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- PDB-3wy6: Structure of hyperthermophilic family 12 endocellulase (E197A) fr... -

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Basic information

Entry
Database: PDB / ID: 3wy6
TitleStructure of hyperthermophilic family 12 endocellulase (E197A) from Pyrococcus furiosus in complex with laminaribiose
ComponentsEndoglucanase A
KeywordsHYDROLASE / Beta-jelly roll / Glycoside hydrolase
Function / homology
Function and homology information


cellulase activity / polysaccharide catabolic process / metal ion binding
Similarity search - Function
Glycoside hydrolase family 12 / Glycosyl hydrolase family 12 / Glycoside hydrolase family 11/12, catalytic domain / Glycoside hydrolase family 11/12 / Concanavalin A-like lectin/glucanase domain superfamily / Jelly Rolls / Sandwich / Mainly Beta
Similarity search - Domain/homology
beta-laminaribiose / beta-D-glucopyranose / Endoglucanase A
Similarity search - Component
Biological speciesPyrococcus furiosus (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.45 Å
AuthorsKataoka, M. / Ishikawa, K.
CitationJournal: To be Published
Title: Structure of hyperthermophilic family 12 endocellulase (E197A) from Pyrococcus furiosus in complex with laminaribiose
Authors: Kataoka, M. / Ishikawa, K.
History
DepositionAug 20, 2014Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Sep 16, 2015Provider: repository / Type: Initial release
Revision 2.0Jul 29, 2020Group: Atomic model / Data collection ...Atomic model / Data collection / Database references / Derived calculations / Structure summary
Category: atom_site / atom_site_anisotrop ...atom_site / atom_site_anisotrop / 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 / pdbx_struct_conn_angle / pdbx_struct_special_symmetry / struct_asym / struct_conn / struct_ref_seq_dif / 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.occupancy / _atom_site.type_symbol / _atom_site_anisotrop.U[1][1] / _atom_site_anisotrop.U[1][2] / _atom_site_anisotrop.U[1][3] / _atom_site_anisotrop.U[2][2] / _atom_site_anisotrop.U[2][3] / _atom_site_anisotrop.U[3][3] / _atom_site_anisotrop.pdbx_auth_asym_id / _atom_site_anisotrop.pdbx_auth_atom_id / _atom_site_anisotrop.pdbx_auth_comp_id / _atom_site_anisotrop.pdbx_auth_seq_id / _atom_site_anisotrop.pdbx_label_asym_id / _atom_site_anisotrop.pdbx_label_atom_id / _atom_site_anisotrop.pdbx_label_comp_id / _atom_site_anisotrop.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_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_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 / _pdbx_struct_special_symmetry.label_asym_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_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_ref_seq_dif.details
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Mar 20, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2
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: Endoglucanase A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,12617
Polymers35,9581
Non-polymers2,16916
Water4,324240
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)58.030, 118.865, 46.873
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP21212
Components on special symmetry positions
IDModelComponents
11A-600-

HOH

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Components

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Protein , 1 types, 1 molecules A

#1: Protein Endoglucanase A


Mass: 35957.543 Da / Num. of mol.: 1 / Mutation: E197A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pyrococcus furiosus (archaea) / Gene: eglA / Production host: Escherichia coli (E. coli) / References: UniProt: Q9V2T0, cellulase

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Sugars , 2 types, 2 molecules

#2: Polysaccharide beta-D-glucopyranose-(1-3)-beta-D-glucopyranose / beta-laminaribiose


Type: oligosaccharide, Oligosaccharide / Class: Antimicrobial / Mass: 342.297 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: oligosaccharide / References: beta-laminaribiose
DescriptorTypeProgram
DGlcpb1-3DGlcpb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/1,2,1/[a2122h-1b_1-5]/1-1/a3-b1WURCSPDB2Glycan 1.1.0
[][b-D-Glcp]{[(3+1)][b-D-Glcp]{}}LINUCSPDB-CARE
#5: Sugar ChemComp-BGC / beta-D-glucopyranose / beta-D-glucose / D-glucose / glucose / Glucose


Type: D-saccharide, beta linking / Mass: 180.156 Da / Num. of mol.: 1
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 , 4 types, 254 molecules

