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- PDB-8gci: Crystal structure of C. elegans LIN-42 PAS-B domain -

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Basic information

Entry
Database: PDB / ID: 8gci
TitleCrystal structure of C. elegans LIN-42 PAS-B domain
ComponentsPeriod protein homolog lin-42
KeywordsGENE REGULATION / PAS domain
Function / homology
Function and homology information


negative regulation of dauer larval development / regulation of development, heterochronic / negative regulation of miRNA transcription / RNA polymerase II-specific DNA-binding transcription factor binding / cell differentiation / nucleus / cytoplasm
Similarity search - Function
: / PAS domain / PAS domain / PAS domain / PAS domain superfamily
Similarity search - Domain/homology
Period protein homolog lin-42
Similarity search - Component
Biological speciesCaenorhabditis elegans (invertebrata)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.42 Å
AuthorsSpangler, B.K. / Coronado, A.R. / Tripathi, S.M. / Ward, J.D. / Partch, C.L.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS) United States
CitationJournal: To Be Published
Title: Crystal structure of C. elegans LIN-42 PAS-B domain
Authors: Spangler, B.K. / Coronado, A.R. / Tripathi, S.M. / Ward, J.D. / Partch, C.L.
History
DepositionMar 1, 2023Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 15, 2023Provider: repository / Type: Initial release
Revision 1.1May 22, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Period protein homolog lin-42


Theoretical massNumber of molelcules
Total (without water)31,1861
Polymers31,1861
Non-polymers00
Water1,31573
1
A: Period protein homolog lin-42

A: Period protein homolog lin-42


Theoretical massNumber of molelcules
Total (without water)62,3712
Polymers62,3712
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_765-x+2,-y+1,z1
Buried area1220 Å2
ΔGint-9 kcal/mol
Surface area17040 Å2
MethodPISA
Unit cell
Length a, b, c (Å)50.733, 105.907, 152.966
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number23
Space group name H-MI222

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Components

#1: Protein Period protein homolog lin-42 / Abnormal cell lineage protein 42


Mass: 31185.611 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Caenorhabditis elegans (invertebrata) / Gene: lin-42, F47F6.1 / Production host: Escherichia coli (E. coli) / References: UniProt: Q65ZG8
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 73 / 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: 3.29 Å3/Da / Density % sol: 62.66 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop
Details: 0.15M Lithium sulfate, 1.5M sodium potassium tartrate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-D / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jun 30, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.42→45.94 Å / Num. obs: 16123 / % possible obs: 99.52 % / Redundancy: 7.1 % / CC1/2: 0.994 / Rmerge(I) obs: 0.14 / Net I/σ(I): 10.2
Reflection shellResolution: 2.42→2.51 Å / Rmerge(I) obs: 0.658 / Mean I/σ(I) obs: 3.3 / Num. unique obs: 1634 / CC1/2: 0.895

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Processing

Software
NameVersionClassification
PHENIX(1.20.1_4487)refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3GEC

3gec


Resolution: 2.42→45.94 Å / SU ML: 0.26 / Cross valid method: FREE R-VALUE / σ(F): 0.04 / Phase error: 28.88 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2929 1556 9.99 %
Rwork0.2627 --
obs0.2657 15583 96.29 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.42→45.94 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1318 0 0 76 1394
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.009
X-RAY DIFFRACTIONf_angle_d1.083
X-RAY DIFFRACTIONf_dihedral_angle_d6.24181
X-RAY DIFFRACTIONf_chiral_restr0.053218
X-RAY DIFFRACTIONf_plane_restr0.009232
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.42-2.50.29471230.24261146X-RAY DIFFRACTION89
2.5-2.590.31461330.25171202X-RAY DIFFRACTION92
2.59-2.690.31491390.24951239X-RAY DIFFRACTION95
2.69-2.810.28281380.24331238X-RAY DIFFRACTION96
2.81-2.960.26541380.23911260X-RAY DIFFRACTION97
2.96-3.150.29721430.24981280X-RAY DIFFRACTION97
3.15-3.390.31311440.24271288X-RAY DIFFRACTION98
3.39-3.730.27111450.24211308X-RAY DIFFRACTION99
3.73-4.270.28381460.25791320X-RAY DIFFRACTION99
4.27-5.380.26281490.26531341X-RAY DIFFRACTION100
5.38-45.940.3341580.33221405X-RAY DIFFRACTION99

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