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- PDB-1pgv: Structural Genomics of Caenorhabditis elegans: tropomodulin C-ter... -

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Basic information

Entry
Database: PDB / ID: 1pgv
TitleStructural Genomics of Caenorhabditis elegans: tropomodulin C-terminal domain
Componentstropomodulin TMD-1
KeywordsPROTEIN BINDING / Structural genomics / tropomodulin / PSI / Protein Structure Initiative / Southeast Collaboratory for Structural Genomics / SECSG
Function / homology
Function and homology information


muscle thin filament assembly / pointed-end actin filament capping / nematode larval development / myofibril assembly / terminal web / negative regulation of actin filament depolymerization / locomotion / embryo development ending in birth or egg hatching / myofibril / sarcomere organization ...muscle thin filament assembly / pointed-end actin filament capping / nematode larval development / myofibril assembly / terminal web / negative regulation of actin filament depolymerization / locomotion / embryo development ending in birth or egg hatching / myofibril / sarcomere organization / tropomyosin binding / striated muscle thin filament / actin filament organization / actin filament binding / cytoskeleton / cytoplasm
Similarity search - Function
Tropomodulin, invertebrate / 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 speciesCaenorhabditis elegans (invertebrata)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsSymersky, J. / Lu, S. / Li, S. / Chen, L. / Meehan, E. / Luo, M. / Qiu, S. / Bunzel, R.J. / Luo, D. / Arabashi, A. ...Symersky, J. / Lu, S. / Li, S. / Chen, L. / Meehan, E. / Luo, M. / Qiu, S. / Bunzel, R.J. / Luo, D. / Arabashi, A. / Nagy, L.A. / Lin, G. / Luan, W.C.-H. / Carson, M. / Gray, R. / Huang, W. / Southeast Collaboratory for Structural Genomics (SECSG)
Citation
Journal: Proteins / Year: 2004
Title: Structural genomics of Caenorhabditis elegans: crystal structure of the tropomodulin C-terminal domain
Authors: Lu, S. / Symersky, J. / Li, S. / Carson, M. / Chen, L. / Meehan, E. / Luo, M.
#1: Journal: Acta Crystallogr.,Sect.D / Year: 2003
Title: Purification, nanocrystallization and preliminary X_ray analysis of a C_terminal part of tropomodulin protein 1, isoform a, from Caenorhabditis elegans
Authors: Ding, H. / Qiu, S. / Bunzel, R.J. / Luo, D. / Arabashi, A. / Lu, S. / Symersky, J. / Nagy, L.A. / Delucas, L.J. / Li, S. / Luo, M.
#2: Journal: 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
DepositionMay 28, 2003Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 10, 2003Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 11, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 1.4Aug 16, 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 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: tropomodulin TMD-1


Theoretical massNumber of molelcules
Total (without water)22,3891
Polymers22,3891
Non-polymers00
Water2,360131
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)31.706, 50.621, 107.132
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Cell settingorthorhombic
Space group name H-MP212121

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Components

#1: Protein tropomodulin TMD-1 / tmd-1 / Tropomodulin protein 1 / isoform a


Mass: 22389.314 Da / Num. of mol.: 1 / Fragment: C-terminal domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Caenorhabditis elegans (invertebrata) / Plasmid: pET28b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)plySs / References: UniProt: O01479
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 131 / 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: 2.08 Å3/Da / Density % sol: 40.5 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 8
Details: RESERVOIR: 28% PEG400, 0.1 M KCL, 10 MM MGCL2, 0.1 M TRIS, PH 8. PROTEIN SOLUTION: 13.7 MG/ML IN 10 MM HEPES, PH 7.5. DROPS: 1 MICROLITER RESERVOIR + 1 MICROLITER PROTEIN SOLUTION. VAPOR ...Details: RESERVOIR: 28% PEG400, 0.1 M KCL, 10 MM MGCL2, 0.1 M TRIS, PH 8. PROTEIN SOLUTION: 13.7 MG/ML IN 10 MM HEPES, PH 7.5. DROPS: 1 MICROLITER RESERVOIR + 1 MICROLITER PROTEIN SOLUTION. VAPOR DIFFUSION, HANGING DROP, temperature 277K
Crystal grow
*PLUS
Temperature: 277 K / pH: 7.5 / Method: vapor diffusion, hanging drop
Details: Ding, H., (2003) Acta Crystallogr.,Sect.D, 59, 1106.
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetailsChemical formula
110 mMHEPES1drop
20.01 %sodium azide1droppH7.5
313.7 mg/mlprotein1drop
428.0 %(v/v)PEG4001reservoir
5100 mM1reservoirKCl
610 mM1reservoirMgCl2
7100 mMTris-HCl1reservoirpH8.0

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 0.984 Å
DetectorType: MARRESEARCH / Detector: CCD / Date: Feb 16, 2003
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.984 Å / Relative weight: 1
ReflectionResolution: 1.8→50 Å / Num. obs: 16153 / % possible obs: 96.9 % / Observed criterion σ(I): -1 / Redundancy: 8.8 % / Biso Wilson estimate: 24.3 Å2 / Rsym value: 0.064 / Net I/σ(I): 10.6
Reflection shellResolution: 1.8→1.86 Å / Redundancy: 3.2 % / Mean I/σ(I) obs: 3.5 / Num. unique all: 1421 / Rsym value: 0.243 / % possible all: 85.3
Reflection
*PLUS
Highest resolution: 1.8 Å / Lowest resolution: 50 Å / Num. obs: 16189 / % possible obs: 96.7 % / Num. measured all: 142014 / Rmerge(I) obs: 0.064
Reflection shell
*PLUS
Highest resolution: 1.8 Å / % possible obs: 85.3 % / Rmerge(I) obs: 0.243

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Processing

Software
NameClassification
MAR345data collection
HKL-2000data reduction
AMoREphasing
ARP/wARPmodel building
CNSrefinement
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 1IO0

1io0


Resolution: 1.8→50 Å / Data cutoff high absF: 10000 / Data cutoff high rms absF: 10000 / Data cutoff low absF: 0 / Isotropic thermal model: isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.234 786 4.9 %random
Rwork0.209 ---
all-16153 --
obs-16153 96.9 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 45.83 Å2 / ksol: 0.39 e/Å3
Displacement parametersBiso mean: 25.5 Å2
Refine analyzeLuzzati coordinate error obs: 0.21 Å / Luzzati d res low obs: 5 Å / Luzzati sigma a obs: 0.13 Å
Refinement stepCycle: LAST / Resolution: 1.8→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1343 0 0 131 1474
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.005
X-RAY DIFFRACTIONc_angle_deg1
X-RAY DIFFRACTIONc_mcbond_it1.2031.5
X-RAY DIFFRACTIONc_mcangle_it1.752
X-RAY DIFFRACTIONc_scbond_it2.472
X-RAY DIFFRACTIONc_scangle_it3.8092.5
LS refinement shellResolution: 1.8→1.84 Å / Total num. of bins used: 15 /
RfactorNum. reflection
Rfree0.31 47
Rwork0.279 -
obs-857
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2WATER_REP.PARAMWATER.TOP
Refinement
*PLUS
Highest resolution: 1.8 Å / % reflection Rfree: 5 %
Solvent computation
*PLUS
Displacement parameters
*PLUS

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