#3: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ca
#4: Chemical
ChemComp-NHE / 2-[N-CYCLOHEXYLAMINO]ETHANE SULFONIC ACID / N-CYCLOHEXYLTAURINE / CHES / CHES (buffer)


Mass: 207.290 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C8H17NO3S / Comment: pH buffer*YM
#6: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C3H8O3
#7: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 240 / 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: 2.25 Å3/Da / Density % sol: 45.28 % / Mosaicity: 0.447 ° / Mosaicity esd: 0.004 °
Crystal growTemperature: 303 K / Method: vapor diffusion, hanging drop / pH: 9
Details: 0.12M CHES, 0.5M potassium sodium tartrate, 0.1M lithium sulfate, pH 9.0, VAPOR DIFFUSION, HANGING DROP, temperature 303.0K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL44XU / Wavelength: 0.9 Å
DetectorType: RAYONIX MX225HE / Detector: CCD / Date: Oct 17, 2012
RadiationMonochromator: double-crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9 Å / Relative weight: 1
ReflectionResolution: 1.45→50 Å / Num. obs: 55555 / % possible obs: 95.6 % / Redundancy: 3.7 % / Rmerge(I) obs: 0.07 / Χ2: 0.981 / Net I/σ(I): 11.2
Reflection shell

Diffraction-ID: 1 / Rejects: 0

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2% possible all
1.45-1.482.70.38425650.79890.7
1.48-1.52.80.35126080.83891.1
1.5-1.532.90.33426180.85390.8
1.53-1.5630.29526180.86291.4
1.56-1.63.10.27326370.91892.2
1.6-1.633.20.24626430.97292.2
1.63-1.673.20.2327060.97693.7
1.67-1.723.30.21226640.99193.2
1.72-1.773.40.18227340.99695
1.77-1.833.50.15627501.04495.9
1.83-1.893.70.12827861.08996.5
1.89-1.973.80.10728421.04597.8
1.97-2.063.90.09628261.03198.3
2.06-2.174.10.09528611.06398.8
2.17-2.34.20.10628831.02198.9
2.3-2.484.20.1229070.9899.3
2.48-2.734.30.11828931.00399
2.73-3.124.40.0829460.98799
3.12-3.944.60.0329690.94899.4
3.94-504.50.02230990.96998.3

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
SCALEPACKdata scaling
MOLREPphasing
REFMAC5.7.0029refinement
PDB_EXTRACT3.15data extraction
HKL-2000data collection
HKL-2000data reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.45→41.55 Å / Cor.coef. Fo:Fc: 0.978 / Cor.coef. Fo:Fc free: 0.963 / WRfactor Rfree: 0.1669 / WRfactor Rwork: 0.1208 / FOM work R set: 0.907 / SU B: 2.387 / SU ML: 0.039 / SU R Cruickshank DPI: 0.0564 / SU Rfree: 0.0595 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.056 / ESU R Free: 0.059 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT U VALUES
RfactorNum. reflection% reflectionSelection details
Rfree0.1779 2790 5 %RANDOM
Rwork0.1255 ---
obs0.1281 55555 95.35 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 124.47 Å2 / Biso mean: 16.696 Å2 / Biso min: 5.27 Å2
Baniso -1Baniso -2Baniso -3
1-0.77 Å2-0 Å2-0 Å2
2---0.06 Å20 Å2
3----0.71 Å2
Refinement stepCycle: LAST / Resolution: 1.45→41.55 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2163 0 137 240 2540
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0240.022447
X-RAY DIFFRACTIONr_angle_refined_deg2.2161.9933356
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.175288
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.82424.854103
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.0315355
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.994157
X-RAY DIFFRACTIONr_chiral_restr0.1740.2381
X-RAY DIFFRACTIONr_gen_planes_refined0.0140.0211814
X-RAY DIFFRACTIONr_rigid_bond_restr6.15832446
X-RAY DIFFRACTIONr_sphericity_free47.729586
X-RAY DIFFRACTIONr_sphericity_bonded16.99852537
LS refinement shellResolution: 1.451→1.488 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.302 177 -
Rwork0.244 3498 -
all-3675 -
obs--86.19 %

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