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- PDB-5f4y: Structure of the SD2 domain of Human Shroom2 -

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Basic information

Entry
Database: PDB / ID: 5f4y
TitleStructure of the SD2 domain of Human Shroom2
ComponentsProtein Shroom2
KeywordsPROTEIN BINDING / coiled-coil / Rock-binding
Function / homology
Function and homology information


eye pigment granule organization / establishment of melanosome localization / cellular pigment accumulation / ligand-gated sodium channel activity / lens morphogenesis in camera-type eye / ear development / camera-type eye morphogenesis / apical protein localization / melanosome organization / camera-type eye development ...eye pigment granule organization / establishment of melanosome localization / cellular pigment accumulation / ligand-gated sodium channel activity / lens morphogenesis in camera-type eye / ear development / camera-type eye morphogenesis / apical protein localization / melanosome organization / camera-type eye development / apical junction complex / bicellular tight junction / actin filament organization / adherens junction / brain development / beta-catenin binding / actin filament binding / cell migration / actin binding / microtubule / cytoskeleton / apical plasma membrane / extracellular exosome / plasma membrane / cytoplasm
Similarity search - Function
Apx/Shrm Domain 1 / Apx/Shroom domain ASD1 / ASD1 domain profile. / Apx/Shrm Domain 2 / Shroom family / Apx/Shroom domain ASD2 / ASD2 domain profile. / PDZ domain / PDZ domain profile. / Domain present in PSD-95, Dlg, and ZO-1/2. ...Apx/Shrm Domain 1 / Apx/Shroom domain ASD1 / ASD1 domain profile. / Apx/Shrm Domain 2 / Shroom family / Apx/Shroom domain ASD2 / ASD2 domain profile. / PDZ domain / PDZ domain profile. / Domain present in PSD-95, Dlg, and ZO-1/2. / PDZ domain / PDZ superfamily
Similarity search - Domain/homology
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.293 Å
AuthorsMo, J.H. / Zalewski, J.K. / Heroux, A. / VanDemark, A.P.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM097204 United States
CitationJournal: J. Biol. Chem. / Year: 2016
Title: Structure of the Shroom-Rho Kinase Complex Reveals a Binding Interface with Monomeric Shroom That Regulates Cell Morphology and Stimulates Kinase Activity.
Authors: Zalewski, J.K. / Mo, J.H. / Heber, S. / Heroux, A. / Gardner, R.G. / Hildebrand, J.D. / VanDemark, A.P.
History
DepositionDec 3, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 19, 2016Provider: repository / Type: Initial release
Revision 1.1Nov 2, 2016Group: Database references
Revision 1.2Dec 14, 2016Group: Database references
Revision 1.3Sep 20, 2017Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.4Dec 25, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.5Sep 27, 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: Protein Shroom2
B: Protein Shroom2


Theoretical massNumber of molelcules
Total (without water)42,1082
Polymers42,1082
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1690 Å2
ΔGint-11 kcal/mol
Surface area20400 Å2
MethodPISA
Unit cell
Length a, b, c (Å)90.887, 110.000, 118.862
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221

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Components

#1: Protein Protein Shroom2 / Apical-like protein / Protein APXL


Mass: 21053.957 Da / Num. of mol.: 2 / Fragment: ASD2 domain residues 1427-1610
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: SHROOM2, APXL / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 (DE3) RIPL / References: UniProt: Q13796

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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: 3.53 Å3/Da / Density % sol: 65.13 % / Description: Thin, square plates
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: 20% PEG 3350, 200 mM Magnesium Chloride, 100 mM Tris pH 8.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X25 / Wavelength: 1.1 Å
DetectorType: PSI PILATUS 6M / Detector: PIXEL / Date: Aug 2, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.1 Å / Relative weight: 1
ReflectionResolution: 3.293→50 Å / Num. obs: 8522 / % possible obs: 92.7 % / Redundancy: 5.6 % / Rmerge(I) obs: 0.08 / Net I/σ(I): 23.7
Reflection shellResolution: 3.293→3.36 Å / Redundancy: 4.1 % / Rmerge(I) obs: 0.524 / Mean I/σ(I) obs: 2.26 / % possible all: 91.8

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Processing

Software
NameVersionClassification
PHENIX(dev_2219)refinement
Cootmodel building
HKL-2000data scaling
PHENIXphasing
HKL-2000data reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3THF

3thf


Resolution: 3.293→14.932 Å / SU ML: 0.53 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 33.44 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2989 1018 12.07 %Random selection
Rwork0.2466 ---
obs0.2531 8431 91.59 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 3.293→14.932 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2575 0 0 0 2575
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0032596
X-RAY DIFFRACTIONf_angle_d0.4533478
X-RAY DIFFRACTIONf_dihedral_angle_d14.1411024
X-RAY DIFFRACTIONf_chiral_restr0.028403
X-RAY DIFFRACTIONf_plane_restr0.002454
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.293-3.46460.39061500.308939X-RAY DIFFRACTION85
3.4646-3.67860.3881050.28851089X-RAY DIFFRACTION92
3.6786-3.95780.34891530.26261110X-RAY DIFFRACTION95
3.9578-4.34710.29371530.25061042X-RAY DIFFRACTION94
4.3471-4.95590.27821530.22431059X-RAY DIFFRACTION92
4.9559-6.16980.34291530.30181065X-RAY DIFFRACTION92
6.1698-14.93210.25731510.21121109X-RAY DIFFRACTION91

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