- PDB-2h7o: Crystal structure of the Rho-GTPase binding domain of YpkA -
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Open data
ID or keywords:
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Basic information
Entry
Database: PDB / ID: 2h7o
Title
Crystal structure of the Rho-GTPase binding domain of YpkA
Components
Protein kinase ypkA
Keywords
SIGNALING PROTEIN / YpkA / YopO / Yersinia / GDI
Function / homology
Function and homology information
non-specific serine/threonine protein kinase / phosphorylation / protein serine kinase activity / protein serine/threonine kinase activity / extracellular region / ATP binding / cytoplasm Similarity search - Function
Rac1-binding domain, N-terminal GTPase binding subdomain / Rac1-binding domain, C-terminal subdomain / Serine/threonine protein kinase, yersinia-type / YpkA, Rac1-binding domain / Rac1-binding domain, C-terminal / Rac1-binding domain, N-terminal / Rac1-binding domain / Four Helix Bundle (Hemerythrin (Met), subunit A) / Methane Monooxygenase Hydroxylase; Chain G, domain 1 / Serine/threonine-protein kinase, active site ...Rac1-binding domain, N-terminal GTPase binding subdomain / Rac1-binding domain, C-terminal subdomain / Serine/threonine protein kinase, yersinia-type / YpkA, Rac1-binding domain / Rac1-binding domain, C-terminal / Rac1-binding domain, N-terminal / Rac1-binding domain / Four Helix Bundle (Hemerythrin (Met), subunit A) / Methane Monooxygenase Hydroxylase; Chain G, domain 1 / Serine/threonine-protein kinase, active site / Serine/Threonine protein kinases active-site signature. / Protein kinase domain / Serine/Threonine protein kinases, catalytic domain / Protein kinase domain profile. / Protein kinase domain / Protein kinase-like domain superfamily / Up-down Bundle / Mainly Alpha Similarity search - Domain/homology
Monochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
Wavelength: 0.979 Å / Relative weight: 1
Reflection
Resolution: 2→99 Å / Num. obs: 30187 / % possible obs: 98.5 % / Redundancy: 9 % / Rsym value: 0.045 / Net I/σ(I): 33.1
Reflection shell
Resolution: 2→2.054 Å / Mean I/σ(I) obs: 3.2 / Rsym value: 0.361 / % possible all: 90.29
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Processing
Software
Name
Version
Classification
NB
REFMAC
5.2.0005
refinement
PDB_EXTRACT
2
dataextraction
HKL-2000
datareduction
HKL-2000
datascaling
SOLVE
phasing
RESOLVE
phasing
Refinement
Method to determine structure: SAD / Resolution: 2→33.88 Å / Cor.coef. Fo:Fc: 0.945 / Cor.coef. Fo:Fc free: 0.939 / SU B: 6.995 / SU ML: 0.103 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.154 / ESU R Free: 0.142 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
Rfactor
Num. reflection
% reflection
Selection details
Rfree
0.237
1485
4.9 %
RANDOM
Rwork
0.208
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all
0.209
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-
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obs
0.209
28539
98.5 %
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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: MASK
Displacement parameters
Biso mean: 40.659 Å2
Baniso -1
Baniso -2
Baniso -3
1-
0.07 Å2
0.03 Å2
0 Å2
2-
-
0.07 Å2
0 Å2
3-
-
-
-0.1 Å2
Refinement step
Cycle: LAST / Resolution: 2→33.88 Å
Protein
Nucleic acid
Ligand
Solvent
Total
Num. atoms
2169
0
0
276
2445
Refine LS restraints
Refine-ID
Type
Dev ideal
Dev ideal target
Number
X-RAY DIFFRACTION
r_bond_refined_d
0.022
0.022
2194
X-RAY DIFFRACTION
r_bond_other_d
0.001
0.02
2065
X-RAY DIFFRACTION
r_angle_refined_deg
1.739
1.968
2953
X-RAY DIFFRACTION
r_angle_other_deg
0.978
3
4796
X-RAY DIFFRACTION
r_dihedral_angle_1_deg
6.803
5
266
X-RAY DIFFRACTION
r_dihedral_angle_2_deg
34.356
24.095
105
X-RAY DIFFRACTION
r_dihedral_angle_3_deg
16.453
15
430
X-RAY DIFFRACTION
r_dihedral_angle_4_deg
17.347
15
20
X-RAY DIFFRACTION
r_chiral_restr
0.121
0.2
351
X-RAY DIFFRACTION
r_gen_planes_refined
0.007
0.02
2374
X-RAY DIFFRACTION
r_gen_planes_other
0.001
0.02
424
X-RAY DIFFRACTION
r_nbd_refined
0.232
0.2
552
X-RAY DIFFRACTION
r_nbd_other
0.189
0.2
2079
X-RAY DIFFRACTION
r_nbtor_refined
0.176
0.2
1083
X-RAY DIFFRACTION
r_nbtor_other
0.089
0.2
1305
X-RAY DIFFRACTION
r_xyhbond_nbd_refined
0.231
0.2
217
X-RAY DIFFRACTION
r_xyhbond_nbd_other
0.24
0.2
1
X-RAY DIFFRACTION
r_symmetry_vdw_refined
0.365
0.2
9
X-RAY DIFFRACTION
r_symmetry_vdw_other
0.308
0.2
81
X-RAY DIFFRACTION
r_symmetry_hbond_refined
0.234
0.2
22
X-RAY DIFFRACTION
r_mcbond_it
1.664
1.5
1764
X-RAY DIFFRACTION
r_mcbond_other
0.336
1.5
545
X-RAY DIFFRACTION
r_mcangle_it
1.921
2
2170
X-RAY DIFFRACTION
r_scbond_it
3.283
3
937
X-RAY DIFFRACTION
r_scangle_it
4.494
4.5
783
LS refinement shell
Resolution: 2→2.054 Å / Total num. of bins used: 20
Rfactor
Num. reflection
% reflection
Rfree
0.302
95
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Rwork
0.248
1829
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obs
-
1924
90.29 %
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