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- PDB-3wt3: New crystal form of a hyperthermophilic endocellulase -

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Basic information

Entry
Database: PDB / ID: 3wt3
TitleNew crystal form of a hyperthermophilic endocellulase
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: To be Published
Title: A new crystal form of a hyperthermophilic endocellulase
Authors: Kataoka, M. / Ishikawa, K.
History
DepositionApr 7, 2014Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Apr 29, 2015Provider: repository / Type: Initial release
Revision 1.1Mar 20, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_conn_angle / struct_conn / struct_ncs_dom_lim / 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_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_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

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)73,48120
Polymers72,0312
Non-polymers1,45018
Water9,170509
1
A: Endoglucanase A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,01713
Polymers36,0161
Non-polymers1,00112
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Endoglucanase A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,4647
Polymers36,0161
Non-polymers4496
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-660-

HOH

21A-876-

HOH

31A-899-

HOH

Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B

NCS domain segments:

Component-ID: _ / Ens-ID: 1 / Beg auth comp-ID: LYS / Beg label comp-ID: LYS / End auth comp-ID: SER / End label comp-ID: SER / Refine code: _ / Auth seq-ID: 50 - 319 / Label seq-ID: 50 - 319

Dom-IDAuth asym-IDLabel asym-ID
1AA
2BB

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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.: 14 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 509 / 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 buffer, 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
Phasing MRModel details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation4.37 Å42.97 Å
Translation4.37 Å42.97 Å

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
PHASER2.5.1phasing
REFMAC5.7.0029refinement
PDB_EXTRACT3.14data extraction
HKL-2000data collection
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.68→43.01 Å / Cor.coef. Fo:Fc: 0.963 / Cor.coef. Fo:Fc free: 0.946 / WRfactor Rfree: 0.2478 / WRfactor Rwork: 0.2044 / FOM work R set: 0.8563 / SU B: 1.838 / SU ML: 0.062 / SU R Cruickshank DPI: 0.0912 / SU Rfree: 0.0949 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.091 / ESU R Free: 0.095 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT U VALUES
RfactorNum. reflection% reflectionSelection details
Rfree0.2184 4096 5 %RANDOM
Rwork0.1808 ---
obs0.1827 81620 99.78 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 89.9 Å2 / Biso mean: 27.321 Å2 / Biso min: 7.94 Å2
Baniso -1Baniso -2Baniso -3
1-0.27 Å2-0 Å2-0.03 Å2
2--0.59 Å20 Å2
3----0.84 Å2
Refinement stepCycle: LAST / Resolution: 1.68→43.01 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4334 0 88 509 4931
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0250.024617
X-RAY DIFFRACTIONr_angle_refined_deg2.451.9556322
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.6365554
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.31224.904208
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.23315697
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.8241515
X-RAY DIFFRACTIONr_chiral_restr0.1880.2699
X-RAY DIFFRACTIONr_gen_planes_refined0.0140.0213541
Refine LS restraints NCS

Ens-ID: 1 / Number: 346 / Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Rms dev position: 0.19 Å / Weight position: 0.05

Dom-IDAuth asym-ID
1A
2B
LS refinement shellResolution: 1.679→1.723 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.299 280 -
Rwork0.246 5594 -
all-5874 -
obs--97.83 %

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