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- PDB-3wr0: Structure of hyperthermophilic family 12 endocellulase mutant fro... -

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Basic information

Entry
Database: PDB / ID: 3wr0
TitleStructure of hyperthermophilic family 12 endocellulase mutant 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: 1.16 Å
AuthorsKataoka, M. / Ishikawa, K.
CitationJournal: To be Published
Title: Structure of hyperthermophilic family 12 endocellulase mutant from Pyrococcus furiosus
Authors: Kataoka, M. / Ishikawa, K.
History
DepositionFeb 6, 2014Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Mar 11, 2015Provider: 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_ref_seq_dif / 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_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_ref_seq_dif.details / _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)36,7298
Polymers35,9581
Non-polymers7717
Water5,531307
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)57.960, 118.270, 46.690
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-735-

HOH

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Components

#1: Protein Endoglucanase A


Mass: 35957.543 Da / Num. of mol.: 1 / Mutation: E290A
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-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
#3: Chemical ChemComp-CA / CALCIUM ION


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


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


Mass: 18.015 Da / Num. of mol.: 307 / 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: 44.72 % / Mosaicity: 0.43 ° / Mosaicity esd: 0.002 °
Crystal growTemperature: 303 K / Method: vapor diffusion, hanging drop / pH: 9
Details: 0.14M 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: Nov 22, 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: 1.16→16.2 Å / Num. all: 101529 / Num. obs: 101529 / % possible obs: 91.2 % / Redundancy: 12.6 % / Rsym value: 0.101 / Net I/σ(I): 15.7
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
1.16-1.2212.90.3881.9183239142430.110.3887.188.5
1.22-1.3130.3122.3174115134310.0880.3128.388.3
1.3-1.39130.2393164648126660.0670.2399.888.6
1.39-1.512.70.1764.1153197120310.050.1761289.9
1.5-1.6412.20.1315.2140848115440.0370.13115.293.7
1.64-1.8311.90.125.2130847109750.0350.1218.497.9
1.83-2.1212.20.102612119599100.0290.10224.599.5
2.12-2.59130.0758.311014984600.0210.0752999.9
2.59-3.6712.70.05811.57909562250.0170.05830.993.9
3.67-14.784100.079.72037120440.0230.0726.653.3

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALA3.3.20data scaling
MOLREPphasing
REFMAC5.7.0029refinement
PDB_EXTRACT3.14data extraction
HKL-2000data collection
MOSFLMdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.16→16.2 Å / Cor.coef. Fo:Fc: 0.974 / Cor.coef. Fo:Fc free: 0.963 / WRfactor Rfree: 0.1604 / WRfactor Rwork: 0.1264 / FOM work R set: 0.9323 / SU B: 0.852 / SU ML: 0.018 / SU R Cruickshank DPI: 0.0291 / SU Rfree: 0.0316 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.029 / 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
Rfree0.1561 5082 5 %RANDOM
Rwork0.1245 ---
obs0.1261 101470 90.82 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 145.29 Å2 / Biso mean: 14.324 Å2 / Biso min: 4.4 Å2
Baniso -1Baniso -2Baniso -3
1-0.6 Å2-0 Å2-0 Å2
2---0.16 Å2-0 Å2
3----0.44 Å2
Refinement stepCycle: LAST / Resolution: 1.16→16.2 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2163 0 46 307 2516
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0240.022404
X-RAY DIFFRACTIONr_angle_refined_deg2.3441.963307
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.3725295
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.64124.667105
X-RAY DIFFRACTIONr_dihedral_angle_3_deg10.77415362
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.567158
X-RAY DIFFRACTIONr_chiral_restr0.2050.2362
X-RAY DIFFRACTIONr_gen_planes_refined0.0170.0211855
X-RAY DIFFRACTIONr_rigid_bond_restr9.27932404
X-RAY DIFFRACTIONr_sphericity_free41.937596
X-RAY DIFFRACTIONr_sphericity_bonded13.78852568
LS refinement shellResolution: 1.16→1.19 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.186 379 -
Rwork0.144 6779 -
all-7158 -
obs--88.41 %

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