- PDB-3vx4: Crystal Structure of the Nucleotide-Binding Domain of S. mutans C... -
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Basic information
Entry
Database: PDB / ID: 3vx4
Title
Crystal Structure of the Nucleotide-Binding Domain of S. mutans ComA, a Bifunctional ATP-binding Cassette Transporter Involved in the Quorum-sensing Pathway
Components
Putative ABC transporter, ATP-binding protein ComA
Keywords
TRANSPORT PROTEIN / ABC transporter / ATP Binding
Function / homology
Function and homology information
single-species submerged biofilm formation / ABC-type bacteriocin transporter activity / ATPase-coupled lipid transmembrane transporter activity / cysteine-type peptidase activity / ATP hydrolysis activity / proteolysis / ATP binding / membrane / metal ion binding Similarity search - Function
Peptidase C39, ABC-type bacteriocin transporter / Peptidase C39 family / Peptidase C39, bacteriocin processing / Peptidase family C39 domain profile. / Type 1 protein exporter / ABC transporter transmembrane region / ABC transporter type 1, transmembrane domain / ABC transporter integral membrane type-1 fused domain profile. / ABC transporter type 1, transmembrane domain superfamily / ABC transporter-like, conserved site ...Peptidase C39, ABC-type bacteriocin transporter / Peptidase C39 family / Peptidase C39, bacteriocin processing / Peptidase family C39 domain profile. / Type 1 protein exporter / ABC transporter transmembrane region / ABC transporter type 1, transmembrane domain / ABC transporter integral membrane type-1 fused domain profile. / ABC transporter type 1, transmembrane domain superfamily / ABC transporter-like, conserved site / ABC transporters family signature. / ABC transporter / ABC transporter-like, ATP-binding domain / ATP-binding cassette, ABC transporter-type domain profile. / P-loop containing nucleotide triphosphate hydrolases / ATPases associated with a variety of cellular activities / AAA+ ATPase domain / P-loop containing nucleoside triphosphate hydrolase / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta Similarity search - Domain/homology
Resolution: 2.69→42.43 Å / Cor.coef. Fo:Fc: 0.918 / Cor.coef. Fo:Fc free: 0.864 / SU B: 10.897 / SU ML: 0.225 / Cross valid method: THROUGHOUT / ESU R: 0.623 / ESU R Free: 0.313 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
Rfactor
Num. reflection
% reflection
Selection details
Rfree
0.24816
994
5.1 %
RANDOM
Rwork
0.19097
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obs
0.19393
18432
99.96 %
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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: 23.486 Å2
Baniso -1
Baniso -2
Baniso -3
1-
0.02 Å2
0.01 Å2
-0 Å2
2-
-
0.02 Å2
-0 Å2
3-
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-0.02 Å2
Refinement step
Cycle: LAST / Resolution: 2.69→42.43 Å
Protein
Nucleic acid
Ligand
Solvent
Total
Num. atoms
3702
0
64
148
3914
Refine LS restraints
Refine-ID
Type
Dev ideal
Dev ideal target
Number
X-RAY DIFFRACTION
r_bond_refined_d
0.016
0.02
3812
X-RAY DIFFRACTION
r_angle_refined_deg
1.3
1.998
5147
X-RAY DIFFRACTION
r_dihedral_angle_1_deg
4.529
5
477
X-RAY DIFFRACTION
r_dihedral_angle_2_deg
33.245
25.155
161
X-RAY DIFFRACTION
r_dihedral_angle_3_deg
15.466
15
713
X-RAY DIFFRACTION
r_dihedral_angle_4_deg
19.719
15
20
X-RAY DIFFRACTION
r_chiral_restr
0.028
0.2
591
X-RAY DIFFRACTION
r_gen_planes_refined
0.003
0.02
2750
LS refinement shell
Resolution: 2.69→2.759 Å / Total num. of bins used: 20
Rfactor
Num. reflection
% reflection
Rfree
0.387
69
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Rwork
0.228
1295
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obs
-
-
100 %
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