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- PDB-3vgi: The crystal structure of hyperthermophilic family 12 endocellulas... -

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Basic information

Entry
Database: PDB / ID: 3vgi
TitleThe crystal structure of hyperthermophilic family 12 endocellulase from Pyrococcus furiosus
ComponentsEndoglucanase A
KeywordsHYDROLASE / Beta-jelly roll fold / Carbohydrate/Sugar Binding
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
Biological speciesPyrococcus furiosus (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.07 Å
AuthorsKataoka, M. / Kim, H.-W. / Ishikawa, K.
CitationJournal: Febs Lett. / Year: 2012
Title: Atomic resolution of the crystal structure of the hyperthermophilic family 12 endocellulase and stabilizing role of the DxDxDG calcium-binding motif in Pyrococcus furiosus.
Authors: Kim, H.-W. / Kataoka, M. / Ishikawa, K.
History
DepositionAug 11, 2011Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Sep 12, 2012Provider: repository / Type: Initial release
Revision 1.1Mar 20, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_conn_angle / struct_conn / 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_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_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_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _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: Endoglucanase A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,48315
Polymers36,0161
Non-polymers1,46814
Water5,909328
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)58.014, 118.665, 46.759
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-596-

HOH

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Components

#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
#2: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca
#3: 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
#4: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 11 / Source method: obtained synthetically / Formula: C3H8O3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 328 / 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: 2.23 Å3/Da / Density % sol: 44.95 % / Mosaicity: 0.358 °
Crystal growTemperature: 303 K / Method: vapor diffusion, hanging drop / pH: 9
Details: 0.1M CHES, 0.5M potassium sodium tartrate, 0.05M lithium sulfate, pH 9.0, VAPOR DIFFUSION, HANGING DROP, temperature 303.0K

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
21001
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL44XU / Wavelength: 0.8000, 0.9000
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Jul 14, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.81
20.91
ReflectionResolution: 1.07→50 Å / Num. obs: 130828 / % possible obs: 92.2 % / Redundancy: 9.1 % / Rmerge(I) obs: 0.062 / Χ2: 1.183 / Net I/σ(I): 18.8
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
1.07-1.0950.32456981.0421,281.2
1.09-1.115.30.30158581.0981,283.5
1.11-1.135.70.27459521.0891,285.3
1.13-1.156.10.25260141.0631,285.7
1.15-1.186.30.23360651.0461,286.2
1.18-1.216.50.22561350.9661,287.6
1.21-1.246.80.20662090.8651,288
1.24-1.2770.19762060.961,288.9
1.27-1.317.30.18463861.0331,290.1
1.31-1.357.50.17564291.121,291.5
1.35-1.47.70.16765431.3281,293
1.4-1.458.10.15967131.5781,295
1.45-1.528.60.15168141.9931,296.2
1.52-1.69.10.14168831.9891,297.4
1.6-1.79.60.11970241.5711,298.8
1.7-1.8310.10.09370240.9921,298.9
1.83-2.0110.30.07570700.8791,298.9
2.01-2.3118.60.06771551.11,299.6
2.31-2.918.50.0572480.7971,299.9
2.9-5013.70.04674021.2691,298.1

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Processing

Software
NameVersionClassificationNB
SCALEPACKdata scaling
REFMACrefinement
PDB_EXTRACT3.1data extraction
HKL-2000data collection
HKL-2000data reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.07→50 Å / Cor.coef. Fo:Fc: 0.983 / Cor.coef. Fo:Fc free: 0.976 / WRfactor Rfree: 0.163 / WRfactor Rwork: 0.1325 / Occupancy max: 1 / Occupancy min: 0 / FOM work R set: 0.9184 / SU B: 0.805 / SU ML: 0.017 / SU R Cruickshank DPI: 0.0232 / SU Rfree: 0.0258 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.026 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES
RfactorNum. reflection% reflectionSelection details
Rfree0.1575 6549 5 %RANDOM
Rwork0.127 ---
obs0.1285 130828 92.11 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso max: 215.29 Å2 / Biso mean: 15.8602 Å2 / Biso min: 4.46 Å2
Baniso -1Baniso -2Baniso -3
1-0.83 Å20 Å20 Å2
2--0.14 Å20 Å2
3----0.96 Å2
Refinement stepCycle: LAST / Resolution: 1.07→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2167 0 93 328 2588
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0250.0222393
X-RAY DIFFRACTIONr_angle_refined_deg2.341.9743269
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.2485288
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.99224.563103
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.02515364
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.555159
X-RAY DIFFRACTIONr_chiral_restr0.1640.2353
X-RAY DIFFRACTIONr_gen_planes_refined0.0160.0211788
X-RAY DIFFRACTIONr_mcbond_it2.6531.51396
X-RAY DIFFRACTIONr_mcangle_it3.722295
X-RAY DIFFRACTIONr_scbond_it4.9873997
X-RAY DIFFRACTIONr_scangle_it6.7234.5967
X-RAY DIFFRACTIONr_rigid_bond_restr2.94632393
LS refinement shellResolution: 1.072→1.1 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.234 420 -
Rwork0.198 7913 -
all-8333 -
obs--80.68 %

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