Type: Cyclic peptide / Class: Antibiotic / Mass: 1159.461 Da / Num. of mol.: 1 / Source method: isolated from a natural source Details: GRAMICIDIN S IS A DECAPEPTIDE, RESIDUES 1 AND 10 FORM A PEPTIDE BOND RESULTING IN CYCLIZATION. Source: (natural) Brevibacillus brevis (bacteria) / References: GRAMICIDIN S
Mass: 18.015 Da / Num. of mol.: 9 / Source method: isolated from a natural source / Formula: H2O
Compound details
GRAMICIDIN S IS A CYCLODECAPEPTIDE, CONSTRUCTED AS TWO IDENTICAL PENTAPEPTIDES JOINED HEAD TO TAIL, ...GRAMICIDIN S IS A CYCLODECAPEPTIDE, CONSTRUCTED AS TWO IDENTICAL PENTAPEPTIDES JOINED HEAD TO TAIL, PRODUCED BY THE GRAM POSITIVE BACTERIUM BACILLUS BREVIS HERE, GRAMICIDIN S IS REPRESENTED BY THE SEQUENCE (SEQRES)
Has ligand of interest
N
-
Experimental details
-
Experiment
Experiment
Method: X-RAY DIFFRACTION / Number of used crystals: 1
-
Sample preparation
Crystal
Density Matthews: 1.78 Å3/Da / Density % sol: 30.93 %
Crystal grow
Details: Urea, HCl, 95% Ethanol
-
Data collection
Diffraction
Mean temperature: 293 K / Serial crystal experiment: N
Diffraction source
Source: ROTATING ANODE / Wavelength: 1.5406 Å
Detector
Type: CUSTOM-MADE / Detector: DIFFRACTOMETER / Date: Jan 1, 1978
Radiation
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
Wavelength: 1.5406 Å / Relative weight: 1
Reflection
Resolution: 0.98→22.34 Å / Num. obs: 4028 / % possible obs: 81.1 % / Net I/σ(I): 210
Method to determine structure: AB INITIO PHASING / Resolution: 0.98→22.34 Å / Cor.coef. Fo:Fc: 0.978 / Cor.coef. Fo:Fc free: 0.988 / SU B: 0.276 / SU ML: 0.015 / Cross valid method: FREE R-VALUE / ESU R: 0.026 / ESU R Free: 0.023 Details: Hydrogens have been added in their riding positions. At this resolution the FreeR is often equal to the overall R factor
Rfactor
Num. reflection
% reflection
Selection details
Rfree
0.1318
205
5.089 %
Random selection
Rwork
0.14
3823
-
-
all
0.14
-
-
-
obs
-
4028
80.738 %
-
Solvent computation
Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT
Displacement parameters
Biso mean: 8.88 Å2
Baniso -1
Baniso -2
Baniso -3
1-
0.064 Å2
0.032 Å2
0 Å2
2-
-
0.064 Å2
-0 Å2
3-
-
-
-0.208 Å2
Refinement step
Cycle: LAST / Resolution: 0.98→22.34 Å /
Protein
Nucleic acid
Ligand
Solvent
Total
Num. atoms
82
0
4
9
95
Refine LS restraints
Refine-ID
Type
Dev ideal
Dev ideal target
Number
X-RAY DIFFRACTION
r_bond_refined_d
0.021
0.012
97
X-RAY DIFFRACTION
r_bond_other_d
0.004
0.015
103
X-RAY DIFFRACTION
r_angle_refined_deg
2.196
1.624
134
X-RAY DIFFRACTION
r_angle_other_deg
0.881
1.564
238
X-RAY DIFFRACTION
r_dihedral_angle_1_deg
7.751
5
12
X-RAY DIFFRACTION
r_dihedral_angle_3_deg
9.574
10
15
X-RAY DIFFRACTION
r_dihedral_angle_6_deg
23.292
10
2
X-RAY DIFFRACTION
r_chiral_restr
1.735
0.2
16
X-RAY DIFFRACTION
r_gen_planes_refined
0.013
0.02
104
X-RAY DIFFRACTION
r_gen_planes_other
0.001
0.02
20
X-RAY DIFFRACTION
r_nbd_refined
0.244
0.2
9
X-RAY DIFFRACTION
