- PDB-1vjt: Crystal structure of Alpha-glucosidase (TM0752) from Thermotoga m... -
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Open data
ID or keywords:
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Basic information
Entry
Database: PDB / ID: 1vjt
Title
Crystal structure of Alpha-glucosidase (TM0752) from Thermotoga maritima at 2.50 A resolution
Components
alpha-glucosidase
Keywords
HYDROLASE / TM0752 / ALPHA-GLUCOSIDASE / STRUCTURAL GENOMICS / JCSG / PSI / Protein Structure Initiative / Joint Center for Structural Genomics
Function / homology
Function and homology information
oxidoreductase activity, acting on the CH-OH group of donors, NAD or NADP as acceptor / hydrolase activity, hydrolyzing O-glycosyl compounds / carbohydrate metabolic process / nucleotide binding / metal ion binding Similarity search - Function
: / : / Glycoside hydrolase, family 4 / Glycosyl hydrolase, family 4, C-terminal / Family 4 glycosyl hydrolase / Family 4 glycosyl hydrolase C-terminal domain / Lactate dehydrogenase/glycoside hydrolase, family 4, C-terminal / NAD(P)-binding Rossmann-like Domain / NAD(P)-binding domain superfamily / Rossmann fold ...: / : / Glycoside hydrolase, family 4 / Glycosyl hydrolase, family 4, C-terminal / Family 4 glycosyl hydrolase / Family 4 glycosyl hydrolase C-terminal domain / Lactate dehydrogenase/glycoside hydrolase, family 4, C-terminal / NAD(P)-binding Rossmann-like Domain / NAD(P)-binding domain superfamily / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta Similarity search - Domain/homology
Resolution: 2.5→50 Å / Num. obs: 15162 / % possible obs: 83.34 % / Redundancy: 3.12 % / Biso Wilson estimate: 44.23 Å2 / Rsym value: 0.057 / Net I/σ(I): 19.08
Reflection shell
Resolution: 2.5→2.59 Å / Redundancy: 2.03 % / Mean I/σ(I) obs: 3.11 / Num. unique all: 758 / Rsym value: 0.264 / % possible all: 42.11
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Processing
Software
Name
Version
Classification
DENZO
datareduction
SCALEPACK
datascaling
autoSHARP
phasing
RESOLVE
modelbuilding
REFMAC
5.2.0001
refinement
RESOLVE
phasing
Refinement
Method to determine structure: MAD / Resolution: 2.5→43.64 Å / Cor.coef. Fo:Fc: 0.932 / Cor.coef. Fo:Fc free: 0.878 / SU B: 22.539 / SU ML: 0.237 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R Free: 0.362 Details: 1. HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS 2. THE NICOTINAMIDE MOIETY OF NAD WAS NOT VISIBLE IN THE DENSITY. 3. RESIDUAL POSITIVE DIFFERENCE DENSITY LIES CLOSE TO THE SIDECHAINS OF ...Details: 1. HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS 2. THE NICOTINAMIDE MOIETY OF NAD WAS NOT VISIBLE IN THE DENSITY. 3. RESIDUAL POSITIVE DIFFERENCE DENSITY LIES CLOSE TO THE SIDECHAINS OF THE ACTIVE SITE RESIDUES SER10 AND PHE13.
Rfactor
Num. reflection
% reflection
Selection details
Rfree
0.25602
754
5 %
RANDOM
Rwork
0.1944
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-
-
obs
0.19754
14406
83.33 %
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Solvent computation
Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parameters
Biso mean: 26.232 Å2
Baniso -1
Baniso -2
Baniso -3
1-
1.18 Å2
0 Å2
0.36 Å2
2-
-
-0.33 Å2
0 Å2
3-
-
-
-0.7 Å2
Refinement step
Cycle: LAST / Resolution: 2.5→43.64 Å
Protein
Nucleic acid
Ligand
Solvent
Total
Num. atoms
3872
0
36
48
3956
Refine LS restraints
Refine-ID
Type
Dev ideal
Dev ideal target
Number
X-RAY DIFFRACTION
r_bond_refined_d
0.01
0.022
4018
X-RAY DIFFRACTION
r_bond_other_d
0.001
0.02
3595
X-RAY DIFFRACTION
r_angle_refined_deg
1.171
1.947
5451
X-RAY DIFFRACTION
r_angle_other_deg
0.804
3
8355
X-RAY DIFFRACTION
r_dihedral_angle_1_deg
5.525
5
470
X-RAY DIFFRACTION
r_dihedral_angle_2_deg
39.312
23.582
201
X-RAY DIFFRACTION
r_dihedral_angle_3_deg
17.788
15
698
X-RAY DIFFRACTION
r_dihedral_angle_4_deg
20.348
15
31
X-RAY DIFFRACTION
r_chiral_restr
0.069
0.2
574
X-RAY DIFFRACTION
r_gen_planes_refined
0.003
0.02
4410
X-RAY DIFFRACTION
r_gen_planes_other
0.001
0.02
839
X-RAY DIFFRACTION
r_nbd_refined
0.197
0.2
874
X-RAY DIFFRACTION
r_nbd_other
0.172
0.2
3685
X-RAY DIFFRACTION
r_nbtor_other
0.084
0.2
2338
X-RAY DIFFRACTION
r_xyhbond_nbd_refined
0.145
0.2
107
X-RAY DIFFRACTION
r_symmetry_vdw_refined
0.228
0.2
11
X-RAY DIFFRACTION
r_symmetry_vdw_other
0.269
0.2
42
X-RAY DIFFRACTION
r_symmetry_hbond_refined
0.283
0.2
8
X-RAY DIFFRACTION
r_mcbond_it
0.57
1.5
2546
X-RAY DIFFRACTION
r_mcbond_other
0.082
1.5
946
X-RAY DIFFRACTION
r_mcangle_it
0.816
2
3812
X-RAY DIFFRACTION
r_scbond_it
1.104
3
1881
X-RAY DIFFRACTION
r_scangle_it
1.702
4.5
1639
LS refinement shell
Resolution: 2.495→2.56 Å / Total num. of bins used: 20
Rfactor
Num. reflection
% reflection
Rfree
0.357
19
3.58 %
Rwork
0.273
512
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Refinement TLS params.
Method: refined / Origin x: 59.5753 Å / Origin y: 9.3396 Å / Origin z: 21.7988 Å
11
12
13
21
22
23
31
32
33
T
-0.0468 Å2
-0.0034 Å2
-0.0251 Å2
-
-0.0221 Å2
-0.0208 Å2
-
-
-0.0112 Å2
L
0.2988 °2
-0.1978 °2
-0.0578 °2
-
0.9307 °2
-0.2684 °2
-
-
1.2814 °2
S
0.0067 Å °
0.1826 Å °
-0.0399 Å °
-0.1821 Å °
0.0214 Å °
0.042 Å °
0.0202 Å °
-0.0437 Å °
-0.0281 Å °
Refinement TLS group
Selection: ALL
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