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- PDB-6v97: Kindlin-3 double deletion mutant short form -

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Basic information

Entry
Database: PDB / ID: 6v97
TitleKindlin-3 double deletion mutant short form
ComponentsFermitin family homolog 3
KeywordsBLOOD CLOTTING / Integrin binding protein
Function / homology
Function and homology information


cell-substrate junction / regulation of cell-cell adhesion mediated by integrin / integrin activation / podosome / leukocyte cell-cell adhesion / substrate adhesion-dependent cell spreading / cell-matrix adhesion / platelet alpha granule lumen / cell projection / integrin-mediated signaling pathway ...cell-substrate junction / regulation of cell-cell adhesion mediated by integrin / integrin activation / podosome / leukocyte cell-cell adhesion / substrate adhesion-dependent cell spreading / cell-matrix adhesion / platelet alpha granule lumen / cell projection / integrin-mediated signaling pathway / platelet aggregation / integrin binding / Platelet degranulation / positive regulation of cell migration / lipid binding / extracellular exosome / extracellular region / membrane
Similarity search - Function
Kindlin/fermitin, PH domain / Kindlin/fermitin / Kindlin-2, N-terminal / Kindlin-2 N-terminal domain / FERM domain signature 2. / FERM central domain / FERM central domain / FERM superfamily, second domain / Band 4.1 domain / Band 4.1 homologues ...Kindlin/fermitin, PH domain / Kindlin/fermitin / Kindlin-2, N-terminal / Kindlin-2 N-terminal domain / FERM domain signature 2. / FERM central domain / FERM central domain / FERM superfamily, second domain / Band 4.1 domain / Band 4.1 homologues / PH domain / PH domain profile. / Pleckstrin homology domain. / Pleckstrin homology domain / PH-like domain superfamily
Similarity search - Domain/homology
Fermitin family homolog 3
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.381 Å
AuthorsXu, Z. / Zhang, T.L. / Xu, Z. / Sun, J.J. / Ding, J.P. / Ma, Y.Q.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Heart, Lung, and Blood Institute (NIH/NHLBI)HL131654 United States
CitationJournal: Blood Adv / Year: 2020
Title: Structure basis of the FERM domain of kindlin-3 in supporting integrin alpha IIb beta 3 activation in platelets.
Authors: Sun, J. / Xiao, D. / Ni, Y. / Zhang, T. / Cao, Z. / Xu, Z. / Nguyen, H. / Zhang, J. / White, G.C. / Ding, J. / Ma, Y.Q. / Xu, Z.
History
DepositionDec 13, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 22, 2020Provider: repository / Type: Initial release
Revision 1.1Oct 11, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Fermitin family homolog 3
B: Fermitin family homolog 3


Theoretical massNumber of molelcules
Total (without water)107,7732
Polymers107,7732
Non-polymers00
Water3,225179
1
A: Fermitin family homolog 3


Theoretical massNumber of molelcules
Total (without water)53,8861
Polymers53,8861
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Fermitin family homolog 3


Theoretical massNumber of molelcules
Total (without water)53,8861
Polymers53,8861
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)67.502, 131.487, 134.151
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Fermitin family homolog 3 / Kindlin-3 / MIG2-like protein / Unc-112-related protein 2


Mass: 53886.457 Da / Num. of mol.: 2 / Mutation: 166-194 deleted, 314-493 deleted
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: FERMT3, KIND3, MIG2B, URP2 / Production host: Escherichia coli (E. coli) / References: UniProt: Q86UX7
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 179 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsThe cDNA of human kindlin-3 (GenBank NM_031471) used for expressing kindlin-3 protein in this study ...The cDNA of human kindlin-3 (GenBank NM_031471) used for expressing kindlin-3 protein in this study is a short variant, resulting in 4 residues (IPRR) missing when compared to Q86UX7 in Uniprot

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.82 Å3/Da / Density % sol: 56.35 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / Details: 11% PEG 3350 and 0.2 M sodium thiocyanate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.97853 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Jan 2, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97853 Å / Relative weight: 1
ReflectionResolution: 2.381→50 Å / Num. obs: 48090 / % possible obs: 99.6 % / Redundancy: 9.3 % / CC1/2: 0.998 / Rmerge(I) obs: 0.047 / Rpim(I) all: 0.016 / Rrim(I) all: 0.05 / Net I/σ(I): 28.1
Reflection shellResolution: 2.4→2.49 Å / Rmerge(I) obs: 0.594 / Num. unique obs: 4708 / CC1/2: 0.859 / Rpim(I) all: 0.207 / Rrim(I) all: 0.63

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Processing

Software
NameVersionClassification
PHENIX1.12_2829refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
HKL-2000data collection
PDB_EXTRACTdata extraction
Cootmodel building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5XPY

5xpy


Resolution: 2.381→46.952 Å / SU ML: 0.32 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 27.11 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2571 2001 4.19 %
Rwork0.2034 45726 -
obs0.2057 47727 98.28 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 151.19 Å2 / Biso mean: 61.1058 Å2 / Biso min: 22.06 Å2
Refinement stepCycle: final / Resolution: 2.381→46.952 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6807 0 0 179 6986
Biso mean---50.7 -
Num. residues----828
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0047008
X-RAY DIFFRACTIONf_angle_d0.7069499
X-RAY DIFFRACTIONf_chiral_restr0.0461019
X-RAY DIFFRACTIONf_plane_restr0.0041225
X-RAY DIFFRACTIONf_dihedral_angle_d8.4915891
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.3815-2.4410.3291210.2711293290
2.441-2.5070.32831450.2463325899
2.507-2.58080.33861470.24323299
2.5808-2.66410.32171380.23713258100
2.6641-2.75930.30421490.2454325699
2.7593-2.86980.30081360.2496326399
2.8698-3.00040.35231470.2503328499
3.0004-3.15850.33321430.24143282100
3.1585-3.35630.26911440.2255332099
3.3563-3.61540.28771430.2139329099
3.6154-3.97910.24411500.1867332199
3.9791-4.55440.20821430.1645332599
4.5544-5.73650.20611490.1781334299
5.7365-46.9520.21271460.1817336395
Refinement TLS params.Method: refined / Origin x: 1.8175 Å / Origin y: -47.0846 Å / Origin z: -16.9992 Å
111213212223313233
T0.2225 Å2-0.0375 Å2-0.0008 Å2-0.2641 Å2-0.0211 Å2--0.2462 Å2
L0.2158 °2-0.1708 °20.0116 °2-0.4117 °20.0741 °2--0.335 °2
S-0.0037 Å °0.0468 Å °0.0415 Å °0.0552 Å °0.0585 Å °-0.0034 Å °0.0057 Å °0.0637 Å °0 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1allA15 - 659
2X-RAY DIFFRACTION1allB15 - 659
3X-RAY DIFFRACTION1allS1 - 180

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