r_symmetry_nbd_other
0.204
0.2
73
X-RAY DIFFRACTION
r_nbtor_refined
0.221
0.2
42
X-RAY DIFFRACTION
r_symmetry_nbtor_other
0.168
0.2
60
X-RAY DIFFRACTION
r_xyhbond_nbd_refined
0.119
0.2
3
X-RAY DIFFRACTION
r_nbd_other
0.114
0.2
12
X-RAY DIFFRACTION
r_symmetry_xyhbond_nbd_refined
0.118
0.2
3
X-RAY DIFFRACTION
r_mcbond_it
1.023
0.62
46
X-RAY DIFFRACTION
r_mcbond_other
1.02
0.62
45
X-RAY DIFFRACTION
r_mcangle_it
1.336
1.126
58
X-RAY DIFFRACTION
r_mcangle_other
1.332
1.122
59
X-RAY DIFFRACTION
r_scbond_it
2.916
0.965
51
X-RAY DIFFRACTION
r_scbond_other
2.927
0.98
50
X-RAY DIFFRACTION
r_scangle_it
4.176
1.583
76
X-RAY DIFFRACTION
r_scangle_other
4.228
1.597
74
X-RAY DIFFRACTION
r_lrange_it
4.488
8.265
87
X-RAY DIFFRACTION
r_lrange_other
4.54
8.032
87
LS refinement shell
Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20
Resolution (Å)
Rfactor Rfree
Num. reflection Rfree
Rfactor Rwork
Num. reflection Rwork
Rfactor all
Num. reflection all
Fsc free
Fsc work
% reflection obs (%)
WRfactor Rwork
0.98-1.005
0.143
7
0.16
141
0.159
354
0.983
0.983
41.8079
0.16
1.005-1.033
0.095
8
0.15
201
0.147
372
0.997
0.984
56.1828
0.15
1.033-1.063
0.144
17
0.138
206
0.139
318
0.987
0.985
70.1258
0.138
1.063-1.095
0.174
12
0.133
244
0.135
333
0.978
0.988
76.8769
0.133
1.095-1.131
0.152
6
0.145
248
0.145
329
0.974
0.986
77.2037
0.145
1.131-1.171
0.116
17
0.137
229
0.135
310
0.99
0.988
79.3548
0.137
1.171-1.215
0.214
13
0.151
233
0.154
308
0.967
0.985
79.8701
0.151
1.215-1.264
0.14
13
0.142
224
0.142
285
0.986
0.986
83.1579
0.142
1.264-1.32
0.204
14
0.137
225
0.141
279
0.964
0.988
85.6631
0.137
1.32-1.384
0.127
9
0.138
226
0.138
271
0.992
0.986
86.7159
0.138
1.384-1.459
0.134
10
0.14
225
0.14
266
0.99
0.986
88.3459
0.14
1.459-1.547
0.113
7
0.149
215
0.147
240
0.992
0.986
92.5
0.149
1.547-1.653
0.181
19
0.163
194
0.164
233
0.983
0.983
91.4163
0.163
1.653-1.785
0.151
12
0.132
191
0.133
214
0.992
0.989
94.8598
0.132
1.785-1.954
0.112
15
0.124
179
0.123
199
0.993
0.988
97.4874
0.124
1.954-2.183
0.033
5
0.119
177
0.116
185
1
0.992
98.3784
0.119
2.183-2.516
0.089
9
0.143
151
0.139
163
0.997
0.988
98.1595
0.143
2.516-3.072
0.205
5
0.142
138
0.145
145
0.992
0.987
98.6207
0.142
3.072-4.304
0.105
5
0.126
108
0.125
113
0.997
0.989
100
0.126
4.304-22.343
0.145
2
0.17
69
0.169
73
0.998
0.984
97.2603
0.17
+
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Function and homology information
Brevibacillus brevis (bacteria)
X-RAY DIFFRACTION / AB INITIO PHASING / Resolution: 0.98 Å 
Authors
Citation
Structure visualization
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PDBj
Assembly
Type: Cyclic peptide / Class: Antibiotic / Mass: 1159.461 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Mass: 60.055 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: CH4N2O
Mass: 18.015 Da / Num. of mol.: 9 / Source method: isolated from a natural source / Formula: H2O
Sample preparation
Processing