Crystal structure of Staphylococcal nuclease variant D+PHS/V23E at pH 6 determined at 100 K
Components
Thermonuclease
Keywords
HYDROLASE / hyperstable / nuclease / pdTp
Function / homology
Function and homology information
endonuclease activity, active with either ribo- or deoxyribonucleic acids and producing 3'-phosphomonoesters / micrococcal nuclease / nucleic acid binding / extracellular region / membrane / metal ion binding Similarity search - Function
Thermonuclease family signature 1. / OB fold (Dihydrolipoamide Acetyltransferase, E2P) - #90 / Thermonuclease active site / Thermonuclease family signature 2. / Staphylococcal nuclease (SNase-like), OB-fold / Staphylococcal nuclease homologue / Thermonuclease domain profile. / Staphylococcal nuclease homologues / SNase-like, OB-fold superfamily / OB fold (Dihydrolipoamide Acetyltransferase, E2P) ...Thermonuclease family signature 1. / OB fold (Dihydrolipoamide Acetyltransferase, E2P) - #90 / Thermonuclease active site / Thermonuclease family signature 2. / Staphylococcal nuclease (SNase-like), OB-fold / Staphylococcal nuclease homologue / Thermonuclease domain profile. / Staphylococcal nuclease homologues / SNase-like, OB-fold superfamily / OB fold (Dihydrolipoamide Acetyltransferase, E2P) / Beta Barrel / Mainly Beta Similarity search - Domain/homology
Mass: 18.015 Da / Num. of mol.: 76 / 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: 2.18 Å3/Da / Density % sol: 43.47 %
Crystal grow
Temperature: 277 K / pH: 6 Details: 22% MPD, 25 mM Potassium Phosphate, pdTp, CaCl2, pH 6, VAPOR DIFFUSION, HANGING DROP, temperature 277K
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Data collection
Diffraction
Mean temperature: 100 K
Diffraction source
Source: SEALED TUBE / Wavelength: 1.5418
Detector
Type: APEX II CCD / Detector: CCD / Date: Dec 14, 2009 / Details: MULTI-LAYER OPTICS
Radiation
Monochromator: GE111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
Wavelength: 1.5418 Å / Relative weight: 1
Reflection
Resolution: 1.9→37.51 Å / Num. obs: 11002 / % possible obs: 99.6 % / Observed criterion σ(I): 0 / Redundancy: 12.13 % / Biso Wilson estimate: 29.9 Å2 / Rmerge(I) obs: 0.0365 / Net I/σ(I): 41.19
Reflection shell
Resolution: 1.9→1.94 Å / Redundancy: 5.21 % / Rmerge(I) obs: 0.2139 / Mean I/σ(I) obs: 5.68 / % possible all: 99.7
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Processing
Software
Name
Version
Classification
APEX
datacollection
PHASER
phasing
REFMAC
5.5.0110
refinement
SAINT
datareduction
XPREP
datareduction
Refinement
Method to determine structure: MOLECULAR REPLACEMENT Starting model: 3BDC WITH NON-PROTEIN ATOMS REMOVED, B-FACTORS SET TO 20 AND RESIDUES 23,113-116 CHANGED TO ALA
Resolution: 1.9→37.51 Å / Cor.coef. Fo:Fc: 0.953 / Cor.coef. Fo:Fc free: 0.935 / SU B: 6.44 / SU ML: 0.108 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.144 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
Rfactor
Num. reflection
% reflection
Selection details
Rfree
0.227
528
4.8 %
RANDOM
Rwork
0.187
-
-
-
obs
0.189
10474
100 %
-
all
-
10474
-
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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: MASK
Displacement parameters
Biso mean: 41.46 Å2
Baniso -1
Baniso -2
Baniso -3
1-
-0.12 Å2
0 Å2
0.15 Å2
2-
-
-0.02 Å2
0 Å2
3-
-
-
0.16 Å2
Refinement step
Cycle: LAST / Resolution: 1.9→37.51 Å
Protein
Nucleic acid
Ligand
Solvent
Total
Num. atoms
1035
0
26
76
1137
Refine LS restraints
Refine-ID
Type
Dev ideal
Dev ideal target
Number
X-RAY DIFFRACTION
r_bond_refined_d
0.018
0.022
1079
X-RAY DIFFRACTION
r_bond_other_d
X-RAY DIFFRACTION
r_angle_refined_deg
1.695
2.006
1451
X-RAY DIFFRACTION
r_angle_other_deg
X-RAY DIFFRACTION
r_dihedral_angle_1_deg
6.546
5
128
X-RAY DIFFRACTION
r_dihedral_angle_2_deg
35.259
25
48
X-RAY DIFFRACTION
r_dihedral_angle_3_deg
16.444
15
209
X-RAY DIFFRACTION
r_dihedral_angle_4_deg
6.915
15
5
X-RAY DIFFRACTION
r_chiral_restr
0.133
0.2
154
X-RAY DIFFRACTION
r_gen_planes_refined
0.011
0.021
785
X-RAY DIFFRACTION
r_gen_planes_other
X-RAY DIFFRACTION
r_nbd_refined
X-RAY DIFFRACTION
r_nbd_other
X-RAY DIFFRACTION
r_nbtor_refined
X-RAY DIFFRACTION
r_nbtor_other
X-RAY DIFFRACTION
r_xyhbond_nbd_refined
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
X-RAY DIFFRACTION
r_symmetry_vdw_other
X-RAY DIFFRACTION
r_symmetry_hbond_refined
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
1.467
1.5
639
X-RAY DIFFRACTION
r_mcbond_other
X-RAY DIFFRACTION
r_mcangle_it
2.522
2
1020
X-RAY DIFFRACTION
r_scbond_it
3.518
3
440
X-RAY DIFFRACTION
r_scangle_it
5.523
4.5
431
X-RAY DIFFRACTION
r_rigid_bond_restr
X-RAY DIFFRACTION
r_sphericity_free
X-RAY DIFFRACTION
r_sphericity_bonded
LS refinement shell
Resolution: 1.9→1.95 Å / Total num. of bins used: 20
Rfactor
Num. reflection
% reflection
Rfree
0.324
46
-
Rwork
0.213
776
-
obs
-
-
99.52 %
Refinement TLS params.
