Escherichia coli SecA, the preprotein translocase dimeric ATPase
Components
Preprotein translocase secA subunit
Keywords
PROTEIN TRANSPORT / ATPase / DNA-RNA helicase / Protein translocation / SecA
Function / homology
Function and homology information
preprotein binding / protein-exporting ATPase activity / cell envelope Sec protein transport complex / protein-secreting ATPase / protein transport by the Sec complex / intracellular protein transmembrane transport / protein import / protein targeting to membrane / protein secretion / protein targeting ...preprotein binding / protein-exporting ATPase activity / cell envelope Sec protein transport complex / protein-secreting ATPase / protein transport by the Sec complex / intracellular protein transmembrane transport / protein import / protein targeting to membrane / protein secretion / protein targeting / ribonucleoprotein complex binding / chaperone-mediated protein folding / cytoplasmic side of plasma membrane / protein transport / ribosome binding / zinc ion binding / ATP binding / identical protein binding / plasma membrane / cytoplasm Similarity search - Function
Protein translocase subunit SecA, preprotein binding domain / Helical scaffold and wing domains of SecA / Helical scaffold and wing domains of SecA / SEC-C motif / SEC-C motif / SecA P-loop domain / SecA, C-terminal helicase domain / cAMP-dependent Protein Kinase, Chain A / Protein translocase subunit SecA / SecA DEAD-like, N-terminal ...Protein translocase subunit SecA, preprotein binding domain / Helical scaffold and wing domains of SecA / Helical scaffold and wing domains of SecA / SEC-C motif / SEC-C motif / SecA P-loop domain / SecA, C-terminal helicase domain / cAMP-dependent Protein Kinase, Chain A / Protein translocase subunit SecA / SecA DEAD-like, N-terminal / SecA Wing/Scaffold / SecA, preprotein cross-linking domain / SecA motor DEAD / SecA conserved site / SecA, Wing/Scaffold superfamily / SecA, preprotein cross-linking domain superfamily / SecA preprotein cross-linking domain / SecA Wing and Scaffold domain / SecA DEAD-like domain / SecA family signature. / SecA family profile. / SecA DEAD-like domain / SecA preprotein cross-linking domain / Helicase, C-terminal / Helicase superfamily 1/2, ATP-binding domain / P-loop containing nucleotide triphosphate hydrolases / Up-down Bundle / Rossmann fold / P-loop containing nucleoside triphosphate hydrolase / Orthogonal Bundle / 3-Layer(aba) Sandwich / Mainly Alpha / Alpha Beta Similarity search - Domain/homology
Mass: 18.015 Da / Num. of mol.: 434 / Source method: isolated from a natural source / Formula: H2O
-
Experimental details
-
Experiment
Experiment
Method: X-RAY DIFFRACTION / Number of used crystals: 2
-
Sample preparation
Crystal
Density Matthews: 2.79 Å3/Da / Density % sol: 55.96 %
-
Data collection
Diffraction
ID
Mean temperature (K)
Crystal-ID
1
100
1
2
100
1
3
1
Diffraction source
Source
Site
Beamline
ID
Wavelength (Å)
SYNCHROTRON
ESRF
ID14-4
1
0.9393
SYNCHROTRON
ESRF
ID14-4
2
0.97955, 0.97939, 0.97550
Detector
Type
ID
Detector
Date
ADSC QUANTUM 4
1
CCD
Aug 2, 2003
ADSC QUANTUM 4
2
CCD
Jun 11, 2004
Radiation
ID
Protocol
Monochromatic (M) / Laue (L)
Scattering type
Wavelength-ID
1
SINGLEWAVELENGTH
M
x-ray
1
2
MAD
M
x-ray
1
Radiation wavelength
ID
Wavelength (Å)
Relative weight
1
0.9393
1
2
0.97955
1
3
0.97939
1
4
0.9755
1
Reflection
Av σ(I) over netI: 6.4 / Number: 481724 / Rmerge(I) obs: 0.096 / Rsym value: 0.096 / D res high: 1.918 Å / D res low: 161.218 Å / Num. obs: 149385 / % possible obs: 88.1 / Redundancy: 3.2 %
ID
1
2
3
Diffraction reflection shell
Highest resolution (Å)
Lowest resolution (Å)
Num. obs
% possible obs (%)
ID
Rmerge(I) obs
Rsym value
Redundancy
6.01
59.95
5526
99.5
1
0.039
0.039
3.4
4.25
6.01
9896
99.8
1
0.045
0.045
3.4
3.47
4.25
12758
100
1
0.053
0.053
3.5
3
3.47
15076
100
1
0.082
0.082
3.6
2.69
3
17091
100
1
0.163
0.163
3.7
2.45
2.69
18789
100
1
0.309
0.309
3.7
2.27
2.45
20491
100
1
0.559
0.559
3.6
2.12
2.27
20158
92.1
1
0.801
0.801
2.9
2
2.12
16788
