The molecular mechanism of the thermostable alpha-galactosidases AgaA and AgaB explained by X-ray crystallography and mutational studies

Merceron, R., Foucault, M., Haser, R., Mattes, R., Watzlawick, H., Gouet, P.

doi:10.1074/jbc.M112.394114

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X-RAY DIFFRACTION

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4FNQ

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Crystallization

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Crystallization Experiments

Method	VAPOR DIFFUSION, HANGING DROP
pH	6.5
Temperature	292.0
Details	1.7M ammonium sulfate 20mM HEPES, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 292K

Crystal Data

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Unit Cell

Length	(Å)	Angle	(°)
a =	87.3	α =	90
b =	113.1	β =	90
c =	161.6	γ =	90

Space Group

Diffraction

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Diffraction Experiment

Diffrn ID	1
Data Collection Temperature	100

Diffraction Detector

Detector	CCD
Type	MAR CCD 165 mm
Collection Date	2005-06-01

Diffraction Radiation

Monochromator	YALE MIRRORS
Diffraction Protocol	SINGLE WAVELENGTH

Diffraction Source

Source	SYNCHROTRON
Type	ESRF BEAMLINE BM30A
Wavelength List	0.98
Site	ESRF
Beamline	BM30A

Refinement Data

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Reflection Details

Observed Criterion Sigma (F)	0.0
Observed Criterion Sigma(I)	-3.0
Resolution(High)	1.7
Resolution(Low)	20
Number Reflections(All)	87928
Number Reflections(Observed)	84878
Percent Possible(Observed)	96.5
B(Isotropic) From Wilson Plot	22.1
Redundancy	5.3

High Resolution Shell Details

Resolution(High)	1.7
Resolution(Low)	1.74
Percent Possible(All)	73.7
R Merge I(Observed)	0.291
Mean I Over Sigma(Observed)	5.1
Redundancy	2.0

Refinement

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Refinement Statistics

Structure Solution Method	MOLECULAR REPLACEMENT
reflnsShellList	1.8
Resolution(Low)	19.471
Cut-off Sigma(F)	1.99
Number of Reflections(all)	84833
Number of Reflections(Observed)	73179
Number of Reflections(R-Free)	3659
Percent Reflections(Observed)	98.75
R-Factor(Observed)	0.1825
R-Work	0.1811
R-Free	0.2089

Temperature Factor Modeling

Anisotropic B[1][1]	0.1456
Anisotropic B[1][2]	0.0
Anisotropic B[1][3]	0.0
Anisotropic B[2][2]	0.0118
Anisotropic B[2][3]	0.0
Anisotropic B[3][3]	-0.1574

