- PDB-2qmq: Crystal structure of a n-myc downstream regulated 2 protein (ndrg... -
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Open data
ID or keywords:
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Basic information
Entry
Database: PDB / ID: 2qmq
Title
Crystal structure of a n-myc downstream regulated 2 protein (ndrg2, syld, ndr2, ai182517, au040374) from mus musculus at 1.70 A resolution
Components
Protein NDRG2
Keywords
SIGNALING PROTEIN / Alpha/beta-hydrolases fold / ndr family / developmental protein / differentiation / neurogenesis / phosphorylation / regulatory protein / structural genomics / Joint Center for Structural Genomics / JCSG / Protein Structure Initiative / PSI-2
Function / homology
Function and homology information
regulation of platelet-derived growth factor production / regulation of vascular endothelial growth factor production / postsynapse organization / negative regulation of cytokine production / negative regulation of smooth muscle cell proliferation / negative regulation of ERK1 and ERK2 cascade / Wnt signaling pathway / nervous system development / growth cone / cell differentiation ...regulation of platelet-derived growth factor production / regulation of vascular endothelial growth factor production / postsynapse organization / negative regulation of cytokine production / negative regulation of smooth muscle cell proliferation / negative regulation of ERK1 and ERK2 cascade / Wnt signaling pathway / nervous system development / growth cone / cell differentiation / glutamatergic synapse / perinuclear region of cytoplasm / Golgi apparatus / signal transduction / nucleus / cytoplasm Similarity search - Function
BIOMOLECULE: 1 SEE REMARK 350 FOR THE AUTHOR PROVIDED AND PROGRAM GENERATED ASSEMBLY INFORMATION ... BIOMOLECULE: 1 SEE REMARK 350 FOR THE AUTHOR PROVIDED AND PROGRAM GENERATED ASSEMBLY INFORMATION FOR THE STRUCTURE IN THIS ENTRY. THE REMARK MAY ALSO PROVIDE INFORMATION ON BURIED SURFACE AREA. SIZE EXCLUSION CHROMATOGRAPHY WITH STATIC LIGHT SCATTERING SUPPORTS THE ASSIGNMENT OF A MONOMER AS A BIOLOGICALLY SIGNIFICANT OLIGOMERIZATION STATE.
Remark 999
SEQUENCE THE CONSTRUCT CONSISTS OF RESIDUES 40-313 OF THE FULL LENGTH PROTEIN. IT WAS EXPRESSED ... SEQUENCE THE CONSTRUCT CONSISTS OF RESIDUES 40-313 OF THE FULL LENGTH PROTEIN. IT WAS EXPRESSED WITH A PURIFICATION TAG MGSDKIHHHHHH.
Resolution: 1.7→29.348 Å / Cor.coef. Fo:Fc: 0.969 / Cor.coef. Fo:Fc free: 0.957 / SU B: 3.438 / SU ML: 0.059 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.098 / ESU R Free: 0.097 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: 1. HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. 2. ATOM RECORD CONTAINS RESIDUAL B FACTORS ONLY. 3. MG AND PEG 400 (2PE) ARE PRESENT IN THE CRYSTALLIZATION CONDITIONS. 4. THE BENZOIC ...Details: 1. HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. 2. ATOM RECORD CONTAINS RESIDUAL B FACTORS ONLY. 3. MG AND PEG 400 (2PE) ARE PRESENT IN THE CRYSTALLIZATION CONDITIONS. 4. THE BENZOIC ACID (BEZ) MOLECULE IS ASSIGNED BASED ON THE ELECTRON DENSITY AND ITS INTERACTION WITH THE PROTEIN. IT COULD BE SOME RELATED COMPOUND WITH A SIMILAR STRUCTURE.
