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- PDB-3wq7: New crystal form of the hyperthermophilic family 12 endo-cellulas... -

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Basic information

Entry
Database: PDB / ID: 3wq7
TitleNew crystal form of the hyperthermophilic family 12 endo-cellulase from Pyrococcus furiosus
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
Biological speciesPyrococcus furiosus (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.68 Å
AuthorsKataoka, M. / Ishikawa, K.
CitationJournal: Acta Crystallogr.,Sect.F / Year: 2014
Title: A new crystal form of a hyperthermophilic endocellulase.
Authors: Kataoka, M. / Ishikawa, K.
History
DepositionJan 23, 2014Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jul 2, 2014Provider: repository / Type: Initial release
Revision 1.1Jul 16, 2014Group: Database references
Revision 1.2Dec 9, 2015Group: Database references
Revision 1.3Nov 22, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 1.4Mar 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_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_alt_id / _pdbx_struct_conn_angle.ptnr1_label_asym_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_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_alt_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 / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_ptnr1_label_alt_id / _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_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

Downloads & links

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Assembly

Deposited unit
A: Endoglucanase A
B: Endoglucanase A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)73,66522
Polymers72,0312
Non-polymers1,63420
Water8,431468
1
A: Endoglucanase A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,38517
Polymers36,0161
Non-polymers1,36916
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Endoglucanase A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,2805
Polymers36,0161
Non-polymers2644
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)134.729, 62.568, 86.284
Angle α, β, γ (deg.)90.000, 95.080, 90.000
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-677-

HOH

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Components

#1: Protein Endoglucanase A


Mass: 36015.578 Da / Num. of mol.: 2
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: Chemical
ChemComp-CA / CALCIUM ION


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


Mass: 92.094 Da / Num. of mol.: 16 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 468 / 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: 2.51 Å3/Da / Density % sol: 51.08 % / Mosaicity: 0.284 ° / Mosaicity esd: 0.002 °
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 5.5
Details: 0.1M CHC, 0.2M lithium sulfate, 5%(v/v) ethanol, pH 5.5, VAPOR DIFFUSION, HANGING DROP, temperature 295.0K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL44XU / Wavelength: 0.9 Å
DetectorType: RAYONIX MX300HE / Detector: CCD / Date: Nov 21, 2013
RadiationMonochromator: double-crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9 Å / Relative weight: 1
ReflectionResolution: 1.68→50 Å / Num. obs: 81623 / % possible obs: 100 % / Redundancy: 3.8 % / Rmerge(I) obs: 0.068 / Χ2: 1.03 / Net I/σ(I): 14.2
Reflection shell

Diffraction-ID: 1 / Rejects: _

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2% possible all
1.68-1.713.80.36740291.081100
1.71-1.743.80.32740791.077100
1.74-1.773.80.28340801.062100
1.77-1.813.80.23340531.036100
1.81-1.853.80.19940741.037100
1.85-1.893.80.17140501.016100
1.89-1.943.80.15240451.033100
1.94-1.993.80.13540711.038100
1.99-2.053.80.12340551.043100
2.05-2.123.80.11540791.013100
2.12-2.193.80.140701.018100
2.19-2.283.80.08640601.011100
2.28-2.383.80.0840991.017100
2.38-2.513.80.07840781.046100
2.51-2.673.80.0840741.003100
2.67-2.873.80.08341181.053100
2.87-3.163.80.06640580.983100
3.16-3.623.80.05441151.00799.9
3.62-4.563.80.04841371.031100
4.56-503.70.04941990.99499.6

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
SCALEPACKdata scaling
MOLREPphasing
REFMAC5.7.0029refinement
PDB_EXTRACT3.14data extraction
HKL-2000data collection
DENZOdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.68→43.01 Å / Cor.coef. Fo:Fc: 0.962 / Cor.coef. Fo:Fc free: 0.946 / WRfactor Rfree: 0.2459 / WRfactor Rwork: 0.2049 / FOM work R set: 0.857 / SU B: 1.826 / SU ML: 0.062 / SU R Cruickshank DPI: 0.091 / SU Rfree: 0.0939 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.091 / ESU R Free: 0.094 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT U VALUES
RfactorNum. reflection% reflectionSelection details
Rfree0.2169 4096 5 %RANDOM
Rwork0.1813 ---
obs0.1831 81582 99.89 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 93.58 Å2 / Biso mean: 27.029 Å2 / Biso min: 7.96 Å2
Baniso -1Baniso -2Baniso -3
1-0.27 Å2-0 Å2-0.03 Å2
2--0.58 Å20 Å2
3----0.84 Å2
Refinement stepCycle: LAST / Resolution: 1.68→43.01 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4334 0 100 468 4902
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0270.024617
X-RAY DIFFRACTIONr_angle_refined_deg2.5381.9586313
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.7715550
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.21724.808208
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.99715694
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.4851516
X-RAY DIFFRACTIONr_chiral_restr0.1990.2699
X-RAY DIFFRACTIONr_gen_planes_refined0.0150.0213526
LS refinement shellResolution: 1.68→1.724 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.298 291 -
Rwork0.244 5673 -
all-5964 -
obs--99.27 %

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