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 / cell envelope Sec protein transport complex / protein-exporting ATPase activity / 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 / cell envelope Sec protein transport complex / protein-exporting ATPase activity / 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 / ribosome binding / protein transport / zinc ion binding / ATP binding / identical protein binding / plasma membrane / cytoplasm Similarity search - Function
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 %
+
About Yorodumi
-
News
-
Feb 9, 2022. New format data for meta-information of EMDB entries
New format data for meta-information of EMDB entries
Version 3 of the EMDB header file is now the official format.
The previous official version 1.9 will be removed from the archive.
In the structure databanks used in Yorodumi, some data are registered as the other names, "COVID-19 virus" and "2019-nCoV". Here are the details of the virus and the list of structure data.
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)
EMDB accession codes are about to change! (news from PDBe EMDB page)
The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
The EM Navigator/Yorodumi systems omit the EMD- prefix.
Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator
Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.
Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi