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- PDB-2yz8: Crystal structure of the 32th Ig-like domain of human obscurin (K... -

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Basic information

Entry
Database: PDB / ID: 2yz8
TitleCrystal structure of the 32th Ig-like domain of human obscurin (KIAA1556)
ComponentsObscurin
KeywordsSTRUCTURAL PROTEIN / obsucurin / KIAA1556 / Ig fold / Structural Genomics / NPPSFA / National Project on Protein Structural and Functional Analyses / RIKEN Structural Genomics/Proteomics Initiative / RSGI
Function / homology
Function and homology information


protein localization to M-band / phosphatidylinositol-5-phosphate binding / phosphatidylinositol-3-phosphate binding / phosphatidylinositol-3,4-bisphosphate binding / M band / phosphatidylinositol-4-phosphate binding / regulation of small GTPase mediated signal transduction / structural constituent of muscle / ankyrin binding / myofibril ...protein localization to M-band / phosphatidylinositol-5-phosphate binding / phosphatidylinositol-3-phosphate binding / phosphatidylinositol-3,4-bisphosphate binding / M band / phosphatidylinositol-4-phosphate binding / regulation of small GTPase mediated signal transduction / structural constituent of muscle / ankyrin binding / myofibril / sarcomere organization / NRAGE signals death through JNK / RHOQ GTPase cycle / phosphatidylinositol-3,4,5-trisphosphate binding / RHOA GTPase cycle / titin binding / phosphatidylinositol-4,5-bisphosphate binding / guanyl-nucleotide exchange factor activity / sarcolemma / Z disc / G alpha (12/13) signalling events / nuclear body / non-specific serine/threonine protein kinase / calmodulin binding / phosphorylation / protein serine kinase activity / protein serine/threonine kinase activity / ATP binding / metal ion binding / plasma membrane / cytosol
Similarity search - Function
Obscurin, SH3 domain / IQ calmodulin-binding motif / Dbl homology (DH) domain superfamily / RhoGEF domain / Guanine nucleotide exchange factor for Rho/Rac/Cdc42-like GTPases / Dbl homology (DH) domain / Dbl homology (DH) domain profile. / Short calmodulin-binding motif containing conserved Ile and Gln residues. / IQ motif profile. / IQ motif, EF-hand binding site ...Obscurin, SH3 domain / IQ calmodulin-binding motif / Dbl homology (DH) domain superfamily / RhoGEF domain / Guanine nucleotide exchange factor for Rho/Rac/Cdc42-like GTPases / Dbl homology (DH) domain / Dbl homology (DH) domain profile. / Short calmodulin-binding motif containing conserved Ile and Gln residues. / IQ motif profile. / IQ motif, EF-hand binding site / Immunoglobulin I-set / Immunoglobulin I-set domain / PH domain / PH domain profile. / Pleckstrin homology domain. / Fibronectin type III domain / Pleckstrin homology domain / Fibronectin type 3 domain / Immunoglobulin subtype 2 / Immunoglobulin C-2 Type / Immunoglobulin V-Type / Fibronectin type-III domain profile. / Fibronectin type III / Fibronectin type III superfamily / Immunoglobulin V-set domain / SH3-like domain superfamily / Src homology 3 (SH3) domain profile. / SH3 domain / Tyrosine protein kinases specific active-site signature. / Immunoglobulin subtype / Immunoglobulin / PH-like domain superfamily / Tyrosine-protein kinase, active site / Ig-like domain profile. / Immunoglobulin-like domain / Serine/threonine-protein kinase, active site / Serine/Threonine protein kinases active-site signature. / Immunoglobulin-like domain superfamily / Protein kinase domain / Serine/Threonine protein kinases, catalytic domain / Immunoglobulins / Protein kinase, ATP binding site / Protein kinases ATP-binding region signature. / Immunoglobulin-like fold / Protein kinase domain profile. / Protein kinase domain / Protein kinase-like domain superfamily / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsSaijo, S. / Ohsawa, N. / Nishino, A. / Kishishita, S. / Chen, L. / Fu, Z.Q. / Chrzas, J. / Wang, B.C. / Shirouzu, M. / Yokoyama, S. / RIKEN Structural Genomics/Proteomics Initiative (RSGI)
CitationJournal: To be Published
Title: Crystal structure of the 32th Ig-like domain of human obscurin (KIAA1556)
Authors: Saijo, S. / Ohsawa, N. / Nishino, A. / Kishishita, S. / Chen, L. / Fu, Z.Q. / Chrzas, J. / Wang, B.C. / Shirouzu, M. / Yokoyama, S.
History
DepositionMay 4, 2007Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0May 6, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2Apr 3, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_conn / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Obscurin


Theoretical massNumber of molelcules
Total (without water)10,8361
Polymers10,8361
Non-polymers00
Water70339
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)43.358, 43.358, 102.316
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212

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Components

#1: Protein Obscurin / Obscurin-myosin light chain kinase / Obscurin-MLCK / Obscurin-RhoGEF


Mass: 10835.966 Da / Num. of mol.: 1 / Fragment: 32th Ig-like domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: OBSCN, KIAA1556 / Plasmid: PK051017-18 / Production host: Cell-free protein synthesis / References: UniProt: Q5VST9
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 39 / Source method: isolated from a natural source / Formula: H2O

