- PDB-2wit: CRYSTAL STRUCTURE OF THE SODIUM-COUPLED GLYCINE BETAINE SYMPORTER... -
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Open data
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Basic information
Entry
Database: PDB / ID: 2wit
Title
CRYSTAL STRUCTURE OF THE SODIUM-COUPLED GLYCINE BETAINE SYMPORTER BETP FROM CORYNEBACTERIUM GLUTAMICUM WITH BOUND SUBSTRATE
Components
GLYCINE BETAINE TRANSPORTER BETP
Keywords
MEMBRANE PROTEIN / CHEMOSENSOR AND OSMOSENSOR / TRIMER / MEMBRANE / TRANSPORT / CELL MEMBRANE / SECONDARY TRANSPORTER / SODIUM COUPLED TRANSPORT / TRANSMEMBRANE / BETAINE TRANSPORT / HYPEROSMOTIC STRESS
Function / homology
Function and homology information
nitrogen compound transport / symporter activity / identical protein binding / metal ion binding / plasma membrane Similarity search - Function
BCCT transporter family / BCCT transporter, conserved site / BCCT, betaine/carnitine/choline family transporter / BCCT family of transporters signature. / Single alpha-helices involved in coiled-coils or other helix-helix interfaces - #430 / Single alpha-helices involved in coiled-coils or other helix-helix interfaces / Up-down Bundle / Mainly Alpha Similarity search - Domain/homology
Type: RAYONIX / Detector: CCD / Date: Feb 12, 2007
Radiation
Monochromator: AL3 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
Wavelength: 0.97944 Å / Relative weight: 1
Reflection
Resolution: 3.35→39.47 Å / Num. obs: 37151 / % possible obs: 90.7 % / Observed criterion σ(I): 1 / Redundancy: 18.9 % / Biso Wilson estimate: 27.351 Å2 / Rmerge(I) obs: 0.1 / Net I/σ(I): 23.2
Reflection shell
Resolution: 3.35→3.55 Å / Redundancy: 1.7 % / Rmerge(I) obs: 0.65 / Mean I/σ(I) obs: 1 / % possible all: 44.1
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Processing
Software
Name
Version
Classification
XDS
datareduction
XSCALE
datascaling
SHELXD
phasing
SHARP
phasing
BUSTER-TNT
2.7.0
refinement
Refinement
Method to determine structure: SAD Starting model: NONE Resolution: 3.35→39.47 Å / Cross valid method: THROUGHOUT / σ(F): 0 Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. NCS IS PRESENT AND WAS USED IN THE REFINEMENT WITH LOCAL STRUCTURE SIMILARITY RESTRAINTS LSSR. SEE PDB FILE REMARK 3 NCS MODEL RESTRAINT ...Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. NCS IS PRESENT AND WAS USED IN THE REFINEMENT WITH LOCAL STRUCTURE SIMILARITY RESTRAINTS LSSR. SEE PDB FILE REMARK 3 NCS MODEL RESTRAINT LSSR REMARK 3 TARGET RESTRAINT LSSR SMART, O. S., M. BRANDL, C. FLENSBURG, P. KELLER, W. PACIOREK, C. VONRHEIN, AND G. BRICOGNE. 2008. REFINEMENT WITH LOCAL STRUCTURE SIMILARITY RESTRAINTS LSSR ENABLES EXPLOITATION OF INFORMATION FROM RELATED STRUCTURES AND FACILITATES USE OF NCS. PRESENTED AT THE ANNUAL MEETING OF THE AMERICAN CRYSTALLOGRAPHIC ASSOCIATION. ABSTRACT TP139, KNOXVILLE TN, U.S.A.
Rfactor
Num. reflection
% reflection
Selection details
Rfree
0.2649
1886
5.08 %
RANDOM
Rwork
0.2568
-
-
-
obs
0.2572
37151
90.44 %
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Displacement parameters
Biso mean: 64.34 Å2
Baniso -1
Baniso -2
Baniso -3
1-
-11.29080734 Å2
0 Å2
0 Å2
2-
-
13.79907882 Å2
0 Å2
3-
-
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-2.50827148 Å2
Refinement step
Cycle: LAST / Resolution: 3.35→39.47 Å
Protein
Nucleic acid
Ligand
Solvent
Total
Num. atoms
11713
0
24
0
11737
Refine LS restraints
Refine-ID
Type
Number
Restraint function
Weight
X-RAY DIFFRACTION
t_bond_d
12029
0.002
2
X-RAY DIFFRACTION
t_angle_deg
16348
0.342
2
X-RAY DIFFRACTION
t_dihedral_angle_d
1910
9.567
0
X-RAY DIFFRACTION
t_incorr_chiral_ct
X-RAY DIFFRACTION
t_pseud_angle
X-RAY DIFFRACTION
t_trig_c_planes
179
0.001
2
X-RAY DIFFRACTION
t_gen_planes
1802
0.006
5
X-RAY DIFFRACTION
t_it
12008
0.526
50
X-RAY DIFFRACTION
t_nbd
43
0.063
5
X-RAY DIFFRACTION
t_omega_torsion
X-RAY DIFFRACTION
t_other_torsion
X-RAY DIFFRACTION
t_improper_torsion
X-RAY DIFFRACTION
t_chiral_improper_torsion
X-RAY DIFFRACTION
t_sum_occupancies
X-RAY DIFFRACTION
t_utility_distance
X-RAY DIFFRACTION
t_utility_angle
X-RAY DIFFRACTION
t_utility_torsion
X-RAY DIFFRACTION
t_ideal_dist_contact
LS refinement shell
Resolution: 3.35→3.55 Å / Total num. of bins used: 9
Rfactor
Num. reflection
% reflection
Rfree
0.2395
140
4.72 %
Rwork
0.2413
2827
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all
0.2412
2967
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obs
-
-
90.44 %
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