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- PDB-4jnd: Structure of a C.elegans sex determining protein -

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Basic information

Entry
Database: PDB / ID: 4jnd
TitleStructure of a C.elegans sex determining protein
ComponentsCa(2+)/calmodulin-dependent protein kinase phosphatase
KeywordsHYDROLASE / novel fold / sex determination / cytosol / male promoting
Function / homology
Function and homology information


masculinization of hermaphroditic germ-line / protein serine/threonine phosphatase activity => GO:0004722 / nematode male tail tip morphogenesis / calmodulin-dependent protein phosphatase activity / peptidyl-threonine dephosphorylation / male sex determination / protein serine/threonine phosphatase activity / protein-serine/threonine phosphatase / positive regulation of cysteine-type endopeptidase activity involved in apoptotic process / phosphoprotein phosphatase activity ...masculinization of hermaphroditic germ-line / protein serine/threonine phosphatase activity => GO:0004722 / nematode male tail tip morphogenesis / calmodulin-dependent protein phosphatase activity / peptidyl-threonine dephosphorylation / male sex determination / protein serine/threonine phosphatase activity / protein-serine/threonine phosphatase / positive regulation of cysteine-type endopeptidase activity involved in apoptotic process / phosphoprotein phosphatase activity / protein dephosphorylation / cell differentiation / apoptotic process / protein-containing complex / metal ion binding
Similarity search - Function
Rna Polymerase Sigma Factor; Chain: A - #220 / Sigma factor PP2C-like phosphatases / PPM-type phosphatase, divalent cation binding / PPM-type phosphatase domain signature. / PPM-type phosphatase domain / Phosphatase 2c; domain 1 / Protein phosphatase 2C / Protein phosphatase 2C family / Rna Polymerase Sigma Factor; Chain: A / Serine/threonine phosphatases, family 2C, catalytic domain ...Rna Polymerase Sigma Factor; Chain: A - #220 / Sigma factor PP2C-like phosphatases / PPM-type phosphatase, divalent cation binding / PPM-type phosphatase domain signature. / PPM-type phosphatase domain / Phosphatase 2c; domain 1 / Protein phosphatase 2C / Protein phosphatase 2C family / Rna Polymerase Sigma Factor; Chain: A / Serine/threonine phosphatases, family 2C, catalytic domain / PPM-type phosphatase domain profile. / PPM-type phosphatase-like domain / PPM-type phosphatase-like domain superfamily / 4-Layer Sandwich / Orthogonal Bundle / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
Protein phosphatase fem-2
Similarity search - Component
Biological speciesCaenorhabditis elegans (invertebrata)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.652 Å
AuthorsFeng, Y. / Zhang, Y. / Ge, J. / Yang, M.
CitationJournal: J.Biol.Chem. / Year: 2013
Title: Structural insight into Caenorhabditis elegans sex-determining protein FEM-2.
Authors: Zhang, Y. / Zhao, H. / Wang, J. / Ge, J. / Li, Y. / Gu, J. / Li, P. / Feng, Y. / Yang, M.
History
DepositionMar 15, 2013Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Jun 19, 2013Provider: repository / Type: Initial release
Revision 1.1Jun 17, 2015Group: Database references
Revision 1.2Mar 20, 2024Group: 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_ref_seq_dif / 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_asym_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.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_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.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.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_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Ca(2+)/calmodulin-dependent protein kinase phosphatase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)51,4203
Polymers51,3711
Non-polymers492
Water6,972387
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)81.399, 160.093, 77.422
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221
Components on special symmetry positions
IDModelComponents
11A-639-

HOH

21A-691-

HOH

31A-855-

HOH

41A-911-

HOH

51A-912-

HOH

61A-922-

HOH

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Components

#1: Protein Ca(2+)/calmodulin-dependent protein kinase phosphatase / CaM-kinase phosphatase / CaMKPase / Feminization of XX and XO animals protein 2 / Sex-determining ...CaM-kinase phosphatase / CaMKPase / Feminization of XX and XO animals protein 2 / Sex-determining protein fem-2


Mass: 51371.234 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Caenorhabditis elegans (invertebrata) / Gene: fem-2, T19C3.8 / Production host: Escherichia coli (E. coli)
References: UniProt: P49594, protein-serine/threonine phosphatase
#2: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 387 / 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: 2.45 Å3/Da / Density % sol: 49.9 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 7.4
Details: 28% PEG 400, 0.2M MgCl2, 0.1M HEPES Sodium pH 7.4, VAPOR DIFFUSION, HANGING DROP, temperature 291K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 0.979 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Aug 20, 2010
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 1.65→50 Å / Num. all: 60896 / Num. obs: 60652 / % possible obs: 99.6 % / Redundancy: 4.7 % / Rmerge(I) obs: 0.091
Reflection shell
Resolution (Å)Diffraction-ID% possible all
1.65-1.71198.2
1.71-1.78199.9
1.78-1.861100
1.86-1.961100
1.96-2.081100
2.08-2.241100

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Processing

Software
NameVersionClassification
HKL-2000data collection
SHELXSphasing
PHENIX(phenix.refine: 1.6.3_473)refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: SAD / Resolution: 1.652→29.796 Å / SU ML: 0.2 / σ(F): 0 / Phase error: 20.05 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2025 2831 5.03 %
Rwork0.1772 --
obs0.1784 56265 92.37 %
Solvent computationShrinkage radii: 0.83 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 39.844 Å2 / ksol: 0.364 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-7.1459 Å2-0 Å2-0 Å2
2---4.0843 Å20 Å2
3----3.0615 Å2
Refinement stepCycle: LAST / Resolution: 1.652→29.796 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3222 0 2 387 3611
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0073310
X-RAY DIFFRACTIONf_angle_d1.054487
X-RAY DIFFRACTIONf_dihedral_angle_d13.0951230
X-RAY DIFFRACTIONf_chiral_restr0.074485
X-RAY DIFFRACTIONf_plane_restr0.005593
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
1.6516-1.680.28381100.252221477
1.68-1.71060.25371250.2498227080
1.7106-1.74350.23871200.243239083
1.7435-1.77910.31561100.2285239383
1.7791-1.81770.25091330.214242285
1.8177-1.860.26051310.2026240184
1.86-1.90650.20571260.1884249187
1.9065-1.95810.22221610.1802259392
1.9581-2.01570.2331330.1777272894
2.0157-2.08070.22291450.1735280597
2.0807-2.15510.20131570.1657278397
2.1551-2.24130.2031750.1629278598
2.2413-2.34330.1991460.1665281498
2.3433-2.46680.2051550.1673283098
2.4668-2.62120.19811460.1782286899
2.6212-2.82350.24321540.185287999
2.8235-3.10740.21211390.19452912100
3.1074-3.55640.15781630.1692911100
3.5564-4.47820.15911440.1422964100
4.4782-29.80120.19871580.1849298197
Refinement TLS params.Method: refined / Origin x: 15.7495 Å / Origin y: 57.5723 Å / Origin z: 36.1272 Å
111213212223313233
T0.0944 Å20.0145 Å20.0104 Å2-0.113 Å20.0036 Å2--0.1101 Å2
L0.4868 °2-0.0764 °2-0.0016 °2-1.065 °20.3161 °2--0.9431 °2
S0.0124 Å °0.0009 Å °-0.0332 Å °-0.0101 Å °-0.0636 Å °0.0138 Å °-0.0396 Å °-0.0152 Å °-0 Å °
Refinement TLS groupSelection details: CHAIN A AND RESID 13:436

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