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- PDB-5gzh: Endo-beta-1,2-glucanase from Chitinophaga pinensis - ligand free form -

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Basic information

Entry
Database: PDB / ID: 5gzh
TitleEndo-beta-1,2-glucanase from Chitinophaga pinensis - ligand free form
ComponentsEndo-beta-1,2-glucanase
KeywordsHYDROLASE / (alpha/alpha)6-barrel
Function / homology
Function and homology information


Glycoside hydrolase 144 (GH144) / Uncharacterised conserved protein UCP028431 / Glycoamylase-like, conserved domain / Putative glucoamylase / Glycosyltransferase / Alpha/alpha barrel / Mainly Alpha
Similarity search - Domain/homology
trehalose / IODIDE ION / Glycoamylase-like domain-containing protein
Similarity search - Component
Biological speciesChitinophaga pinensis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsAbe, K. / Nakajima, M. / Arakawa, T. / Fushinobu, S. / Taguchi, H.
CitationJournal: J. Biol. Chem. / Year: 2017
Title: Biochemical and structural analyses of a bacterial endo-beta-1,2-glucanase reveal a new glycoside hydrolase family
Authors: Abe, K. / Nakajima, M. / Yamashita, T. / Matsunaga, H. / Kamisuki, S. / Nihira, T. / Takahashi, Y. / Sugimoto, N. / Miyanaga, A. / Nakai, H. / Arakawa, T. / Fushinobu, S. / Taguchi, H.
History
DepositionSep 28, 2016Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Mar 15, 2017Provider: repository / Type: Initial release
Revision 1.1May 24, 2017Group: Database references
Revision 2.0Jul 29, 2020Group: Atomic model / Data collection ...Atomic model / Data collection / Derived calculations / Non-polymer description / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / entity / entity_name_com / pdbx_branch_scheme / pdbx_chem_comp_identifier / pdbx_entity_branch / pdbx_entity_branch_descriptor / pdbx_entity_branch_link / pdbx_entity_branch_list / pdbx_entity_nonpoly / pdbx_molecule_features / pdbx_nonpoly_scheme / pdbx_struct_assembly_gen / struct_asym / struct_conn / struct_site / struct_site_gen
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_asym_id / _atom_site.auth_atom_id / _atom_site.auth_comp_id / _atom_site.auth_seq_id / _atom_site.label_asym_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _atom_site.label_entity_id / _atom_site.type_symbol / _chem_comp.formula / _chem_comp.formula_weight / _chem_comp.id / _chem_comp.mon_nstd_flag / _chem_comp.name / _chem_comp.pdbx_synonyms / _chem_comp.type / _entity.formula_weight / _entity.pdbx_description / _entity.src_method / _entity.type / _pdbx_struct_assembly_gen.asym_id_list / _struct_asym.entity_id
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Nov 8, 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: Endo-beta-1,2-glucanase
B: Endo-beta-1,2-glucanase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)106,31528
Polymers102,5852
Non-polymers3,73026
Water11,512639
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A: Endo-beta-1,2-glucanase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)53,41116
Polymers51,2921
Non-polymers2,11915
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area16000 Å2
MethodPISA
2
B: Endo-beta-1,2-glucanase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)52,90412
Polymers51,2921
Non-polymers1,61111
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area360 Å2
ΔGint-4 kcal/mol
Surface area16100 Å2
MethodPISA
Unit cell
Length a, b, c (Å)90.965, 90.965, 124.086
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number144
Space group name H-MP31

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Components

#1: Protein Endo-beta-1,2-glucanase


Mass: 51292.422 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Chitinophaga pinensis (strain ATCC 43595 / DSM 2588 / NCIB 11800 / UQM 2034) (bacteria)
Strain: ATCC 43595 / DSM 2588 / NCIB 11800 / UQM 2034 / Gene: Cpin_6279 / Plasmid: pET-30a / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: C7PIC2
#2: Polysaccharide alpha-D-glucopyranose-(1-1)-alpha-D-glucopyranose / trehalose


Type: oligosaccharide, Oligosaccharide / Class: Nutrient / Mass: 342.297 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: oligosaccharide with reducing-end-to-reducing-end glycosidic bond
References: trehalose
DescriptorTypeProgram
DGlcpa1-1DGlcpaGlycam Condensed SequenceGMML 1.0
WURCS=2.0/1,2,1/[a2122h-1a_1-5]/1-1/a1-b1WURCSPDB2Glycan 1.1.0
[][a-D-Glcp]{[(1+1)][a-D-Glcp]{}}LINUCSPDB-CARE
#3: Chemical...
ChemComp-IOD / IODIDE ION


Mass: 126.904 Da / Num. of mol.: 24 / Source method: obtained synthetically / Formula: I
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 639 / 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: 2.95 Å3/Da / Density % sol: 58.4 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / Details: 0.1 M ammonium iodide, 7% PEG 3350

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: AR-NW12A / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Jun 28, 2015
RadiationMonochromator: Numerical link type Si(111) double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.8→50 Å / Num. obs: 105566 / % possible obs: 99 % / Redundancy: 5.3 % / Biso Wilson estimate: 19.7 Å2 / Rmerge(I) obs: 0.098 / Net I/σ(I): 21.3
Reflection shellResolution: 1.8→1.83 Å / Redundancy: 5.6 % / Rmerge(I) obs: 0.682 / Mean I/σ(I) obs: 2.3 / CC1/2: 0.823 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.8.0107refinement
HKL-2000data reduction
HKL-2000data scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3EU8

3eu8


Resolution: 1.8→48.74 Å / Cor.coef. Fo:Fc: 0.962 / Cor.coef. Fo:Fc free: 0.945 / SU B: 2.307 / SU ML: 0.071 / Cross valid method: THROUGHOUT / ESU R: 0.103 / ESU R Free: 0.104 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.20437 5317 5 %RANDOM
Rwork0.16807 ---
obs0.1699 100115 98.99 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 28.34 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refinement stepCycle: 1 / Resolution: 1.8→48.74 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6934 0 70 639 7643
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.020.0197240
X-RAY DIFFRACTIONr_bond_other_d0.0020.026454
X-RAY DIFFRACTIONr_angle_refined_deg1.8521.9259842
X-RAY DIFFRACTIONr_angle_other_deg1.098314864
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.2425854
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.86823.967368
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.133151114
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.1691526
X-RAY DIFFRACTIONr_chiral_restr0.1260.2968
X-RAY DIFFRACTIONr_gen_planes_refined0.0120.0218312
X-RAY DIFFRACTIONr_gen_planes_other0.0020.021858
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it2.3872.6163416
X-RAY DIFFRACTIONr_mcbond_other2.3872.6163415
X-RAY DIFFRACTIONr_mcangle_it2.9593.9114270
X-RAY DIFFRACTIONr_mcangle_other2.9583.9124271
X-RAY DIFFRACTIONr_scbond_it3.1042.93824
X-RAY DIFFRACTIONr_scbond_other3.1042.93824
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other4.3924.2395573
X-RAY DIFFRACTIONr_long_range_B_refined5.61422.4989183
X-RAY DIFFRACTIONr_long_range_B_other5.61422.59184
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.8→1.847 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.259 484 -
Rwork0.226 7394 -
obs--100 %

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