- PDB-3un6: 2.0 Angstrom Crystal Structure of Ligand Binding Component of ABC... -
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Basic information
Entry
Database: PDB / ID: 3un6
Title
2.0 Angstrom Crystal Structure of Ligand Binding Component of ABC-type Import System from Staphylococcus aureus with Zinc bound
Components
ABC transporter substrate-binding protein
Keywords
UNKNOWN FUNCTION / Structural Genomics / Center for Structural Genomics of Infectious Diseases / CSGID / Ligand Binding Component of ABC-type Import System
Function / homology
NMT1-like family / transmembrane transporter activity / Periplasmic binding protein-like II / D-Maltodextrin-Binding Protein; domain 2 / 3-Layer(aba) Sandwich / metal ion binding / Alpha Beta / PHOSPHATE ION / Uncharacterized protein
Type: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Nov 10, 2011 / Details: Mirrors
Radiation
Monochromator: Si {1,1,1} / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
Wavelength: 0.97903 Å / Relative weight: 1
Reflection
Resolution: 2→30 Å / Num. all: 17064 / Num. obs: 17064 / % possible obs: 97.7 % / Observed criterion σ(I): -3 / Redundancy: 4.3 % / Biso Wilson estimate: 25.5 Å2 / Rmerge(I) obs: 0.098 / Net I/σ(I): 14.2
Reflection shell
Resolution: 2→2.03 Å / Redundancy: 3.7 % / Rmerge(I) obs: 0.43 / Mean I/σ(I) obs: 2.7 / Num. unique all: 804 / % possible all: 93.1
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Processing
Software
Name
Version
Classification
Blu-Ice
Max
datacollection
BUCCANEER
modelbuilding
REFMAC
5.5.0102
refinement
HKL-3000
datareduction
HKL-3000
datascaling
BUCCANEER
phasing
Refinement
Method to determine structure: SAD / Resolution: 2.01→28.99 Å / Cor.coef. Fo:Fc: 0.965 / Cor.coef. Fo:Fc free: 0.944 / SU B: 8.328 / SU ML: 0.11 Isotropic thermal model: Thermal Factors Individually Refined Cross valid method: THROUGHOUT / ESU R Free: 0.166 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
Rfactor
Num. reflection
% reflection
Selection details
Rfree
0.20571
865
5.1 %
RANDOM
Rwork
0.16352
-
-
-
all
0.16561
16184
-
-
obs
0.16561
16184
96.67 %
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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
Displacement parameters
Biso mean: 27.013 Å2
Baniso -1
Baniso -2
Baniso -3
1-
2.84 Å2
0 Å2
0.29 Å2
2-
-
-2.18 Å2
0 Å2
3-
-
-
-0.65 Å2
Refinement step
Cycle: LAST / Resolution: 2.01→28.99 Å
Protein
Nucleic acid
Ligand
Solvent
Total
Num. atoms
2320
0
17
105
2442
Refine LS restraints
Refine-ID
Type
Dev ideal
Dev ideal target
Number
X-RAY DIFFRACTION
r_bond_refined_d
0.013
0.021
2424
X-RAY DIFFRACTION
r_bond_other_d
0.001
0.02
1645
X-RAY DIFFRACTION
r_angle_refined_deg
1.424
1.958
3278
X-RAY DIFFRACTION
r_angle_other_deg
0.848
3
4035
X-RAY DIFFRACTION
r_dihedral_angle_1_deg
3.405
5
298
X-RAY DIFFRACTION
r_dihedral_angle_2_deg
33.888
24.643
112
X-RAY DIFFRACTION
r_dihedral_angle_3_deg
11.097
15
433
X-RAY DIFFRACTION
r_dihedral_angle_4_deg
13.794
15
8
X-RAY DIFFRACTION
r_chiral_restr
0.1
0.2
344
X-RAY DIFFRACTION
r_gen_planes_refined
0.005
0.021
2693
X-RAY DIFFRACTION
r_gen_planes_other
0.001
0.02
469
X-RAY DIFFRACTION
r_mcbond_it
1.033
1.5
1471
X-RAY DIFFRACTION
r_mcbond_other
0.313
1.5
597
X-RAY DIFFRACTION
r_mcangle_it
1.84
2
2369
X-RAY DIFFRACTION
r_scbond_it
3.282
3
953
X-RAY DIFFRACTION
r_scangle_it
4.982
4.5
909
LS refinement shell
Resolution: 2.005→2.057 Å / Total num. of bins used: 20
Rfactor
Num. reflection
% reflection
Rfree
0.237
70
-
Rwork
0.213
992
-
obs
-
992
80.27 %
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
0.9848
0.0834
-0.1805
1.3776
-0.3399
1.6035
-0.015
-0.0633
0.0547
0.1451
-0.021
0.0245
-0.0514
-0.0624
0.0359
0.051
0.0061
-0.0244
0.0098
-0.0119
0.0265
-22.9669
11.7647
-5.761
2
1.7066
-0.0853
-0.5788
0.9431
0.027
1.3872
-0.0176
0.065
0.0357
-0.0568
-0.0036
-0.0622
-0.0597
0.0445
0.0212
0.0456
-0.0077
-0.0272
0.022
0.0075
0.0273
-16.839
12.939
-15.8322
3
0.8656
0.2296
-0.0669
2.0875
0.1132
0.7873
-0.0052
0.0807
-0.0046
0.0089
-0.0029
0.1415
0.0451
-0.0733
0.0081
0.0514
0.0002
-0.0221
0.0386
-0.0099
0.0221
-27.0471
9.7933
-13.9531
Refinement TLS group
ID
Refine-ID
Refine TLS-ID
Auth asym-ID
Auth seq-ID
1
X-RAY DIFFRACTION
1
A
34 - 131
2
X-RAY DIFFRACTION
2
A
132 - 257
3
X-RAY DIFFRACTION
3
A
258 - 324
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