- PDB-3b0z: Crystal structure of cytoplasmic domain of FlhB from Salmonella t... -
+
Open data
ID or keywords:
Loading...
-
Basic information
Entry
Database: PDB / ID: 3b0z
Title
Crystal structure of cytoplasmic domain of FlhB from Salmonella typhimurium
Components
(Flagellar biosynthetic protein flhB) x 2
Keywords
PROTEIN TRANSPORT / flagella / type III secretion system / membrane protein
Function / homology
Function and homology information
bacterial-type flagellum assembly / protein secretion / membrane => GO:0016020 / plasma membrane Similarity search - Function
Single alpha-helices involved in coiled-coils or other helix-helix interfaces - #2080 / Flagellar biosynthetic protein FlhB / secretion proteins EscU / name from scop / Type III secretion system substrate exporter / Type III secretion system substrate exporter, C-terminal / FlhB HrpN YscU SpaS Family / Single alpha-helices involved in coiled-coils or other helix-helix interfaces / Helix non-globular / Special ...Single alpha-helices involved in coiled-coils or other helix-helix interfaces - #2080 / Flagellar biosynthetic protein FlhB / secretion proteins EscU / name from scop / Type III secretion system substrate exporter / Type III secretion system substrate exporter, C-terminal / FlhB HrpN YscU SpaS Family / Single alpha-helices involved in coiled-coils or other helix-helix interfaces / Helix non-globular / Special / 3-Layer(aba) Sandwich / Alpha Beta Similarity search - Domain/homology
Mass: 18.015 Da / Num. of mol.: 20 / 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
ID
Density Matthews (Å3/Da)
Density % sol (%)
1
2.29
46.32
2
Crystal grow
Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5 Details: 0.1M sodium cacodylate, 0.2M zinc acetate, 25% propylene glycol, pH 5.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K
-
Data collection
Diffraction
ID
Mean temperature (K)
Crystal-ID
1
100
1
2
100
2
Diffraction source
Source
Site
Beamline
ID
Wavelength (Å)
SYNCHROTRON
SPring-8
BL44XU
1
0.9
SYNCHROTRON
SPring-8
BL44XU
2
0.97894, 0.97919
Detector
Type
ID
Detector
Date
RAYONIX MX225HE
1
CCD
Jul 15, 2010
RAYONIX MX225HE
2
CCD
Jul 15, 2010
Radiation
ID
Monochromator
Protocol
Monochromatic (M) / Laue (L)
Scattering type
Wavelength-ID
1
Si111
SINGLEWAVELENGTH
M
x-ray
1
2
Si111
MAD
M
x-ray
2
Radiation wavelength
ID
Wavelength (Å)
Relative weight
1
0.9
1
2
0.97894
1
3
0.97919
1
Reflection
Resolution: 2.45→40.45 Å / Num. obs: 6875
Reflection shell
Resolution: 2.45→2.58 Å / % possible all: 100
-
Processing
Software
Name
Version
Classification
HKL-2000
datacollection
SHELXCD
phasing
SHELXE
modelbuilding
REFMAC
5.5.0109
refinement
HKL-2000
datareduction
HKL-2000
datascaling
Refinement
Method to determine structure: MAD / Resolution: 2.45→28.07 Å / Cor.coef. Fo:Fc: 0.937 / Cor.coef. Fo:Fc free: 0.918 / SU B: 18.131 / SU ML: 0.202 / Cross valid method: THROUGHOUT / ESU R Free: 0.247 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
Rfactor
Num. reflection
% reflection
Selection details
Rfree
0.24709
346
5.1 %
RANDOM
Rwork
0.23077
-
-
-
obs
0.23163
6416
98.16 %
-
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: 76.147 Å2
Baniso -1
Baniso -2
Baniso -3
1-
0.02 Å2
0 Å2
0 Å2
2-
-
0.02 Å2
0 Å2
3-
-
-
-0.05 Å2
Refinement step
Cycle: LAST / Resolution: 2.45→28.07 Å
Protein
Nucleic acid
Ligand
Solvent
Total
Num. atoms
992
0
4
20
1016
Refine LS restraints
Refine-ID
Type
Dev ideal
Dev ideal target
Number
X-RAY DIFFRACTION
r_bond_refined_d
0.021
0.022
1013
X-RAY DIFFRACTION
r_angle_refined_deg
2.09
1.953
1370
X-RAY DIFFRACTION
r_dihedral_angle_1_deg
8.288
5
123
X-RAY DIFFRACTION
r_dihedral_angle_2_deg
39.01
23.191
47
X-RAY DIFFRACTION
r_dihedral_angle_3_deg
20.003
15
178
X-RAY DIFFRACTION
r_dihedral_angle_4_deg
21.668
15
10
X-RAY DIFFRACTION
r_chiral_restr
0.126
0.2
148
X-RAY DIFFRACTION
r_gen_planes_refined
0.01
0.021
767
X-RAY DIFFRACTION
r_mcbond_it
0.92
1.5
625
X-RAY DIFFRACTION
r_mcangle_it
1.745
2
1001
X-RAY DIFFRACTION
r_scbond_it
2.804
3
388
X-RAY DIFFRACTION
r_scangle_it
4.814
4.5
369
LS refinement shell
Resolution: 2.453→2.516 Å / Total num. of bins used: 20
Rfactor
Num. reflection
% reflection
Rfree
0.302
22
-
Rwork
0.278
393
-
obs
-
-
99.76 %
Refinement TLS params.
Method: refined / Refine-ID: X-RAY DIFFRACTION
ID
L11 (°2)
L12 (°2)
L13 (°2)
L22 (°2)
L23 (°2)
L33 (°2)
S11 (Å °)
S12 (Å °)
S13 (Å °)
S21 (Å °)
S22 (Å °)
S23 (Å °)
S31 (Å °)
S32 (Å °)
S33 (Å °)
T11 (Å2)
T12 (Å2)
T13 (Å2)
T22 (Å2)
T23 (Å2)
T33 (Å2)
Origin x (Å)
Origin y (Å)
Origin z (Å)
1
2.8647
3.3859
-3.04
6.1244
-5.2456
6.6661
-0.1538
-0.3054
-0.5064
-0.2451
-0.0648
-0.3059
0.5336
-0.3527
0.2186
0.1535
-0.0945
-0.037
0.7405
0.0555
0.3406
35.9695
-8.7095
28.1112
2
4.2332
-0.0158
1.2918
4.9885
-0.8158
6.5148
-0.0638
-0.4331
0.164
-0.1875
0.1286
0.1137
-0.4167
-0.5925
-0.0648
0.0558
0.0444
0.0446
0.4347
-0.0214
0.1311
38.1911
9.0329
12.5737
Refinement TLS group
ID
Refine-ID
Refine TLS-ID
Auth asym-ID
Auth seq-ID
1
X-RAY DIFFRACTION
1
A
229 - 269
2
X-RAY DIFFRACTION
2
B
270 - 353
+
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