- PDB-4w7z: Tetrameric BAP29 vDED without disulfide bonds -
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Open data
ID or keywords:
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Basic information
Entry
Database: PDB / ID: 4w7z
Title
Tetrameric BAP29 vDED without disulfide bonds
Components
B-cell receptor-associated protein 29
Keywords
TRANSPORT PROTEIN / Coiled coil / nanomaterial
Function / homology
Function and homology information
protein localization to endoplasmic reticulum exit site / endoplasmic reticulum to Golgi vesicle-mediated transport / intracellular protein transport / osteoblast differentiation / apoptotic process / endoplasmic reticulum membrane / membrane Similarity search - Function
B-cell receptor-associated protein 29/31 / BAP29/BAP31, transmembrane domain / Bap31/Bap29 cytoplasmic coiled-coil domain / Bap31/Bap29 transmembrane region / Bap31/Bap29 cytoplasmic coiled-coil domain / Single alpha-helices involved in coiled-coils or other helix-helix interfaces - #110 / Single alpha-helices involved in coiled-coils or other helix-helix interfaces / Up-down Bundle / Mainly Alpha Similarity search - Domain/homology
Mass: 18.015 Da / Num. of mol.: 194 / Source method: isolated from a natural source / Formula: H2O
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Experimental details
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Experiment
Experiment
Method: X-RAY DIFFRACTION
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Sample preparation
Crystal
Density Matthews: 4.65 Å3/Da / Density % sol: 73.57 %
Crystal grow
Temperature: 277.15 K / Method: vapor diffusion / pH: 4.6 Details: The crystal grew in 1.8 M ammonium sulfate, 100 mM Na acetate pH 4.6 and 5 mM TCEP using protein purified in 20 mM Tris pH 8, 150 mM NaCl and 0.5 mM TCEP and concentrated to ~14 mg/mL
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
Wavelength: 0.97949 Å / Relative weight: 1
Reflection
Resolution: 2.2→29.27 Å / Num. obs: 28934 / % possible obs: 98.9 % / Observed criterion σ(I): -3 / Redundancy: 10.1 % / Rsym value: 0.072 / Net I/σ(I): 19.05
Reflection shell
Resolution: 2.2→2.26 Å / Redundancy: 9.7 % / % possible all: 97.1
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Processing
Software
Name
Version
Classification
PHENIX
(phenix.refine: 1.8.2_1309)
refinement
XDS
datareduction
XSCALE
datascaling
PHENIX
phasing
Refinement
Method to determine structure: MOLECULAR REPLACEMENT Starting model: Model at lower resolution build based on selenomethionine SAD phases Resolution: 2.2→29.265 Å / SU ML: 0.16 / Cross valid method: THROUGHOUT / σ(F): 1.36 / Phase error: 20.08 / Stereochemistry target values: ML
Rfactor
Num. reflection
% reflection
Selection details
Rfree
0.201
1192
4.12 %
RANDOM
Rwork
0.1834
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-
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obs
0.1842
28929
98.95 %
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Solvent computation
Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement step
Cycle: LAST / Resolution: 2.2→29.265 Å
Protein
Nucleic acid
Ligand
Solvent
Total
Num. atoms
2017
0
84
194
2295
Refine LS restraints
Refine-ID
Type
Dev ideal
Number
X-RAY DIFFRACTION
f_bond_d
0.008
2110
X-RAY DIFFRACTION
f_angle_d
0.976
2815
X-RAY DIFFRACTION
f_dihedral_angle_d
13.861
862
X-RAY DIFFRACTION
f_chiral_restr
0.063
305
X-RAY DIFFRACTION
f_plane_restr
0.003
357
LS refinement shell
Resolution (Å)
Rfactor Rfree
Num. reflection Rfree
Rfactor Rwork
Num. reflection Rwork
Refine-ID
% reflection obs (%)
2.2001-2.2882
0.2031
131
0.1941
3007
X-RAY DIFFRACTION
98
2.2882-2.3922
0.2455
138
0.177
3007
X-RAY DIFFRACTION
99
2.3922-2.5183
0.1767
127
0.1742
3036
X-RAY DIFFRACTION
99
2.5183-2.676
0.2014
121
0.1758
3055
X-RAY DIFFRACTION
99
2.676-2.8824
0.2146
143
0.1822
3039
X-RAY DIFFRACTION
99
2.8824-3.1722
0.2377
144
0.2021
3063
X-RAY DIFFRACTION
99
3.1722-3.6305
0.1896
122
0.1547
3106
X-RAY DIFFRACTION
99
3.6305-4.5712
0.1432
130
0.1606
3144
X-RAY DIFFRACTION
100
4.5712-29.2677
0.2295
136
0.2197
3280
X-RAY DIFFRACTION
99
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
6.3891
-2.7283
-0.5323
3.4328
0.0609
2.5539
0.1842
-0.0081
-0.6235
-0.3575
-0.2248
0.2954
0.2012
-0.0305
0.0548
0.1604
0.0036
0.0169
0.215
0.0002
0.1479
-28.5317
-32.9523
-13.8982
2
6.2075
-3.252
-1.0326
4.1431
-0.1133
2.4034
0.0536
-0.2009
0.5874
0.0634
-0.1026
-0.4287
-0.368
0.1843
0.0017
0.1997
0.0208
-0.0652
0.1931
-0.0023
0.1833
-27.1939
-22.1152
-11.3313
3
5.2334
-1.3841
-0.8908
2.9999
0.1054
2.4658
0.0931
-0.3712
-0.7165
0.0059
-0.1151
0.1939
0.1761
-0.111
-0.0732
0.2174
-0.0205
0.0191
0.1915
0.0292
0.1448
-29.6266
-33.4343
-7.8907
4
7.3664
-2.4544
-1.4592
3.1169
0.1103
3.0586
0.0347
-0.5123
0.5805
0.096
-0.037
-0.1923
-0.2093
0.1307
-0.0354
0.2699
-0.0027
-0.0616
0.2314
-0.0232
0.1299
-26.6039
-24.6251
-5.7458
Refinement TLS group
ID
Refine-ID
Refine TLS-ID
Selection details
1
X-RAY DIFFRACTION
1
chain 'A'
2
X-RAY DIFFRACTION
2
chain 'B'
3
X-RAY DIFFRACTION
3
chain 'C'
4
X-RAY DIFFRACTION
4
chain 'D'
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