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

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Basic information

Entry
Database: PDB / ID: 4lqr
TitleStructure of CBM32-3 from a family 31 glycoside hydrolase from Clostridium perfringens
ComponentsGlycosyl hydrolase, family 31/fibronectin type III domain protein
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) / 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
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: 1.58 Å
AuthorsGrondin, J.M. / Furness, H.S. / Duan, D. / 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 19, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 23, 2014Provider: repository / Type: Initial release
Revision 1.1Mar 8, 2017Group: Database references
Revision 1.2Sep 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_seq_id / _pdbx_struct_conn_angle.ptnr2_label_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_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)19,0743
Polymers18,9941
Non-polymers802
Water3,477193
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)38.766, 52.562, 70.169
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.: 1 / Fragment: CBM32-3, UNP residues 1640-1785
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Clostridium perfringens (bacteria) / Strain: ATCC 13124 / 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: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 193 / 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: 1.94 Å3/Da / Density % sol: 36.11 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 20% PEG 10000, 100mM HEPES 50mM NaCl, pH 7.5, 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: Oct 5, 2009
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: 1.58→50 Å / Num. obs: 20155 / % possible obs: 98.9 % / Redundancy: 5.4 % / Rmerge(I) obs: 0.042
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allDiffraction-ID% possible all
1.58-1.647.60.0841833191
1.64-1.77.90.07519861100
1.7-1.787.90.06619971100
1.78-1.8780.05720011100
1.87-1.9980.0520061100
1.99-2.1480.04420281100
2.14-2.3680.04220151100
2.36-2.780.04120491100
2.7-3.47.90.03720751100
3.4-507.10.0352165198.4

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Processing

Software
NameVersionClassificationNB
REFMAC5.7.0032refinement
PDB_EXTRACT3.11data extraction
Blu-Icelikedata collection
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2J1A

2j1a


Resolution: 1.58→33.96 Å / Cor.coef. Fo:Fc: 0.953 / Cor.coef. Fo:Fc free: 0.938 / Occupancy max: 1 / Occupancy min: 0.3 / SU B: 1.249 / SU ML: 0.046 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.087 / ESU R Free: 0.087 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.194 1024 5.1 %RANDOM
Rwork0.1609 ---
obs0.1626 20155 99.83 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 44.13 Å2 / Biso mean: 9.8579 Å2 / Biso min: 2.49 Å2
Baniso -1Baniso -2Baniso -3
1--0.42 Å2-0 Å20 Å2
2---0.11 Å20 Å2
3---0.53 Å2
Refinement stepCycle: LAST / Resolution: 1.58→33.96 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1238 0 2 193 1433
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0240.021309
X-RAY DIFFRACTIONr_angle_refined_deg2.2481.9441790
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.1945171
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.042570
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.03715218
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.052158
X-RAY DIFFRACTIONr_chiral_restr0.1780.2196
X-RAY DIFFRACTIONr_gen_planes_refined0.0140.021032
LS refinement shellResolution: 1.58→1.64 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.196 77 -
Rwork0.167 1383 -
all-1460 -
obs--99.86 %

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