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- PDB-3wq0: Structure of hyperthermophilic family 12 endocellulase from Pyroc... -

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Basic information

Entry
Database: PDB / ID: 3wq0
TitleStructure of hyperthermophilic family 12 endocellulase from Pyrococcus furiosus in complex with gluco-oligosaccharide
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-cellotetraose / Endoglucanase A
Similarity search - Component
Biological speciesPyrococcus furiosus (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.22 Å
AuthorsKataoka, M. / Ishikawa, K.
CitationJournal: To be Published
Title: Structure of hyperthermophilic family 12 endocellulase from Pyrococcus furiosus in complex with gluco-oligosaccharide
Authors: Kataoka, M. / Ishikawa, K.
History
DepositionJan 21, 2014Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Feb 25, 2015Provider: repository / Type: Initial release
Revision 2.0Jul 29, 2020Group: Atomic model / Data collection ...Atomic model / Data collection / 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_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 / _entity.formula_weight / _entity.pdbx_description / _entity.pdbx_number_of_molecules / _entity.src_method / _entity.type / _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_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
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)37,4539
Polymers36,0161
Non-polymers1,4388
Water5,423301
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)57.900, 118.180, 46.700
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-678-

HOH

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Components

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Protein / Sugars , 2 types, 2 molecules A

#1: Protein Endoglucanase A


Mass: 36015.578 Da / Num. of mol.: 1
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
#2: Polysaccharide beta-D-glucopyranose-(1-4)-beta-D-glucopyranose-(1-4)-beta-D-glucopyranose-(1-4)-beta-D-glucopyranose / beta-cellotetraose


Type: oligosaccharide, Oligosaccharide / Class: Metabolism / Mass: 666.578 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: oligosaccharide / References: beta-cellotetraose
DescriptorTypeProgram
DGlcpb1-4DGlcpb1-4DGlcpb1-4DGlcpb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/1,4,3/[a2122h-1b_1-5]/1-1-1-1/a4-b1_b4-c1_c4-d1WURCSPDB2Glycan 1.1.0
[][b-D-Glcp]{[(4+1)][b-D-Glcp]{[(4+1)][b-D-Glcp]{[(4+1)][b-D-Glcp]{}}}}LINUCSPDB-CARE

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Non-polymers , 4 types, 308 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


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


Mass: 92.094 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3H8O3
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 301 / 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: 2.22 Å3/Da / Density % sol: 44.55 % / Mosaicity: 0.36 °
Crystal growTemperature: 303 K / Method: vapor diffusion, hanging drop / pH: 9
Details: 0.12M CHES, 0.5M potassium sodium tartrate, 0.15M 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 19, 2011
RadiationMonochromator: double-crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9 Å / Relative weight: 1
ReflectionResolution: 1.22→16 Å / Num. all: 94867 / Num. obs: 94867 / % possible obs: 98.8 % / Redundancy: 13.6 % / Rsym value: 0.112 / Net I/σ(I): 16.1
Reflection shell

Diffraction-ID: 1 / Rejects: _

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allRpim(I) allRsym valueNet I/σ(I) obs% possible all
1.22-1.2913.90.3582193469138760.0990.3588.1100
1.29-1.36140.2932.4183119131240.0810.2939.4100
1.36-1.4613.80.2183.2171610124030.0610.21811.4100
1.46-1.5813.60.1564.5156567114760.0430.1561499.9
1.58-1.7313.50.1345143977106320.0370.13416.899.7
1.73-1.9313.50.1274.913002096440.0350.12720.599.9
1.93-2.2313.60.1095.611689685810.030.10924.6100
2.23-2.7313.90.0827.410152772830.0230.08226.9100
2.73-3.8613.10.0728.57273455400.0220.07227.996.8
3.86-15.96710.50.0857.42413823080.0290.08524.470.2

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
SCALA3.3.20data scaling
MOLREPphasing
REFMAC5.7.0029refinement
PDB_EXTRACT3.14data extraction
HKL-2000data collection
MOSFLMdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.22→15.97 Å / Cor.coef. Fo:Fc: 0.976 / Cor.coef. Fo:Fc free: 0.967 / WRfactor Rfree: 0.1522 / WRfactor Rwork: 0.1204 / FOM work R set: 0.9358 / SU B: 0.924 / SU ML: 0.019 / SU R Cruickshank DPI: 0.0297 / SU Rfree: 0.0316 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.03 / ESU R Free: 0.032 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT U VALUES
RfactorNum. reflection% reflectionSelection details
Rfree0.146 4746 5 %RANDOM
Rwork0.1172 ---
obs0.1186 94805 98.65 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 159.09 Å2 / Biso mean: 13.564 Å2 / Biso min: 4.18 Å2
Baniso -1Baniso -2Baniso -3
1-0.79 Å2-0 Å2-0 Å2
2---0.03 Å2-0 Å2
3----0.77 Å2
Refinement stepCycle: LAST / Resolution: 1.22→15.97 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2163 0 91 301 2555
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0230.022485
X-RAY DIFFRACTIONr_angle_refined_deg2.2581.983425
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.3195300
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.92324.528106
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.15915368
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.263159
X-RAY DIFFRACTIONr_chiral_restr0.1650.2389
X-RAY DIFFRACTIONr_gen_planes_refined0.0160.0211880
X-RAY DIFFRACTIONr_rigid_bond_restr8.6432485
X-RAY DIFFRACTIONr_sphericity_free53.35591
X-RAY DIFFRACTIONr_sphericity_bonded15.77152623
LS refinement shellResolution: 1.22→1.252 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.164 349 -
Rwork0.128 6611 -
all-6960 -
obs--100 %

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