- PDB-3dgt: The 1.5 A crystal structure of endo-1,3-beta-glucanase from Strep... -
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Open data
ID or keywords:
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Basic information
Entry
Database: PDB / ID: 3dgt
Title
The 1.5 A crystal structure of endo-1,3-beta-glucanase from Streptomyces sioyaensis
Components
Endo-1,3-beta-glucanase
Keywords
HYDROLASE / GHF16 / 1 / 3-beta-glucanase
Function / homology
Function and homology information
hydrolase activity, hydrolyzing O-glycosyl compounds / carbohydrate binding / carbohydrate metabolic process / metal ion binding Similarity search - Function
Cellulose binding, type IV / Cellulose Binding Domain Type IV / Carbohydrate binding module (family 6) / Glycosyl hydrolases family 16 / Glycoside hydrolase family 16 / Glycosyl hydrolases family 16 (GH16) domain profile. / CBM6 (carbohydrate binding type-6) domain profile. / Carbohydrate binding module family 6 / Twin arginine translocation (Tat) signal profile. / Twin-arginine translocation pathway, signal sequence ...Cellulose binding, type IV / Cellulose Binding Domain Type IV / Carbohydrate binding module (family 6) / Glycosyl hydrolases family 16 / Glycoside hydrolase family 16 / Glycosyl hydrolases family 16 (GH16) domain profile. / CBM6 (carbohydrate binding type-6) domain profile. / Carbohydrate binding module family 6 / Twin arginine translocation (Tat) signal profile. / Twin-arginine translocation pathway, signal sequence / Jelly Rolls - #200 / Galactose-binding-like domain superfamily / Concanavalin A-like lectin/glucanase domain superfamily / Jelly Rolls / Sandwich / Mainly Beta Similarity search - Domain/homology
Mass: 18.015 Da / Num. of mol.: 150 / Source method: isolated from a natural source / Formula: H2O
Sequence details
THERE ARE CONFLICTS BETWEEN THE GIVEN SEQUENCE AND THE DATABASE REFERENCE SEQUENCE. THESE RESIDUES ...THERE ARE CONFLICTS BETWEEN THE GIVEN SEQUENCE AND THE DATABASE REFERENCE SEQUENCE. THESE RESIDUES IDENTIFIED IN THE STRUCTURE DETERMINTION WORK SOULD BE THE CORRECT SEQUENCE OF THE PROTEIN. THE DEPOSITORS ALSO DID THE SEQUENCING OF THE PLASMID AND CONFIRMED THESE RESIDUE SEQUENCES ARE CONSISTENT WITH THE X-RAY STRUCTURE.
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Experimental details
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Experiment
Experiment
Method: X-RAY DIFFRACTION / Number of used crystals: 1
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Sample preparation
Crystal
Density Matthews: 2.03 Å3/Da / Density % sol: 39.54 %
Monochromator: MSC blue-optics / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
Wavelength: 1.5418 Å / Relative weight: 1
Reflection
Resolution: 1.5→20 Å / Num. obs: 38840 / % possible obs: 99 % / Observed criterion σ(I): -3 / Redundancy: 4.2 % / Biso Wilson estimate: 10.246 Å2 / Rmerge(I) obs: 0.048 / Net I/σ(I): 34.8
Reflection shell
Resolution: 1.5→1.57 Å / Redundancy: 3.39 % / Rmerge(I) obs: 0.098 / Mean I/σ(I) obs: 14.4 / Num. unique all: 4632 / % possible all: 96.3
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Processing
Software
Name
Version
Classification
REFMAC
5.2.0019
refinement
CrystalClear
datacollection
DENZO
datareduction
SCALEPACK
datascaling
SHELXCD
phasing
SHELXE
modelbuilding
Refinement
Method to determine structure: SAD / Resolution: 1.5→19.75 Å / Cor.coef. Fo:Fc: 0.945 / Cor.coef. Fo:Fc free: 0.939 / SU B: 1.016 / SU ML: 0.04 / Cross valid method: THROUGHOUT / ESU R: 0.079 / ESU R Free: 0.074 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
Rfactor
Num. reflection
% reflection
Selection details
Rfree
0.19832
1949
5 %
RANDOM
Rwork
0.18284
-
-
-
obs
0.18361
36838
99.03 %
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Solvent computation
Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parameters
Biso mean: 13.559 Å2
Baniso -1
Baniso -2
Baniso -3
1-
-0.01 Å2
0 Å2
0 Å2
2-
-
0 Å2
0 Å2
3-
-
-
0 Å2
Refinement step
Cycle: LAST / Resolution: 1.5→19.75 Å
Protein
Nucleic acid
Ligand
Solvent
Total
Num. atoms
2053
0
1
150
2204
Refine LS restraints
Refine-ID
Type
Dev ideal
Dev ideal target
Number
X-RAY DIFFRACTION
r_bond_refined_d
0.008
0.021
2117
X-RAY DIFFRACTION
r_bond_other_d
X-RAY DIFFRACTION
r_angle_refined_deg
1.244
1.916
2901
X-RAY DIFFRACTION
r_angle_other_deg
X-RAY DIFFRACTION
r_dihedral_angle_1_deg
6.882
5
277
X-RAY DIFFRACTION
r_dihedral_angle_2_deg
38.268
24.624
93
X-RAY DIFFRACTION
r_dihedral_angle_3_deg
10.491
15
274
X-RAY DIFFRACTION
r_dihedral_angle_4_deg
15.983
15
9
X-RAY DIFFRACTION
r_chiral_restr
0.082
0.2
304
X-RAY DIFFRACTION
r_gen_planes_refined
0.004
0.02
1701
X-RAY DIFFRACTION
r_gen_planes_other
X-RAY DIFFRACTION
r_nbd_refined
0.198
0.2
1005
X-RAY DIFFRACTION
r_nbd_other
X-RAY DIFFRACTION
r_nbtor_refined
0.305
0.2
1459
X-RAY DIFFRACTION
r_nbtor_other
X-RAY DIFFRACTION
r_xyhbond_nbd_refined
0.08
0.2
128
X-RAY DIFFRACTION
r_xyhbond_nbd_other
X-RAY DIFFRACTION
r_metal_ion_refined
X-RAY DIFFRACTION
r_metal_ion_other
X-RAY DIFFRACTION
r_symmetry_vdw_refined
0.163
0.2
35
X-RAY DIFFRACTION
r_symmetry_vdw_other
X-RAY DIFFRACTION
r_symmetry_hbond_refined
0.064
0.2
27
X-RAY DIFFRACTION
r_symmetry_hbond_other
X-RAY DIFFRACTION
r_symmetry_metal_ion_refined
X-RAY DIFFRACTION
r_symmetry_metal_ion_other
X-RAY DIFFRACTION
r_mcbond_it
0.476
1.5
1393
X-RAY DIFFRACTION
r_mcbond_other
X-RAY DIFFRACTION
r_mcangle_it
0.811
2
2196
X-RAY DIFFRACTION
r_scbond_it
1.249
3
849
X-RAY DIFFRACTION
r_scangle_it
1.642
4.5
705
X-RAY DIFFRACTION
r_rigid_bond_restr
X-RAY DIFFRACTION
r_sphericity_free
X-RAY DIFFRACTION
r_sphericity_bonded
LS refinement shell
Resolution: 1.5→1.539 Å / Total num. of bins used: 20
Rfactor
Num. reflection
% reflection
Rfree
0.184
153
-
Rwork
0.158
2559
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obs
-
-
95.19 %
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