- PDB-4g6c: Crystal structure of beta-hexosaminidase 1 from Burkholderia ceno... -
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Open data
ID or keywords:
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Basic information
Entry
Database: PDB / ID: 4g6c
Title
Crystal structure of beta-hexosaminidase 1 from Burkholderia cenocepacia J2315
Components
Beta-hexosaminidase 1
Keywords
HYDROLASE / SSGCID / NIAID / BETA- HEXOSAMINIDASE / Structural Genomics / National Institute of Allergy and Infectious Diseases / Seattle Structural Genomics Center for Infectious Disease
Function / homology
Function and homology information
beta-N-acetylhexosaminidase activity / beta-N-acetylhexosaminidase / peptidoglycan turnover / N-acetyl-beta-D-galactosaminidase activity / peptidoglycan biosynthetic process / cell wall organization / regulation of cell shape / carbohydrate metabolic process / cell cycle / cell division / cytoplasm Similarity search - Function
Beta-hexosaminidase, bacterial / Glycoside hydrolase, family 3, N-terminal domain / Glycoside hydrolase, family 3, N-terminal / Glycoside hydrolase, family 3, N-terminal domain superfamily / Glycosyl hydrolase family 3 N terminal domain / Glycoside hydrolase superfamily / TIM Barrel / Alpha-Beta Barrel / Alpha Beta Similarity search - Domain/homology
Mass: 18.015 Da / Num. of mol.: 558 / Source method: isolated from a natural source / Formula: H2O
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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: 1.98 Å3/Da / Density % sol: 37.89 %
Crystal grow
Temperature: 289 K / Method: vapor diffusion, sitting drop / pH: 8.5 Details: EBS INTERNAL TRACKING NUMBER 234629B12. : BUCEA.18451.A PW36254 AT 20 MG/ML IN 25 MM HEPES (pH 7.0), 500 mM NaCl, 2 mM DTT, 0.025% sodium azide, 5% glycerol, 0.4 uL x 0.4 uL drop with ...Details: EBS INTERNAL TRACKING NUMBER 234629B12. : BUCEA.18451.A PW36254 AT 20 MG/ML IN 25 MM HEPES (pH 7.0), 500 mM NaCl, 2 mM DTT, 0.025% sodium azide, 5% glycerol, 0.4 uL x 0.4 uL drop with MORPHEUS SCREEN B12: 90 mM Halogens (NaF, NaBr, NaI, 0.1 M Tris/Bicine pH 8.5, 37.5% MPD-PEG1000-PEG3350, VAPOR DIFFUSION, SITTING DROP, temperature 289K
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Data collection
Diffraction
ID
Mean temperature (K)
Crystal-ID
1
100
1
2
100
1
Diffraction source
Source
Site
Beamline
Type
ID
Wavelength
Wavelength (Å)
SYNCHROTRON
SSRL
BL7-1
1
1.03317
1.03317
ROTATING ANODE
RIGAKU FR-E+ SUPERBRIGHT
2
1.54
1.54
Detector
Type
ID
Detector
Date
ADSC QUANTUM 315r
1
CCD
May 31, 2012
RIGAKU SATURN 944+
2
CCD
May 25, 2012
Radiation
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
ID
Wavelength (Å)
Relative weight
1
1.03317
1
2
1.54
1
Reflection
Number: 588960 / Rmerge(I) obs: 0.035 / D res high: 1.7 Å / Num. obs: 123462 / % possible obs: 98.9
Diffraction reflection shell
Highest resolution (Å)
Lowest resolution (Å)
Num. obs
% possible obs (%)
ID
Rmerge(I) obs
1.7
1.74
8203
88.8
1
0.18
1.74
1.79
8865
98.6
1
0.164
1.79
1.84
8611
99.1
1
0.139
1.84
1.9
8475
99.3
1
0.12
1.9
1.96
8259
99.8
1
0.096
1.96
2.03
7990
100
1
0.078
2.03
2.11
7642
100
1
0.068
2.11
2.19
7409
100
1
0.057
2.19
2.29
7073
100
1
0.052
2.29
2.4
6784
100
1
0.045
2.4
2.53
6464
100
1
0.041
2.69
2.87
5723
100
1
0.036
2.87
3.1
5330
100
1
0.033
3.1
3.4
4907
100
1
0.029
3.4
3.8
4447
100
1
0.026
3.8
4.39
3910
100
1
0.025
4.39
5.38
3295
100
1
0.024
5.38
7.6
2556
100
1
0.026
Reflection
Resolution: 1.38→99.7 Å / Num. obs: 118123 / % possible obs: 99.7 % / Observed criterion σ(I): -3 / Biso Wilson estimate: 18.888 Å2 / Rmerge(I) obs: 0.047 / Net I/σ(I): 22.51
Reflection shell
Resolution (Å)
Rmerge(I) obs
Mean I/σ(I) obs
Num. measured obs
Num. unique obs
Diffraction-ID
% possible all
1.38-1.42
0.492
3.6
47521
8708
1
99.9
1.42-1.45
0.403
4.42
46622
8508
1
99.9
1.45-1.5
0.332
5.38
45485
8288
1
99.9
1.5-1.54
0.254
6.93
44160
8009
1
99.8
1.54-1.59
0.213
8.36
43075
7787
1
99.8
1.59-1.65
0.167
10.49
41699
7523
1
99.9
1.65-1.71
0.14
12.44
40479
7278
1
99.8
1.71-1.78
0.11
15.2
39029
6991
1
99.8
1.78-1.86
0.087
18.55
37686
6746
1
99.8
1.86-1.95
0.065
23.57
36046
6419
1
99.8
1.95-2.06
0.051
29.06
33954
6072
1
99.8
2.06-2.18
0.043
33.84
32457
5785
1
99.7
2.18-2.33
0.037
38.04
30528
5437
1
99.8
2.33-2.52
0.033
42.75
27996
5029
1
99.8
2.52-2.76
0.031
46.41
25698
4667
1
99.6
2.76-3.09
0.027
50.3
22577
4239
1
99.8
3.09-3.56
0.023
58.26
20782
3726
1
100
3.56-4.36
0.022
62.87
17424
3172
1
99.9
4.36-6.17
0.022
62.64
13369
2471
1
99.9
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Phasing
Phasing
Method
SAD
molecular replacement
Phasing MR
Model details: Phaser MODE: MR_AUTO
Highest resolution
Lowest resolution
Rotation
2.5 Å
19.7 Å
Translation
2.5 Å
19.7 Å
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Processing
Software
Name
Version
Classification
NB
XSCALE
datascaling
PHASER
2.3.0
phasing
REFMAC
refinement
PDB_EXTRACT
3.11
dataextraction
XDS
datareduction
Refinement
Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.38→99.7 Å / Cor.coef. Fo:Fc: 0.969 / Cor.coef. Fo:Fc free: 0.956 / WRfactor Rfree: 0.1892 / WRfactor Rwork: 0.1668 / Occupancy max: 1 / Occupancy min: 0.5 / FOM work R set: 0.8823 / SU B: 1.968 / SU ML: 0.036 / SU R Cruickshank DPI: 0.0599 / SU Rfree: 0.0608 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.065 / ESU R Free: 0.059 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT U VALUES : WITH TLS ADDED
Rfactor
Num. reflection
% reflection
Selection details
Rfree
0.188
5916
5 %
RANDOM
Rwork
0.155
-
-
-
obs
0.157
118094
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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: MASK
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