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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: 2.22 Å3/Da / Density % sol: 44.56 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 5.6
Details: 0.2M potassium sodium tartrate tetrahydrate, 0.1M tri-sodium citrate dihydrate pH 5.6, 2M ammonium sulfate , VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-BM / Wavelength: 0.97901 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Jan 31, 2007
RadiationMonochromator: Si 111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97901 Å / Relative weight: 1
ReflectionResolution: 2→50 Å / Num. all: 7165 / Num. obs: 6566 / % possible obs: 91.7 % / Observed criterion σ(I): 0 / Redundancy: 6 % / Biso Wilson estimate: 6.9 Å2 / Rsym value: 0.061 / Net I/σ(I): 14.1
Reflection shellResolution: 2→2.07 Å / Redundancy: 4.2 % / Mean I/σ(I) obs: 4.5 / Num. unique all: 390 / Rsym value: 0.247 / % possible all: 56.1

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Processing

Software
NameVersionClassification
REFMAC5.2.0005refinement
HKL-2000data collection
HKL-2000data reduction
HKL-2000data scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: homology-model (SWISS-MODEL)

Resolution: 2→39.94 Å / Cor.coef. Fo:Fc: 0.946 / Cor.coef. Fo:Fc free: 0.928 / SU B: 9.269 / SU ML: 0.13 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.215 / ESU R Free: 0.193 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: The structure was refined also with CNS 1.1
RfactorNum. reflection% reflectionSelection details
Rfree0.261 648 9.9 %RANDOM
Rwork0.209 ---
obs0.214 5904 92.11 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 21.164 Å2
Baniso -1Baniso -2Baniso -3
1-0.21 Å20 Å20 Å2
2--0.21 Å20 Å2
3----0.43 Å2
Refinement stepCycle: LAST / Resolution: 2→39.94 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms673 0 0 39 712
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0060.022684
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.1391.976930
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.832589
X-RAY DIFFRACTIONr_dihedral_angle_2_deg26.89522.59327
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.23515108
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.004157
X-RAY DIFFRACTIONr_chiral_restr0.0590.2110
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.02511
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.1830.2226
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.2930.2455
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1130.238
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1640.237
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1510.25
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.3451.5455
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it0.6592717
X-RAY DIFFRACTIONr_scbond_it1.0163256
X-RAY DIFFRACTIONr_scangle_it1.4924.5213
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2→2.052 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.225 28 -
Rwork0.225 251 -
obs-279 53.55 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
131.139312.5841-11.88087.72031.180918.1151-0.6834-0.0438-0.5867-0.24790.2304-0.37430.07421.63760.45310.1141-0.0325-0.03860.14120.1747-0.124816.75116.89740.956
215.1152-8.4455-3.0644.74021.3148.0447-0.21040.08420.64140.09540.1307-0.1333-0.5953-0.54140.07970.31470.0180.01960.07850.0041-0.0013-1.14920.67247.531
34.04894.1084-6.06858.9418-2.637511.6918-0.03970.1486-0.3837-0.7262-0.5818-0.27950.01930.16120.62150.21940.0252-0.00990.27690.0868-0.007913.85414.64634.761
49.978-2.43.452415.83931.74571.6294-0.00750.2206-0.2518-0.23920.0006-0.26350.5365-0.30380.00680.1215-0.03310.00960.1366-0.0558-0.15983.6236.46444.199
512.82276.1438-5.24347.2612-4.39817.6667-0.05610.3487-0.0558-0.18190.1820.31510.214-0.7807-0.12590.1259-0.02310.01040.17370.0236-0.09940.58813.02835.574
677.803515.1459-41.45944.9309-15.369648.96431.29721.23482.1870.7285-0.19741.543-1.20120.2781-1.09970.2517-0.04230.0090.2516-0.0469-0.09494.7318.05537.611
742.92591.1879-39.35925.373-14.192168.2394-0.03763.23870.0209-0.10640.38810.29830.0842-4.5244-0.35050.2041-0.1321-0.02910.4992-0.0250.0139-7.76914.73843.972
839.7578-8.1266-1.19785.1417-0.91299.4222-0.6477-0.7168-0.97310.04850.4950.50930.3336-1.14830.15270.1558-0.01120.02490.20730.0111-0.135-2.67911.49351.574
99.5947-0.7842-5.83794.27582.29826.7725-0.07130.1381-0.1271-0.0717-0.1738-0.41110.09560.37260.24510.1404-0.00020.00460.12430.065-0.131610.85211.13844.514
1031.8458-8.3698-11.699113.00073.268611.90370.44290.70541.2353-0.216-0.04370.4092-0.928-1.7458-0.39920.21740.11930.00360.31520.05-0.1131-8.68620.91854.511
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA459 - 4668 - 15
2X-RAY DIFFRACTION2AA467 - 48016 - 29
3X-RAY DIFFRACTION3AA481 - 49130 - 40
4X-RAY DIFFRACTION4AA492 - 49941 - 48
5X-RAY DIFFRACTION5AA500 - 51249 - 61
6X-RAY DIFFRACTION6AA513 - 51762 - 66
7X-RAY DIFFRACTION7AA518 - 52267 - 71
8X-RAY DIFFRACTION8AA523 - 52872 - 77
9X-RAY DIFFRACTION9AA529 - 54278 - 91
10X-RAY DIFFRACTION10AA543 - 54892 - 97

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