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- PDB-4lpl: Structure of CBM32-1 from a family 31 glycoside hydrolase from Cl... -

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Basic information

Entry
Database: PDB / ID: 4lpl
TitleStructure of CBM32-1 from a family 31 glycoside hydrolase from Clostridium perfringens
ComponentsGlycosyl hydrolase, family 31/fibronectin type III domain proteinGlycoside hydrolase
KeywordsSUGAR BINDING PROTEIN / B-sandwich / carbohydrate-binding
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) / Invasin/intimin cell-adhesion fragments / Bacterial Ig-like domain (group 2) / Glycoside hydrolase family 31, N-terminal domain / Glycosyl hydrolase 31 N-terminal galactose mutarotase-like domain / Bacterial Ig-like domain 2 / Bacterial Ig-like domain, group 2 ...Alpha-glucosidase, N-terminal / : / Domain of unknown function DUF5110 / Domain of unknown function (DUF5110) / Invasin/intimin cell-adhesion fragments / Bacterial Ig-like domain (group 2) / Glycoside hydrolase family 31, N-terminal domain / Glycosyl hydrolase 31 N-terminal galactose mutarotase-like domain / 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
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: 1.35 Å
AuthorsGrondin, J.M. / Duan, D. / Heather, F.S. / Spencer, C.A. / 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 16, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 16, 2014Provider: repository / Type: Initial release
Revision 1.1Mar 8, 2017Group: Database references
Revision 1.2Jul 17, 2019Group: Data collection / Refinement description / Category: software
Item: _software.contact_author / _software.contact_author_email ..._software.contact_author / _software.contact_author_email / _software.language / _software.location / _software.name / _software.type / _software.version
Revision 1.3Sep 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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_comp_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr2_label_atom_id / _pdbx_struct_conn_angle.ptnr2_label_comp_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_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_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)21,0613
Polymers20,9971
Non-polymers642
Water2,054114
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)55.620, 55.671, 88.700
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number20
Space group name H-MC2221

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Components

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


Mass: 20996.625 Da / Num. of mol.: 1 / Fragment: CBM32-1, UNP residues 935-1095
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.: 1 / Source method: obtained synthetically / Formula: Ca
#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 114 / 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: 1.93 Å3/Da / Density % sol: 35.9 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 8
Details: 32% PEG 4000, 225mM MgCl2 100mM Tris, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 93.15 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-B / Wavelength: 1.033 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Jul 16, 2010
RadiationMonochromator: Si (III) double crystal cryo-cooled / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.033 Å / Relative weight: 1
ReflectionResolution: 1.35→30 Å / Num. obs: 30335 / % possible obs: 98.9 % / Redundancy: 11 % / Rmerge(I) obs: 0.063 / Net I/σ(I): 28.9
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allDiffraction-ID% possible all
1.35-1.45.10.4492971197.7
1.4-1.455.50.3653017199.7
1.45-1.525.60.3083000199.5
1.52-1.65.60.2213008199.8
1.6-1.75.70.1483051199.9
1.7-1.835.70.1130341100
1.83-2.025.80.0723075199.9
2.02-2.315.90.0663067199.7
2.31-2.915.90.0543065198.8
2.91-305.80.0443047194.2

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Processing

Software
NameVersionClassificationNB
PHENIX1.6.1_357refinement
PDB_EXTRACT3.11data extraction
Blu-Icelikedata collection
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing
REFMACrefinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2J1A

2j1a


Resolution: 1.35→23.637 Å / Occupancy max: 1 / Occupancy min: 0.01 / SU ML: 0.12 / σ(F): 0.1 / Phase error: 19.85 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2073 1485 5.06 %
Rwork0.1878 --
obs0.1888 29352 95.76 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 40.474 Å2 / ksol: 0.399 e/Å3
Displacement parametersBiso max: 43.8 Å2 / Biso mean: 16.0366 Å2 / Biso min: 6.37 Å2
Baniso -1Baniso -2Baniso -3
1-4.438 Å2-0 Å2-0 Å2
2---2.8207 Å20 Å2
3----1.6173 Å2
Refinement stepCycle: LAST / Resolution: 1.35→23.637 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1146 0 2 114 1262
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONf_bond_d0.006
X-RAY DIFFRACTIONf_angle_d1.066
X-RAY DIFFRACTIONf_chiral_restr0.076
X-RAY DIFFRACTIONf_plane_restr0.004
X-RAY DIFFRACTIONf_dihedral_angle_d12.7424
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkRefine-ID% reflection obs (%)
1.35-1.40.2691230.2272X-RAY DIFFRACTION87
1.4-1.450.2471270.2033X-RAY DIFFRACTION91
1.45-1.520.22811200.1909X-RAY DIFFRACTION96
1.52-1.60.20371100.1862X-RAY DIFFRACTION97
1.6-1.70.20791550.1763X-RAY DIFFRACTION98
1.7-1.830.21451440.1862X-RAY DIFFRACTION99
1.83-2.020.19371240.175X-RAY DIFFRACTION100
2.02-2.310.2061560.1744X-RAY DIFFRACTION99
2.31-2.910.20131430.1991X-RAY DIFFRACTION99
2.91-300.19521430.1838X-RAY DIFFRACTION94

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