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- PDB-1io0: CRYSTAL STRUCTURE OF TROPOMODULIN C-TERMINAL HALF -

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Basic information

Entry
Database: PDB / ID: 1io0
TitleCRYSTAL STRUCTURE OF TROPOMODULIN C-TERMINAL HALF
ComponentsTROPOMODULIN
KeywordsPROTEIN BINDING / LRR protein / right-handed super-helix
Function / homology
Function and homology information


pointed-end actin filament capping / costamere / tropomyosin binding / sarcomere / sarcolemma / actin filament binding / metal ion binding
Similarity search - Function
Tropomodulin-1 / Tropomodulin / Tropomodulin / Leucine-rich repeat, LRR (right-handed beta-alpha superhelix) / Ribonuclease Inhibitor / Alpha-Beta Horseshoe / Leucine-rich repeat domain superfamily / Alpha Beta
Similarity search - Domain/homology
Biological speciesGallus gallus (chicken)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.45 Å
AuthorsKrieger, I. / Kostyukova, A. / Yamashita, A. / Maeda, Y.
CitationJournal: Biophys.J. / Year: 2002
Title: Crystal structure of the C-terminal half of tropomodulin and structural basis of actin filament pointed-end capping.
Authors: Krieger, I. / Kostyukova, A. / Yamashita, A. / Nitanai, Y. / Maeda, Y.
History
DepositionDec 14, 2000Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Nov 27, 2002Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 23, 2019Group: Data collection / Database references / Category: citation
Item: _citation.journal_abbrev / _citation.pdbx_database_id_DOI / _citation.title
Revision 1.4Dec 27, 2023Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr1_symmetry / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.ptnr3_symmetry / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr1_symmetry / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_conn.ptnr2_symmetry / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Remark 600HETEROGEN ZN IS ALSO COORDINATED WITH OD2 ASP 194 AND OD2 ASP 196 IN A SYMMTERY_RELATED MOLECULE.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: TROPOMODULIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)20,7152
Polymers20,6501
Non-polymers651
Water4,161231
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)69.294, 69.294, 101.223
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number146
Space group name H-MH3

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Components

#1: Protein TROPOMODULIN /


Mass: 20649.510 Da / Num. of mol.: 1 / Fragment: C-TERMINAL DOMAIN
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Gallus gallus (chicken) / Plasmid: PET(HIS)TMOD / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)PLYSE / References: UniProt: Q9DEA6
#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 231 / 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: 2.3 Å3/Da / Density % sol: 45.3 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: PEG 400, zinc sulfate, MES, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 295K
Crystal grow
*PLUS
Temperature: 22 ℃ / Method: vapor diffusion
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetailsChemical formula
110 mg/mlprotein1drop
225 mMglycine1droppH3.0
30.1 MMES-NaOH1droppH6.5
424 %(v/v)PEG4001drop
510 mM1dropZnSO4
60.1 MMES- NaOH1reservoirpH6.5
715 %(v/v)PEG4001reservoir
86 mM1reservoirZnSO4

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL44B2 / Wavelength: 0.7 Å
DetectorType: MARRESEARCH / Detector: CCD / Date: Oct 13, 2000
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.7 Å / Relative weight: 1
ReflectionResolution: 1.45→20 Å / Num. all: 31971 / Num. obs: 31954 / % possible obs: 100 % / Observed criterion σ(I): 0 / Redundancy: 11.2 % / Biso Wilson estimate: 17.31 Å2 / Rmerge(I) obs: 0.076 / Net I/σ(I): 13.4
Reflection shellResolution: 1.45→1.5 Å / Rmerge(I) obs: 0.286 / % possible all: 100
Reflection
*PLUS
Lowest resolution: 20 Å / % possible obs: 100 % / Num. measured all: 357913
Reflection shell
*PLUS
Lowest resolution: 1.5 Å / % possible obs: 100 %

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Processing

Software
NameVersionClassification
DENZOdata reduction
SCALEPACKdata scaling
SOLVEphasing
DMmodel building
ARP/wARPmodel building
X-PLOR3.851refinement
DMphasing
RefinementMethod to determine structure: MAD / Resolution: 1.45→10 Å / Data cutoff high absF: 1000000 / Data cutoff low absF: 0.001 / Cross valid method: THROUGHOUT / σ(F): 2 / Stereochemistry target values: Engh & Huber
Details: THE PROGRAM REFMAC (CCP4) WAS ALSO USED IN REFINEMENT PROCESS FOR DATA AT 20.0-1.45 A
RfactorNum. reflection% reflectionSelection details
Rfree0.22 1602 5 %RANDOM
Rwork0.203 ---
all-31866 --
obs-31866 99.4 %-
Displacement parametersBiso mean: 18.89 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.195 Å0.181 Å
Luzzati d res low-5 Å
Luzzati sigma a0.161 Å0.174 Å
Refinement stepCycle: LAST / Resolution: 1.45→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1297 0 1 231 1529
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONx_angle_deg1.052
X-RAY DIFFRACTIONx_bond_d0.005
X-RAY DIFFRACTIONx_dihedral_angle_d24.073
X-RAY DIFFRACTIONx_improper_angle_d0.566
X-RAY DIFFRACTIONx_mcbond_it1.0031.5
X-RAY DIFFRACTIONx_mcangle_it1.5872
X-RAY DIFFRACTIONx_scbond_it2.4122
X-RAY DIFFRACTIONx_scangle_it3.9592.5
LS refinement shellResolution: 1.45→1.52 Å / Total num. of bins used: 8
RfactorNum. reflection% reflection
Rfree0.283 165 4.14 %
Rwork0.286 3641 -
obs--95.5 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramtophcsdx.pro.top
X-RAY DIFFRACTION2toph19.sol.top
Refinement
*PLUS
% reflection Rfree: 5 % / Rfactor Rfree: 0.22
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_deg24.073
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg0.566

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