- PDB-3a2a: The structure of the carboxyl-terminal domain of the human voltag... -
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Basic information
Entry
Database: PDB / ID: 3a2a
Title
The structure of the carboxyl-terminal domain of the human voltage-gated proton channel Hv1
Components
Voltage-gated hydrogen channel 1
Keywords
TRANSPORT PROTEIN / voltage-gated proton channel / Alternative splicing / Coiled coil / Ion transport / Ionic channel / Membrane / Transmembrane / Transport / Voltage-gated channel
Function / homology
Function and homology information
Sperm Motility And Taxes / voltage-gated proton channel activity / regulation of acrosome reaction / cellular response to pH / ROS and RNS production in phagocytes / voltage-gated monoatomic cation channel activity / regulation of reactive oxygen species biosynthetic process / response to pH / cellular response to zinc ion / monoatomic ion channel complex ...Sperm Motility And Taxes / voltage-gated proton channel activity / regulation of acrosome reaction / cellular response to pH / ROS and RNS production in phagocytes / voltage-gated monoatomic cation channel activity / regulation of reactive oxygen species biosynthetic process / response to pH / cellular response to zinc ion / monoatomic ion channel complex / response to zinc ion / sperm flagellum / single fertilization / specific granule membrane / positive regulation of superoxide anion generation / proton transmembrane transport / secretory granule membrane / cell redox homeostasis / regulation of intracellular pH / phagocytic vesicle membrane / apical plasma membrane / innate immune response / Neutrophil degranulation / protein homodimerization activity / identical protein binding / membrane / plasma membrane Similarity search - Function
Voltage-gated hydrogen channel 1, C-terminal membrane-localisation domain / Voltage-gated hydrogen channel 1 / C-terminal membrane-localisation domain of ion-channel, VCN1 / Single alpha-helices involved in coiled-coils or other helix-helix interfaces - #170 / Voltage-dependent channel domain superfamily / Single alpha-helices involved in coiled-coils or other helix-helix interfaces / Ion transport domain / Ion transport protein / Up-down Bundle / Mainly Alpha Similarity search - Domain/homology
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
Wavelength: 1 Å / Relative weight: 1
Reflection
Resolution: 2→37.65 Å / Num. obs: 12915 / % possible obs: 100 % / Redundancy: 6.2 % / Biso Wilson estimate: 43.48 Å2 / Rmerge(I) obs: 0.081 / Net I/σ(I): 12
Reflection shell
Resolution: 2→2.11 Å / Redundancy: 6.2 % / Rmerge(I) obs: 0.323 / Mean I/σ(I) obs: 4.5 / % possible all: 100
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Processing
Software
Name
Version
Classification
REFMAC
5.5.0066
refinement
ADSC
Quantum
datacollection
MOSFLM
datareduction
SCALA
datascaling
SOLVE
phasing
Refinement
Method to determine structure: MIR / Resolution: 2→37.65 Å / Cor.coef. Fo:Fc: 0.919 / Cor.coef. Fo:Fc free: 0.925 / SU B: 3.684 / SU ML: 0.099 / Cross valid method: THROUGHOUT / ESU R: 0.052 / ESU R Free: 0.04 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
Rfactor
Num. reflection
% reflection
Selection details
Rfree
0.26621
630
4.9 %
RANDOM
Rwork
0.25191
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-
-
obs
0.25259
12236
99.98 %
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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: 34.952 Å2
Baniso -1
Baniso -2
Baniso -3
1-
3.47 Å2
0 Å2
0 Å2
2-
-
3.47 Å2
0 Å2
3-
-
-
-6.93 Å2
Refinement step
Cycle: LAST / Resolution: 2→37.65 Å
Protein
Nucleic acid
Ligand
Solvent
Total
Num. atoms
1396
0
2
68
1466
Refine LS restraints
Refine-ID
Type
Dev ideal
Dev ideal target
Number
X-RAY DIFFRACTION
r_bond_refined_d
0.03
0.021
1406
X-RAY DIFFRACTION
r_bond_other_d
X-RAY DIFFRACTION
r_angle_refined_deg
2.314
1.975
1864
X-RAY DIFFRACTION
r_angle_other_deg
X-RAY DIFFRACTION
r_dihedral_angle_1_deg
10.094
5
160
X-RAY DIFFRACTION
r_dihedral_angle_2_deg
31.997
24.5
80
X-RAY DIFFRACTION
r_dihedral_angle_3_deg
22.395
15
328
X-RAY DIFFRACTION
r_dihedral_angle_4_deg
18.676
15
16
X-RAY DIFFRACTION
r_chiral_restr
0.145
0.2
208
X-RAY DIFFRACTION
r_gen_planes_refined
0.01
0.02
1004
X-RAY DIFFRACTION
r_gen_planes_other
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
1.633
1.5
816
X-RAY DIFFRACTION
r_mcbond_other
X-RAY DIFFRACTION
r_mcangle_it
2.729
2
1304
X-RAY DIFFRACTION
r_scbond_it
4.651
3
590
X-RAY DIFFRACTION
r_scangle_it
7.208
4.5
560
X-RAY DIFFRACTION
r_rigid_bond_restr
X-RAY DIFFRACTION
r_sphericity_free
X-RAY DIFFRACTION
r_sphericity_bonded
LS refinement shell
Resolution: 2→2.052 Å / Total num. of bins used: 20
Rfactor
Num. reflection
% reflection
Rfree
0.345
50
-
Rwork
0.27
930
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obs
-
-
99.8 %
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