- PDB-2xi1: Crystal structure of the HIV-1 Nef sequenced from a patient's sample -
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Open data
ID or keywords:
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Basic information
Entry
Database: PDB / ID: 2xi1
Title
Crystal structure of the HIV-1 Nef sequenced from a patient's sample
Components
(NEF) x 2
Keywords
VIRAL PROTEIN / AIDS
Function / homology
Function and homology information
symbiont-mediated suppression of host adaptive immune response / symbiont-mediated suppression of host antigen processing and presentation of peptide antigen via MHC class I / symbiont-mediated suppression of host antigen processing and presentation of peptide antigen via MHC class II / virion component => GO:0044423 / suppression by virus of host autophagy / host cell Golgi membrane / : / SH3 domain binding / GTP binding / host cell plasma membrane ...symbiont-mediated suppression of host adaptive immune response / symbiont-mediated suppression of host antigen processing and presentation of peptide antigen via MHC class I / symbiont-mediated suppression of host antigen processing and presentation of peptide antigen via MHC class II / virion component => GO:0044423 / suppression by virus of host autophagy / host cell Golgi membrane / : / SH3 domain binding / GTP binding / host cell plasma membrane / extracellular region / membrane Similarity search - Function
Type: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Details: VARIMAX-HF
Radiation
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
Wavelength: 1.5418 Å / Relative weight: 1
Reflection
Resolution: 3.5→29.9 Å / Num. obs: 7262 / % possible obs: 93 % / Observed criterion σ(I): 2 / Redundancy: 5.7 % / Biso Wilson estimate: 56.37 Å2 / Rmerge(I) obs: 0.12 / Net I/σ(I): 7.1
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Processing
Software
Name
Version
Classification
PHENIX
(PHENIX.REFINE)
refinement
MOSFLM
datareduction
SCALA
datascaling
Refinement
Method to determine structure: OTHER Starting model: NONE Resolution: 3.5→29.551 Å / SU ML: 0.45 / σ(F): 1.36 / Phase error: 26.11 / Stereochemistry target values: ML / Details: 1-75 AND 152-178 ARE DISORDERED
Rfactor
Num. reflection
% reflection
Rfree
0.288
331
4.6 %
Rwork
0.2239
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obs
0.2268
7239
92.99 %
Solvent computation
Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 34.873 Å2 / ksol: 0.335 e/Å3
Displacement parameters
Biso mean: 37 Å2
Baniso -1
Baniso -2
Baniso -3
1-
0 Å2
0 Å2
0 Å2
2-
-
0 Å2
0 Å2
3-
-
-
0 Å2
Refinement step
Cycle: LAST / Resolution: 3.5→29.551 Å
Protein
Nucleic acid
Ligand
Solvent
Total
Num. atoms
1681
0
0
0
1681
Refine LS restraints
Refine-ID
Type
Dev ideal
Number
X-RAY DIFFRACTION
f_bond_d
0.01
1747
X-RAY DIFFRACTION
f_angle_d
1.393
2372
X-RAY DIFFRACTION
f_dihedral_angle_d
19.225
608
X-RAY DIFFRACTION
f_chiral_restr
0.075
235
X-RAY DIFFRACTION
f_plane_restr
0.008
294
LS refinement shell
Resolution (Å)
Rfactor Rfree
Num. reflection Rfree
Rfactor Rwork
Num. reflection Rwork
Refine-ID
% reflection obs (%)
3.5001-4.4075
0.2894
156
0.219
3280
X-RAY DIFFRACTION
91
4.4075-29.5519
0.2867
175
0.2273
3628
X-RAY DIFFRACTION
95
Refinement TLS params.
Method: refined / Origin x: -35.9128 Å / Origin y: 40.169 Å / Origin z: 10.8204 Å
11
12
13
21
22
23
31
32
33
T
0.106 Å2
-0.0405 Å2
-0.0282 Å2
-
0.1779 Å2
0.0557 Å2
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-
0.1009 Å2
L
0.9383 °2
0.3268 °2
0.0565 °2
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1.1059 °2
0.022 °2
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-
0.749 °2
S
0.0649 Å °
-0.328 Å °
-0.1363 Å °
0.3199 Å °
-0.179 Å °
0.0845 Å °
0.086 Å °
-0.0703 Å °
-0.2082 Å °
Refinement TLS group
Selection details: ALL
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