Rfactor
Num. reflection
% reflection
Selection details
Rfree
0.183
1449
5.1 %
RANDOM
Rwork
0.145
-
-
-
obs
0.147
28649
100 %
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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: 14.36 Å2
Baniso -1
Baniso -2
Baniso -3
1-
0.35 Å2
0.18 Å2
0 Å2
2-
-
0.35 Å2
0 Å2
3-
-
-
-0.53 Å2
Refinement step
Cycle: LAST / Resolution: 1.7→29.348 Å
Protein
Nucleic acid
Ligand
Solvent
Total
Num. atoms
2152
0
27
314
2493
Refine LS restraints
Refine-ID
Type
Dev ideal
Dev ideal target
Number
X-RAY DIFFRACTION
r_bond_refined_d
0.016
0.022
2304
X-RAY DIFFRACTION
r_bond_other_d
0.008
0.02
1525
X-RAY DIFFRACTION
r_angle_refined_deg
1.561
1.968
3151
X-RAY DIFFRACTION
r_angle_other_deg
0.953
3
3758
X-RAY DIFFRACTION
r_dihedral_angle_1_deg
6.579
5
301
X-RAY DIFFRACTION
r_dihedral_angle_2_deg
32.568
25
104
X-RAY DIFFRACTION
r_dihedral_angle_3_deg
11.741
15
363
X-RAY DIFFRACTION
r_dihedral_angle_4_deg
21.224
15
7
X-RAY DIFFRACTION
r_chiral_restr
0.094
0.2
346
X-RAY DIFFRACTION
r_gen_planes_refined
0.007
0.02
2603
X-RAY DIFFRACTION
r_gen_planes_other
0.001
0.02
445
X-RAY DIFFRACTION
r_nbd_refined
0.223
0.2
469
X-RAY DIFFRACTION
r_nbd_other
0.193
0.2
1583
X-RAY DIFFRACTION
r_nbtor_refined
0.188
0.2
1128
X-RAY DIFFRACTION
r_nbtor_other
0.087
0.2
1160
X-RAY DIFFRACTION
r_xyhbond_nbd_refined
0.165
0.2
223
X-RAY DIFFRACTION
r_xyhbond_nbd_other
X-RAY DIFFRACTION
r_metal_ion_refined
0.047
0.2
1
X-RAY DIFFRACTION
r_metal_ion_other
X-RAY DIFFRACTION
r_symmetry_vdw_refined
0.15
0.2
13
X-RAY DIFFRACTION
r_symmetry_vdw_other
0.254
0.2
40
X-RAY DIFFRACTION
r_symmetry_hbond_refined
0.169
0.2
31
X-RAY DIFFRACTION
r_symmetry_hbond_other
X-RAY DIFFRACTION
r_symmetry_metal_ion_refined
X-RAY DIFFRACTION
r_symmetry_metal_ion_other
X-RAY DIFFRACTION
r_mcbond_it
1.454
2
1522
X-RAY DIFFRACTION
r_mcbond_other
0.402
2
572
X-RAY DIFFRACTION
r_mcangle_it
1.977
3
2313
X-RAY DIFFRACTION
r_scbond_it
2.751
4
964
X-RAY DIFFRACTION
r_scangle_it
3.742
5
826
X-RAY DIFFRACTION
r_rigid_bond_restr
X-RAY DIFFRACTION
r_sphericity_free
X-RAY DIFFRACTION
r_sphericity_bonded
LS refinement shell
Resolution: 1.7→1.74 Å / Total num. of bins used: 20
Rfactor
Num. reflection
% reflection
Rfree
0.243
69
-
Rwork
0.189
1302
-
obs
-
-
100 %
Refinement TLS params.
Method: refined / Origin x: 3.7832 Å / Origin y: 34.5458 Å / Origin z: 16.8449 Å
11
12
13
21
22
23
31
32
33
T
-0.0432 Å2
-0.0243 Å2
-0.004 Å2
-
-0.0141 Å2
0.0002 Å2
-
-
-0.0311 Å2
L
0.7468 °2
0.2506 °2
0.1012 °2
-
0.5567 °2
0.1081 °2
-
-
0.6603 °2
S
0.013 Å °
-0.1019 Å °
-0.0032 Å °
0.0357 Å °
-0.0449 Å °
-0.0177 Å °
0.036 Å °
0.0075 Å °
0.0319 Å °
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