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- PDB-1mg7: Crystal Structure of xol-1 -

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ID or keywords:

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Basic information

Entry
Database: PDB / ID: 1mg7
TitleCrystal Structure of xol-1
Componentsearly switch protein xol-1 2.2k splice form
KeywordsGENE REGULATION / alpha-beta
Function / homology
Function and homology information


dosage compensation by hypoactivation of X chromosome / male sex determination / cell differentiation / nucleus
Similarity search - Function
Switch protein XOL-1, GHMP-like / Switch protein XOL-1, N-terminal / Switch protein XOL-1, GHMP-like / : / Switch protein XOL-1, N-terminal / Switch protein XOL-1, GHMP-like / GHMP kinase, C-terminal domain superfamily / Ribosomal Protein S5; domain 2 - #10 / Ribosomal Protein S5; domain 2 / Ribosomal protein S5 domain 2-type fold, subgroup ...Switch protein XOL-1, GHMP-like / Switch protein XOL-1, N-terminal / Switch protein XOL-1, GHMP-like / : / Switch protein XOL-1, N-terminal / Switch protein XOL-1, GHMP-like / GHMP kinase, C-terminal domain superfamily / Ribosomal Protein S5; domain 2 - #10 / Ribosomal Protein S5; domain 2 / Ribosomal protein S5 domain 2-type fold, subgroup / Ribosomal protein S5 domain 2-type fold / Alpha-Beta Plaits / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Biological speciesCaenorhabditis elegans (invertebrata)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.55 Å
AuthorsLuz, J.G. / Hassig, C.A. / Godzik, A. / Meyer, B.J. / Wilson, I.A.
CitationJournal: Genes Dev. / Year: 2003
Title: XOL-1, primary determinant of sexual fate in C. elegans, is a GHMP kinase family member and a structural prototype for a class of developmental regulators
Authors: Luz, J.G. / Hassig, C.A. / Pickle, C. / Godzik, A. / Meyer, B.J. / Wilson, I.A.
History
DepositionAug 14, 2002Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 22, 2003Provider: repository / Type: Initial release
Revision 1.1Apr 28, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 11, 2017Group: Refinement description / Category: software
Revision 1.4Feb 14, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: early switch protein xol-1 2.2k splice form
B: early switch protein xol-1 2.2k splice form


Theoretical massNumber of molelcules
Total (without water)94,4272
Polymers94,4272
Non-polymers00
Water10,557586
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)116.071, 86.023, 80.240
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212

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Components

#1: Protein early switch protein xol-1 2.2k splice form


Mass: 47213.629 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Caenorhabditis elegans (invertebrata) / Plasmid: pRSETA / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21DE3 / References: UniProt: Q23229
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 586 / 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: 3

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Sample preparation

CrystalDensity Matthews: 2.12 Å3/Da / Density % sol: 41.99 %
Crystal growTemperature: 277.15 K / Method: vapor diffusion, sitting drop / pH: 7.8
Details: peg 400, magnesium chloride, hepes, dtt, pH 7.8, VAPOR DIFFUSION, SITTING DROP, temperature 277.15K
Crystal
*PLUS
Density Matthews: 2.4 Å3/Da
Crystal grow
*PLUS
Temperature: 4 ℃ / Method: vapor diffusion
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetailsChemical formula
180 mg/mlprotein1drop
20.1 MHEPES1reservoirpH7.8
30.2 M1reservoirMgCl2
417.5 %PEG4001reservoir
55 %MPD1reservoir

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Data collection

DiffractionMean temperature: 93 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL11-1 / Wavelength: 0.98 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Nov 19, 2001
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 1.55→50 Å / Num. obs: 125315 / % possible obs: 97.3 % / Observed criterion σ(I): -3 / Redundancy: 3.8 % / Rsym value: 0.054 / Net I/σ(I): 25.2
Reflection shellResolution: 1.5→1.55 Å / Mean I/σ(I) obs: 1.6 / Num. unique all: 12180 / Rsym value: 0.73 / % possible all: 95.6
Reflection
*PLUS
Lowest resolution: 50 Å / Num. obs: 113135 / Rmerge(I) obs: 0.054
Reflection shell
*PLUS
% possible obs: 96.9 % / Num. unique obs: 12340 / Rmerge(I) obs: 0.54 / Mean I/σ(I) obs: 2.4

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Processing

Software
NameVersionClassification
HKL-2000data collection
SCALEPACKdata scaling
SOLVEphasing
ARP/wARPmodel building
CNS1.1refinement
HKL-2000data reduction
RefinementMethod to determine structure: MAD / Resolution: 1.55→50 Å / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.2124 5468 -random
Rwork0.2036 ---
all-108727 --
obs-103259 93 %-
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-0.739 Å20 Å20 Å2
2---2.181 Å20 Å2
3---1.442 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.19 Å0.18 Å
Luzzati d res low-50 Å
Luzzati sigma a0.14 Å0.12 Å
Refinement stepCycle: LAST / Resolution: 1.55→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5544 0 0 586 6130
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_angle_deg1.3
X-RAY DIFFRACTIONc_bond_d0.005
X-RAY DIFFRACTIONc_dihedral_angle_d22.9
X-RAY DIFFRACTIONc_improper_angle_d0.79
Xplor file
Refine-IDSerial noParam file
X-RAY DIFFRACTION1protein_rep.param
X-RAY DIFFRACTION2water_rep.param
Refinement
*PLUS
Lowest resolution: 50 Å / % reflection Rfree: 5 % / Rfactor Rfree: 0.213 / Rfactor Rwork: 0.203
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.006
X-RAY DIFFRACTIONc_angle_deg1.4
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg22.9
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg0.79

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