Resolution Shells

Refinement method	X-RAY DIFFRACTION
Shell Resolution(High)	1.8
Shell Resolution(Low)	1.8237
Number of Reflections(R-Free)	136
Number of Reflections(R-Work)	2606
R-Factor(R-Work)	0.2202
R-Factor(R-Free)	0.2802
Percent Reflections(Observed)	98.0
Refinement method	X-RAY DIFFRACTION
Shell Resolution(High)	1.8237
Shell Resolution(Low)	1.8486
Number of Reflections(R-Free)	138
Number of Reflections(R-Work)	2615
R-Factor(R-Work)	0.222
R-Factor(R-Free)	0.2154
Percent Reflections(Observed)	98.0
Refinement method	X-RAY DIFFRACTION
Shell Resolution(High)	1.8486
Shell Resolution(Low)	1.875
Number of Reflections(R-Free)	136
Number of Reflections(R-Work)	2584
R-Factor(R-Work)	0.2263
R-Factor(R-Free)	0.2641
Percent Reflections(Observed)	96.0
Refinement method	X-RAY DIFFRACTION
Shell Resolution(High)	1.875
Shell Resolution(Low)	1.903
Number of Reflections(R-Free)	136
Number of Reflections(R-Work)	2583
R-Factor(R-Work)	0.2267
R-Factor(R-Free)	0.2845
Percent Reflections(Observed)	96.0
Refinement method	X-RAY DIFFRACTION
Shell Resolution(High)	1.903
Shell Resolution(Low)	1.9327
Number of Reflections(R-Free)	138
Number of Reflections(R-Work)	2624
R-Factor(R-Work)	0.2137
R-Factor(R-Free)	0.2293
Percent Reflections(Observed)	98.0
Refinement method	X-RAY DIFFRACTION
Shell Resolution(High)	1.9327
Shell Resolution(Low)	1.9644
Number of Reflections(R-Free)	139
Number of Reflections(R-Work)	2640
R-Factor(R-Work)	0.2052
R-Factor(R-Free)	0.221
Percent Reflections(Observed)	99.0
Refinement method	X-RAY DIFFRACTION
Shell Resolution(High)	1.9644
Shell Resolution(Low)	1.9982
Number of Reflections(R-Free)	143
Number of Reflections(R-Work)	2704
R-Factor(R-Work)	0.1842
R-Factor(R-Free)	0.2178
Percent Reflections(Observed)	100.0
Refinement method	X-RAY DIFFRACTION
Shell Resolution(High)	1.9982
Shell Resolution(Low)	2.0345
Number of Reflections(R-Free)	140
Number of Reflections(R-Work)	2671
R-Factor(R-Work)	0.1719
R-Factor(R-Free)	0.2097
Percent Reflections(Observed)	100.0
Refinement method	X-RAY DIFFRACTION
Shell Resolution(High)	2.0345
Shell Resolution(Low)	2.0736
Number of Reflections(R-Free)	143
Number of Reflections(R-Work)	2706
R-Factor(R-Work)	0.1676
R-Factor(R-Free)	0.2181
Percent Reflections(Observed)	100.0
Refinement method	X-RAY DIFFRACTION
Shell Resolution(High)	2.0736
Shell Resolution(Low)	2.1159
Number of Reflections(R-Free)	139
Number of Reflections(R-Work)	2648
R-Factor(R-Work)	0.1672
R-Factor(R-Free)	0.202
Percent Reflections(Observed)	100.0
Refinement method	X-RAY DIFFRACTION
Shell Resolution(High)	2.1159
Shell Resolution(Low)	2.1618
Number of Reflections(R-Free)	141
Number of Reflections(R-Work)	2686
R-Factor(R-Work)	0.179
R-Factor(R-Free)	0.2221
Percent Reflections(Observed)	100.0
Refinement method	X-RAY DIFFRACTION
Shell Resolution(High)	2.1618
Shell Resolution(Low)	2.212
Number of Reflections(R-Free)	140
Number of Reflections(R-Work)	2656
R-Factor(R-Work)	0.1813
R-Factor(R-Free)	0.2119
Percent Reflections(Observed)	99.0
Refinement method	X-RAY DIFFRACTION
Shell Resolution(High)	2.212
Shell Resolution(Low)	2.2673
Number of Reflections(R-Free)	141
Number of Reflections(R-Work)	2681
R-Factor(R-Work)	0.174
R-Factor(R-Free)	0.1829
Percent Reflections(Observed)	99.0
Refinement method	X-RAY DIFFRACTION
Shell Resolution(High)	2.2673
Shell Resolution(Low)	2.3285
Number of Reflections(R-Free)	140
Number of Reflections(R-Work)	2651
R-Factor(R-Work)	0.1764
R-Factor(R-Free)	0.204
Percent Reflections(Observed)	99.0
Refinement method	X-RAY DIFFRACTION
Shell Resolution(High)	2.3285
Shell Resolution(Low)	2.3969
Number of Reflections(R-Free)	141
