- PDB-3lr1: The crystal structure of the tungstate ABC transporter from Geoba... -
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Open data
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Basic information
Entry
Database: PDB / ID: 3lr1
Title
The crystal structure of the tungstate ABC transporter from Geobacter sulfurreducens
Components
Tungstate ABC transporter, periplasmic tungstate-binding protein
Keywords
TRANSPORT PROTEIN / The tungstate ABC transporter / periplasmic tungstate-binding protein / structural genomics / PSI / MCSG / Protein Structure Initiative / Midwest Center for Structural Genomics
Function / homology
Function and homology information
ATPase-coupled transmembrane transporter activity / outer membrane-bounded periplasmic space Similarity search - Function
Resolution: 1.8→1.847 Å / Redundancy: 7.4 % / Rmerge(I) obs: 0.817 / Mean I/σ(I) obs: 1.88 / Num. unique all: 1554 / % possible all: 96.72
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Processing
Software
Name
Version
Classification
SBC-Collect
datacollection
HKL-3000
phasing
REFMAC
5.5.0102
refinement
HKL-3000
datareduction
HKL-3000
datascaling
Refinement
Method to determine structure: SAD / Resolution: 1.8→49.54 Å / Cor.coef. Fo:Fc: 0.957 / Cor.coef. Fo:Fc free: 0.926 / SU B: 6.939 / SU ML: 0.099 / Cross valid method: THROUGHOUT / ESU R: 0.341 / ESU R Free: 0.155 Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
Rfactor
Num. reflection
% reflection
Selection details
Rfree
0.26527
1068
5.1 %
RANDOM
Rwork
0.18106
-
-
-
obs
0.18516
19739
98.34 %
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all
-
20072
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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: 18.39 Å2
Baniso -1
Baniso -2
Baniso -3
1-
-0.17 Å2
0 Å2
0 Å2
2-
-
-0.97 Å2
0 Å2
3-
-
-
1.14 Å2
Refinement step
Cycle: LAST / Resolution: 1.8→49.54 Å
Protein
Nucleic acid
Ligand
Solvent
Total
Num. atoms
1776
0
8
173
1957
Refine LS restraints
Refine-ID
Type
Dev ideal
Dev ideal target
Number
X-RAY DIFFRACTION
r_bond_refined_d
0.023
0.022
1814
X-RAY DIFFRACTION
r_bond_other_d
0.004
0.02
1241
X-RAY DIFFRACTION
r_angle_refined_deg
1.954
1.977
2447
X-RAY DIFFRACTION
r_angle_other_deg
1.085
3
3047
X-RAY DIFFRACTION
r_dihedral_angle_1_deg
6.916
5
230
X-RAY DIFFRACTION
r_dihedral_angle_2_deg
37.775
24.789
71
X-RAY DIFFRACTION
r_dihedral_angle_3_deg
17.306
15
322
X-RAY DIFFRACTION
r_dihedral_angle_4_deg
17.905
15
7
X-RAY DIFFRACTION
r_chiral_restr
0.14
0.2
277
X-RAY DIFFRACTION
r_gen_planes_refined
0.009
0.021
1991
X-RAY DIFFRACTION
r_gen_planes_other
0.001
0.02
346
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
1.8
1.5
1145
X-RAY DIFFRACTION
r_mcbond_other
0.556
1.5
476
X-RAY DIFFRACTION
r_mcangle_it
2.829
2
1837
X-RAY DIFFRACTION
r_scbond_it
4.707
3
669
X-RAY DIFFRACTION
r_scangle_it
6.86
4.5
610
X-RAY DIFFRACTION
r_rigid_bond_restr
2.028
3
3055
X-RAY DIFFRACTION
r_sphericity_free
X-RAY DIFFRACTION
r_sphericity_bonded
LS refinement shell
Resolution: 1.8→1.847 Å / Total num. of bins used: 20
Rfactor
Num. reflection
% reflection
Rfree
0.31
89
-
Rwork
0.221
1414
-
obs
-
1503
96.72 %
Refinement TLS params.
Method: refined / Origin x: 7.043 Å / Origin y: 15.043 Å / Origin z: 8.062 Å
11
12
13
21
22
23
31
32
33
T
0.0443 Å2
-0.0033 Å2
0.0195 Å2
-
0.0717 Å2
0.0136 Å2
-
-
0.1069 Å2
L
0.8669 °2
-0.05 °2
-0.244 °2
-
0.5024 °2
0.1551 °2
-
-
1.7225 °2
S
-0.0144 Å °
0.1101 Å °
0.0268 Å °
-0.0743 Å °
-0.0132 Å °
-0.064 Å °
-0.0984 Å °
-0.093 Å °
0.0276 Å °
Refinement TLS group
ID
Refine-ID
Refine TLS-ID
Auth asym-ID
Auth seq-ID
1
X-RAY DIFFRACTION
1
A
-1 - 50
2
X-RAY DIFFRACTION
1
A
51 - 100
3
X-RAY DIFFRACTION
1
A
101 - 150
4
X-RAY DIFFRACTION
1
A
151 - 200
5
X-RAY DIFFRACTION
1
A
201 - 233
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