- PDB-4hbd: Crystal structure of KANK2 ankyrin repeats -
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Open data
ID or keywords:
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Basic information
Entry
Database: PDB / ID: 4hbd
Title
Crystal structure of KANK2 ankyrin repeats
Components
KN motif and ankyrin repeat domain-containing protein 2
Keywords
PROTEIN BINDING / Structural Genomics Consortium / SGC
Function / homology
Function and homology information
negative regulation of vitamin D receptor signaling pathway / kidney epithelium development / podocyte cell migration / negative regulation of intracellular estrogen receptor signaling pathway / negative regulation of actin filament polymerization / regulation of Rho protein signal transduction / negative regulation of programmed cell death / negative regulation of G1/S transition of mitotic cell cycle / negative regulation of cell population proliferation / apoptotic process ...negative regulation of vitamin D receptor signaling pathway / kidney epithelium development / podocyte cell migration / negative regulation of intracellular estrogen receptor signaling pathway / negative regulation of actin filament polymerization / regulation of Rho protein signal transduction / negative regulation of programmed cell death / negative regulation of G1/S transition of mitotic cell cycle / negative regulation of cell population proliferation / apoptotic process / negative regulation of transcription by RNA polymerase II / mitochondrion / cytoplasm Similarity search - Function
KNmotifandankyrinrepeatdomain-containingprotein2 / Ankyrin repeat domain-containing protein 25 / Matrix-remodeling-associated protein 3 / SRC-1- ...Ankyrin repeat domain-containing protein 25 / Matrix-remodeling-associated protein 3 / SRC-1-interacting protein / SRC1-interacting protein
Mass: 30162.223 Da / Num. of mol.: 1 / Fragment: UNP residues 578-832 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: KANK2, ANKRD25, KIAA1518, MXRA3, SIP / Plasmid: pET28-MHL / Production host: Escherichia coli (E. coli) / Strain (production host): BL21-V2R-pRARE2 / References: UniProt: Q63ZY3
Resolution: 1.72→75.031 Å / Num. all: 31276 / Num. obs: 31276 / % possible obs: 100 % / Redundancy: 7.1 % / Rsym value: 0.072 / Net I/σ(I): 17.7
Reflection shell
Diffraction-ID: 1
Resolution (Å)
Redundancy (%)
Rmerge(I) obs
Mean I/σ(I) obs
Num. measured all
Num. unique all
Rsym value
% possible all
1.72-1.81
7.3
0.961
0.8
32689
4483
0.961
100
1.81-1.92
7.3
0.602
1.2
31103
4262
0.602
100
1.92-2.06
7.3
0.324
2.3
29168
4000
0.324
100
2.06-2.22
7.3
0.187
3.9
27039
3720
0.187
100
2.22-2.43
7.3
0.117
6.4
24975
3439
0.117
100
2.43-2.72
7.2
0.084
8.9
22675
3135
0.084
100
2.72-3.14
7.1
0.055
13.3
19954
2810
0.055
100
3.14-3.85
6.9
0.037
18
16420
2390
0.037
100
3.85-5.44
6.7
0.031
18.9
12699
1903
0.031
100
5.44-37.515
6
0.033
12.4
6829
1134
0.033
99.7
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Phasing
Phasing
Method: molecular replacement
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Processing
Software
Name
Version
Classification
NB
SCALA
3.3.20
datascaling
SHELX
phasing
REFMAC
5.7.0027
refinement
PDB_EXTRACT
3.11
dataextraction
XDS
datareduction
PHASER
phasing
Refinement
Method to determine structure: MOLECULAR REPLACEMENT Starting model: UNPUBLISHED MODEL OF SAME PROTEIN BUT DIFFERENT CRYSTAL DIMENSIONS (P21212; A,B,C=61.46,63.59,163.08 FOR DERIVATIVE (IODIDE?, DIFFRACTION INTENSITIES INCLUDED). THAT STRUCTURE WAS ...Starting model: UNPUBLISHED MODEL OF SAME PROTEIN BUT DIFFERENT CRYSTAL DIMENSIONS (P21212; A,B,C=61.46,63.59,163.08 FOR DERIVATIVE (IODIDE?, DIFFRACTION INTENSITIES INCLUDED). THAT STRUCTURE WAS SOLVED WITH SHELX, SIRAS (ISOMORPHOUS "NATIVE" DATA NOT PROVIDED AS SAD DOES ALSO WORK) Resolution: 1.72→37.54 Å / Cor.coef. Fo:Fc: 0.965 / Cor.coef. Fo:Fc free: 0.957 / WRfactor Rfree: 0.1973 / WRfactor Rwork: 0.1619 / Occupancy max: 1 / Occupancy min: 0.3 / FOM work R set: 0.8638 / SU B: 4.465 / SU ML: 0.073 / SU R Cruickshank DPI: 0.0974 / SU Rfree: 0.0967 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.097 / ESU R Free: 0.097 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. U VALUES: WITH TLS ADDED. ELECTRON DENSITY AT RESIDUES HIS-677 AND HIS-782 IS NOT CONSISTENT WITH THAT RESIDUE TYPE.
Rfactor
Num. reflection
% reflection
Selection details
Rfree
0.2072
1583
5.1 %
RANDOM
Rwork
0.1765
-
-
-
obs
0.1781
31215
99.98 %
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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
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