Number of Reflections(R-Work)	2690
R-Factor(R-Work)	0.1735
R-Factor(R-Free)	0.2314
Percent Reflections(Observed)	99.0
Refinement method	X-RAY DIFFRACTION
Shell Resolution(High)	2.3969
Shell Resolution(Low)	2.4741
Number of Reflections(R-Free)	140
Number of Reflections(R-Work)	2663
R-Factor(R-Work)	0.1806
R-Factor(R-Free)	0.1975
Percent Reflections(Observed)	99.0
Refinement method	X-RAY DIFFRACTION
Shell Resolution(High)	2.4741
Shell Resolution(Low)	2.5623
Number of Reflections(R-Free)	143
Number of Reflections(R-Work)	2710
R-Factor(R-Work)	0.1785
R-Factor(R-Free)	0.1968
Percent Reflections(Observed)	99.0
Refinement method	X-RAY DIFFRACTION
Shell Resolution(High)	2.5623
Shell Resolution(Low)	2.6647
Number of Reflections(R-Free)	140
Number of Reflections(R-Work)	2656
R-Factor(R-Work)	0.1812
R-Factor(R-Free)	0.2142
Percent Reflections(Observed)	99.0
Refinement method	X-RAY DIFFRACTION
Shell Resolution(High)	2.6647
Shell Resolution(Low)	2.7856
Number of Reflections(R-Free)	142
Number of Reflections(R-Work)	2693
R-Factor(R-Work)	0.1784
R-Factor(R-Free)	0.1957
Percent Reflections(Observed)	99.0
Refinement method	X-RAY DIFFRACTION
Shell Resolution(High)	2.7856
Shell Resolution(Low)	2.932
Number of Reflections(R-Free)	142
Number of Reflections(R-Work)	2706
R-Factor(R-Work)	0.1854
R-Factor(R-Free)	0.2224
Percent Reflections(Observed)	99.0
Refinement method	X-RAY DIFFRACTION
Shell Resolution(High)	2.932
Shell Resolution(Low)	3.115
Number of Reflections(R-Free)	142
Number of Reflections(R-Work)	2695
R-Factor(R-Work)	0.1809
R-Factor(R-Free)	0.2003
Percent Reflections(Observed)	99.0
Refinement method	X-RAY DIFFRACTION
Shell Resolution(High)	3.115
Shell Resolution(Low)	3.3544
Number of Reflections(R-Free)	144
Number of Reflections(R-Work)	2731
R-Factor(R-Work)	0.1741
R-Factor(R-Free)	0.206
Percent Reflections(Observed)	100.0
Refinement method	X-RAY DIFFRACTION
Shell Resolution(High)	3.3544
Shell Resolution(Low)	3.6899
Number of Reflections(R-Free)	143
Number of Reflections(R-Work)	2714
R-Factor(R-Work)	0.1668
R-Factor(R-Free)	0.2015
Percent Reflections(Observed)	100.0
Refinement method	X-RAY DIFFRACTION
Shell Resolution(High)	3.6899
Shell Resolution(Low)	4.2191
Number of Reflections(R-Free)	143
Number of Reflections(R-Work)	2730
R-Factor(R-Work)	0.1615
R-Factor(R-Free)	0.1695
Percent Reflections(Observed)	99.0
Refinement method	X-RAY DIFFRACTION
Shell Resolution(High)	4.2191
Shell Resolution(Low)	5.2979
Number of Reflections(R-Free)	144
Number of Reflections(R-Work)	2732
R-Factor(R-Work)	0.1653
R-Factor(R-Free)	0.1808
Percent Reflections(Observed)	98.0
Refinement method	X-RAY DIFFRACTION
Shell Resolution(High)	5.2979
Shell Resolution(Low)	19.4724
Number of Reflections(R-Free)	145
Number of Reflections(R-Work)	2745
R-Factor(R-Work)	0.2111
R-Factor(R-Free)	0.2575
Percent Reflections(Observed)	95.0

RMS Deviations

Parameter Type	Deviation from Ideal
f_plane_restr	0.005
f_chiral_restr	0.083
f_dihedral_angle_d	14.239
f_angle_d	1.172
f_bond_d	0.007

Number of Non-Hydrogen Atoms Used in Refinement

Protein Atoms	5832
Nucleic Acid Atoms	0
Heterogen Atoms	4
Solvent Atoms	396

Software and Computing

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Computing

Data Collection	ADSC Quantum
Data Reduction (intensity integration)	XDS
Data Reduction (data scaling)	XSCALE
Structure Solution	MOLREP
Structure Refinement	PHENIX (phenix.refine: 1.8_1069)

Software

refinement	PHENIX version: (phenix.refine: 1.7.1_743)
model building	MOLREP
data collection	ADSC version: Quantum

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