72.1
1
1.384
1.384
2.3
1.9
2
12812
52.3
1
3.669
3.669
2
6.01
59.95
5526
99.5
2
0.039
0.039
3.4
4.25
6.01
9896
99.8
2
0.045
0.045
3.4
3.47
4.25
12758
100
2
0.053
0.053
3.5
3
3.47
15076
100
2
0.082
0.082
3.6
2.69
3
17091
100
2
0.163
0.163
3.7
2.45
2.69
18789
100
2
0.309
0.309
3.7
2.27
2.45
20491
100
2
0.559
0.559
3.6
2.12
2.27
20158
92.1
2
0.801
0.801
2.9
2
2.12
16788
72.1
2
1.384
1.384
2.3
1.9
2
12812
52.3
2
3.669
3.669
2
6.01
59.95
5526
99.5
3
0.039
0.039
3.4
4.25
6.01
9896
99.8
3
0.045
0.045
3.4
3.47
4.25
12758
100
3
0.053
0.053
3.5
3
3.47
15076
100
3
0.082
0.082
3.6
2.69
3
17091
100
3
0.163
0.163
3.7
2.45
2.69
18789
100
3
0.309
0.309
3.7
2.27
2.45
20491
100
3
0.559
0.559
3.6
2.12
2.27
20158
92.1
3
0.801
0.801
2.9
2
2.12
16788
72.1
3
1.384
1.384
2.3
1.9
2
12812
52.3
3
3.669
3.669
2
Reflection
Resolution: 2→20 Å / Num. all: 144187 / Num. obs: 140049 / % possible obs: 97.13 % / Redundancy: 3.2 % / Biso Wilson estimate: 50.972 Å2 / Rmerge(I) obs: 0.042 / Net I/σ(I): 12.49
Reflection shell
Resolution (Å)
Highest resolution (Å)
Redundancy (%)
Rmerge(I) obs
Mean I/σ(I) obs
Num. measured obs
Num. unique obs
% possible all
2-2.1
2.3
0.352
2.3
32034
16916
86.7
2.1-2.2
0.247
3.1
28757
14955
92.5
2.2-2.3
0.185
3.9
23770
12458
92.5
2.3-2.4
0.139
4.8
20512
10673
94.5
2.4-2.5
0.11
5.7
17661
9176
95.3
2.5-2.7
0.08
7.2
27706
14477
95.8
2.7-3
0.057
11.2
31847
15432
97
3-4
0.046
24.8
89547
24199
98.1
4-5
0.034
33.3
33419
8768
98.6
5-6
0.036
32.7
14595
3829
98
6
0.034
32.1
15064
4162
97
-
Processing
Software
Name
Version
Classification
NB
XSCALE
datascaling
REFMAC
5.2.0005
refinement
PDB_EXTRACT
1.701
dataextraction
XDS
datareduction
MOSFLM
datareduction
CCP4
(SCALA)
datascaling
SHELXD
phasing
SHARP
phasing
Refinement
Method to determine structure: MAD / Resolution: 2→19.98 Å / Cor.coef. Fo:Fc: 0.952 / Cor.coef. Fo:Fc free: 0.928 / SU B: 9.476 / SU ML: 0.135 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.161 / ESU R Free: 0.158 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
Rfactor
Num. reflection
% reflection
Selection details
Rfree
0.261
7010
5 %
RANDOM
Rwork
0.213
-
-
-
all
0.215
144187
-
-
obs
-
140049
97.13 %
-
Solvent computation
Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parameters
Biso mean: 46.246 Å2
Baniso -1
Baniso -2
Baniso -3
1-
0.02 Å2
0 Å2
0 Å2
2-
-
-0.02 Å2
0 Å2
3-
-
-
0.01 Å2
Refinement step
Cycle: LAST / Resolution: 2→19.98 Å
Protein
Nucleic acid
Ligand
Solvent
Total
Num. atoms
11203
0
0
434
11637
Refine LS restraints
Refine-ID
Type
Dev ideal
Dev ideal target
Number
X-RAY DIFFRACTION
r_bond_refined_d
0.029
0.022
11385
X-RAY DIFFRACTION
r_bond_other_d
0.005
0.02
10525
X-RAY DIFFRACTION
r_angle_refined_deg
2.21
1.967
15361
X-RAY DIFFRACTION
r_angle_other_deg
1.084
3
24450
X-RAY DIFFRACTION
r_dihedral_angle_1_deg
8.287
5
1404
X-RAY DIFFRACTION
r_dihedral_angle_2_deg
36.257
24.167
564
X-RAY DIFFRACTION
r_dihedral_angle_3_deg
19.515
15
2102
X-RAY DIFFRACTION
r_dihedral_angle_4_deg
17.722
15
102
X-RAY DIFFRACTION
r_chiral_restr
0.146
0.2
1709
X-RAY DIFFRACTION
r_gen_planes_refined
0.01
0.02
12662
X-RAY DIFFRACTION
r_gen_planes_other
0.002
0.02
2260
X-RAY DIFFRACTION
r_nbd_refined
0.241
0.2
2866
X-RAY DIFFRACTION
r_nbd_other
0.217
0.2
11006
X-RAY DIFFRACTION
r_nbtor_refined
0.186
0.2
5445
X-RAY DIFFRACTION
r_nbtor_other
0.096
0.2
6639
X-RAY DIFFRACTION
r_xyhbond_nbd_refined
0.215
0.2
537
X-RAY DIFFRACTION
r_xyhbond_nbd_other
0.11
0.2
10
X-RAY DIFFRACTION
r_symmetry_vdw_refined
0.232
0.2
42
X-RAY DIFFRACTION
r_symmetry_vdw_other
0.263
0.2
191
X-RAY DIFFRACTION
r_symmetry_hbond_refined
0.343
0.2
9
X-RAY DIFFRACTION
r_mcbond_it
2.102
1.5
8899
X-RAY DIFFRACTION
r_mcbond_other
0.377
1.5
2850
X-RAY DIFFRACTION
r_mcangle_it
2.207
2
11280
X-RAY DIFFRACTION
r_scbond_it
3.626
3
4944
X-RAY DIFFRACTION
r_scangle_it
5.085
4.5
4081
LS refinement shell
Resolution: 2→2.052 Å / Total num. of bins used: 20
Rfactor
Num. reflection
% reflection
Rfree
0.31
491
-
Rwork
0.282
9587
-
obs
-
10078
95.37 %
+
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