Method: refined / Refine-ID: X-RAY DIFFRACTION
ID
L11 (°2)
L12 (°2)
L13 (°2)
L22 (°2)
L23 (°2)
L33 (°2)
S11 (Å °)
S12 (Å °)
S13 (Å °)
S21 (Å °)
S22 (Å °)
S23 (Å °)
S31 (Å °)
S32 (Å °)
S33 (Å °)
T11 (Å2)
T12 (Å2)
T13 (Å2)
T22 (Å2)
T23 (Å2)
T33 (Å2)
Origin x (Å)
Origin y (Å)
Origin z (Å)
1
2.6811
-0.9278
-0.3643
1.6046
0.3817
-0.1394
-0.1357
-0.081
-0.3107
0.0863
0.0381
0.0592
0.0104
0.0467
0.0975
0.3097
0.0177
-0.0471
0.255
0.0091
0.2394
11.615
-4.57
3.448
2
1.8878
-1.0752
0.252
1.1336
0.4302
-0.2603
-0.0662
-0.0307
0.0421
0.0359
0.1047
-0.1718
0.0338
0.0143
-0.0385
0.3196
0.0163
-0.0315
0.2882
-0.0137
0.2575
15.268
1.254
4.175
3
5.3953
-1.1129
0.4964
2.3563
2.4891
0.534
-0.8644
-1.9679
-0.3175
0.1785
0.7149
0.1499
0.1295
-0.0667
0.1495
0.4379
0.2342
-0.0368
0.6938
0.0969
0.0653
10.843
4.302
16.301
4
2.3906
-2.3962
-0.1133
4.7576
-0.804
-0.5779
0.3326
0.3932
-0.8897
-0.1739
-0.231
0.5165
-0.1318
0.1207
-0.1017
0.316
-0.0195
-0.111
0.2823
-0.0429
0.3649
7.406
-3.036
-1.443
5
1.7246
0.3164
-0.0815
2.2036
-0.6994
-0.0182
0.0787
0.1626
-0.1519
-0.0339
0.0627
0.016
0.0556
0.0445
-0.1414
0.2999
-0.0092
-0.0104
0.2919
-0.0137
0.2763
12.049
1.795
0.054
6
3.7443
-2.1016
-0.429
1.1664
0.6359
0.6252
0
-0.0189
0.1864
-0.0389
0.1069
0.2353
0.0383
0.0321
-0.1069
0.2994
-0.0198
-0.0427
0.2848
0.0398
0.2484
4.968
9.833
2.633
7
2.5206
0.4704
1.903
1.8618
-0.0442
2.2723
-0.191
-0.2151
0.49
-0.0182
0.1978
0.3253
-0.0562
-0.1135
-0.0068
0.2425
0.0465
0.0389
0.3129
-0.0553
0.3345
-0.675
14.89
10.967
Refinement TLS group
ID
Refine-ID
Refine TLS-ID
Auth asym-ID
Auth seq-ID
1
X-RAY DIFFRACTION
1
A
7 - 20
2
X-RAY DIFFRACTION
2
A
21 - 50
3
X-RAY DIFFRACTION
3
A
51 - 68
4
X-RAY DIFFRACTION
4
A
69 - 80
5
X-RAY DIFFRACTION
5
A
81 - 97
6
X-RAY DIFFRACTION
6
A
98 - 123
7
X-RAY DIFFRACTION
7
A
124 - 141
+
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