608-1.70230.23281590.185626502809100
1.7023-1.74830.22531610.185226082769100
1.7483-1.79980.23561300.180726692799100
1.7998-1.85790.19791370.170126792816100
1.8579-1.92430.20051490.17182662281199
1.9243-2.00130.20581450.16242649279499
2.0013-2.09240.21211460.16712637278399
2.0924-2.20260.2051600.17372688284899
2.2026-2.34060.17631270.16912652277999
2.3406-2.52120.24911230.17582698282199
2.5212-2.77480.21420.18732678282099
2.7748-3.1760.21031340.17712687282198
3.176-40.15441520.14962680283297
4-30.66520.17531560.16892727288395

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