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- PDB-5gzk: Endo-beta-1,2-glucanase from Chitinophaga pinensis - sophorotrios... -

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Basic information

Entry
Database: PDB / ID: 5gzk
TitleEndo-beta-1,2-glucanase from Chitinophaga pinensis - sophorotriose and glucose complex
ComponentsUncharacterized protein
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
beta-D-glucopyranose / : / DI(HYDROXYETHYL)ETHER / PHOSPHATE ION / Glycoamylase-like domain-containing protein
Similarity search - Component
Biological speciesChitinophaga pinensis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.7 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 / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / entity / 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_nonpoly_scheme / pdbx_struct_assembly_gen / pdbx_struct_conn_angle / pdbx_struct_special_symmetry / struct_asym / struct_conn / struct_conn_type / 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.name / _chem_comp.type / _pdbx_entity_nonpoly.entity_id / _pdbx_entity_nonpoly.name / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_symmetry / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_symmetry / _pdbx_struct_conn_angle.value / _pdbx_struct_special_symmetry.label_asym_id / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _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_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_conn.ptnr2_symmetry / _struct_conn_type.id
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Nov 8, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_conn
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI ..._chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Uncharacterized protein
B: Uncharacterized protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)106,99714
Polymers104,7852
Non-polymers2,21112
Water11,998666
1
A: Uncharacterized protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)53,5127
Polymers52,3931
Non-polymers1,1196
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area14620 Å2
MethodPISA
2
B: Uncharacterized protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)53,4857
Polymers52,3931
Non-polymers1,0926
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area130 Å2
ΔGint-12 kcal/mol
Surface area14640 Å2
MethodPISA
Unit cell
Length a, b, c (Å)126.106, 117.401, 75.554
Angle α, β, γ (deg.)90.00, 92.56, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-910-

HOH

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein Uncharacterized protein


Mass: 52392.637 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-28b / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: C7PIC2

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Sugars , 2 types, 4 molecules

#2: Polysaccharide beta-D-glucopyranose-(1-2)-beta-D-glucopyranose-(1-2)-beta-D-glucopyranose


Type: oligosaccharide / Mass: 504.438 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGlcpb1-2DGlcpb1-2DGlcpb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/1,3,2/[a2122h-1b_1-5]/1-1-1/a2-b1_b2-c1WURCSPDB2Glycan 1.1.0
[][b-D-Glcp]{[(2+1)][b-D-Glcp]{[(2+1)][b-D-Glcp]{}}}LINUCSPDB-CARE
#5: Sugar ChemComp-BGC / beta-D-glucopyranose / beta-D-glucose / D-glucose / glucose


Type: D-saccharide, beta linking / Mass: 180.156 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Formula: C6H12O6
IdentifierTypeProgram
DGlcpbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
b-D-glucopyranoseCOMMON NAMEGMML 1.0
b-D-GlcpIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcSNFG CARBOHYDRATE SYMBOLGMML 1.0

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Non-polymers , 7 types, 674 molecules

#3: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: PO4
#4: Chemical ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: K
#6: Chemical ChemComp-PG4 / TETRAETHYLENE GLYCOL


Mass: 194.226 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H18O5 / Comment: precipitant*YM
#7: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O3
#8: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#9: Chemical ChemComp-1PE / PENTAETHYLENE GLYCOL / PEG400


Mass: 238.278 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H22O6 / Comment: precipitant*YM
#10: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 666 / 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: 2.67 Å3/Da / Density % sol: 53.95 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 6.2
Details: 0.2 M sodium chloride, 0.1 M sodium/potassium phosphate (pH 6.2), 10% PEG 8000

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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: Nov 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: 1.7→50 Å / Num. obs: 120399 / % possible obs: 99.9 % / Redundancy: 3.7 % / Biso Wilson estimate: 8.2 Å2 / Rmerge(I) obs: 0.11 / Net I/σ(I): 13.1
Reflection shellResolution: 1.7→1.73 Å / Redundancy: 3.6 % / Rmerge(I) obs: 0.68 / Mean I/σ(I) obs: 2 / CC1/2: 0.696 / % 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: 5GZH

5gzh


Resolution: 1.7→49.46 Å / Cor.coef. Fo:Fc: 0.961 / Cor.coef. Fo:Fc free: 0.944 / SU B: 1.902 / SU ML: 0.063 / Cross valid method: THROUGHOUT / ESU R: 0.086 / ESU R Free: 0.088 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.19875 5990 5 %RANDOM
Rwork0.16598 ---
obs0.16761 114356 99.9 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 18.848 Å2
Baniso -1Baniso -2Baniso -3
1--0.01 Å20 Å20 Å2
2--0.01 Å20 Å2
3---0 Å2
Refinement stepCycle: 1 / Resolution: 1.7→49.46 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6770 0 141 666 7577
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0250.0197135
X-RAY DIFFRACTIONr_bond_other_d0.0020.026379
X-RAY DIFFRACTIONr_angle_refined_deg2.1581.9439688
X-RAY DIFFRACTIONr_angle_other_deg1.167314703
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.6165834
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.02424.034352
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.279151084
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.5161526
X-RAY DIFFRACTIONr_chiral_restr0.1470.2968
X-RAY DIFFRACTIONr_gen_planes_refined0.0130.0218076
X-RAY DIFFRACTIONr_gen_planes_other0.0020.021790
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_it1.8461.6823342
X-RAY DIFFRACTIONr_mcbond_other1.8461.6813341
X-RAY DIFFRACTIONr_mcangle_it2.3692.5164174
X-RAY DIFFRACTIONr_mcangle_other2.3692.5174175
X-RAY DIFFRACTIONr_scbond_it2.6151.9163793
X-RAY DIFFRACTIONr_scbond_other2.6151.9163793
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other3.7152.7795515
X-RAY DIFFRACTIONr_long_range_B_refined5.21214.8919222
X-RAY DIFFRACTIONr_long_range_B_other5.21214.8939223
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.7→1.744 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.219 470 -
Rwork0.181 8411 -
obs--99.92 %

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