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- PDB-6ap0: Crystal structure of human FLASH N-terminal domain C54S/C83A (Cry... -

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Basic information

Entry
Database: PDB / ID: 6ap0
TitleCrystal structure of human FLASH N-terminal domain C54S/C83A (Crystal form 2)
ComponentsCASP8-associated protein 2
KeywordsGENE REGULATION / coiled-coil
Function / homology
Function and homology information


SUMO polymer binding / Fas signaling pathway / peptidase activator activity involved in apoptotic process / death receptor binding / cysteine-type endopeptidase activator activity involved in apoptotic process / extrinsic apoptotic signaling pathway via death domain receptors / SUMOylation of transcription cofactors / apoptotic signaling pathway / cellular response to mechanical stimulus / PML body ...SUMO polymer binding / Fas signaling pathway / peptidase activator activity involved in apoptotic process / death receptor binding / cysteine-type endopeptidase activator activity involved in apoptotic process / extrinsic apoptotic signaling pathway via death domain receptors / SUMOylation of transcription cofactors / apoptotic signaling pathway / cellular response to mechanical stimulus / PML body / transcription corepressor activity / signal transduction / mitochondrion / nucleoplasm / nucleus / cytoplasm
Similarity search - Function
CASP8-associated protein 2 / : / Myb-like DNA-binding domain / Homeobox-like domain superfamily
Similarity search - Domain/homology
CASP8-associated protein 2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.581 Å
AuthorsAik, W.S. / Tong, L.
CitationJournal: PLoS ONE / Year: 2017
Title: The N-terminal domains of FLASH and Lsm11 form a 2:1 heterotrimer for histone pre-mRNA 3'-end processing.
Authors: Aik, W.S. / Lin, M.H. / Tan, D. / Tripathy, A. / Marzluff, W.F. / Dominski, Z. / Chou, C.Y. / Tong, L.
History
DepositionAug 16, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 15, 2017Provider: repository / Type: Initial release
Revision 1.1Oct 4, 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
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
B: CASP8-associated protein 2
A: CASP8-associated protein 2


Theoretical massNumber of molelcules
Total (without water)22,6682
Polymers22,6682
Non-polymers00
Water18010
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: light scattering
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4280 Å2
ΔGint-45 kcal/mol
Surface area12660 Å2
MethodPISA
Unit cell
Length a, b, c (Å)63.478, 44.346, 68.433
Angle α, β, γ (deg.)90.00, 98.65, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein CASP8-associated protein 2 / FLICE-associated huge protein


Mass: 11333.769 Da / Num. of mol.: 2 / Fragment: UNP residues 51-137 / Mutation: C54S, C83A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CASP8AP2, FLASH, KIAA1315, RIP25 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9UKL3
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 10 / 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: 2.1 Å3/Da / Density % sol: 41.44 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 100 mM sodium formate, 15% (w/v) PEG 3350, 3% (v/v) 1,6-hexanediol

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-E / Wavelength: 0.9792 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Mar 10, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 2.58→36.216 Å / Num. obs: 11542 / % possible obs: 99.6 % / Redundancy: 3.8 % / CC1/2: 0.998 / Rmerge(I) obs: 0.079 / Net I/σ(I): 13.42
Reflection shellResolution: 2.58→2.74 Å / Redundancy: 3.7 % / Rmerge(I) obs: 0.467 / Mean I/σ(I) obs: 3.82 / Num. unique obs: 1848 / CC1/2: 0.898 / % possible all: 99.2

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6ANO

6ano


Resolution: 2.581→36.216 Å / SU ML: 0.37 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 27
RfactorNum. reflection% reflection
Rfree0.2487 575 4.98 %
Rwork0.2138 --
obs0.2156 11536 99.58 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.581→36.216 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1389 0 0 10 1399
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0031412
X-RAY DIFFRACTIONf_angle_d0.5341890
X-RAY DIFFRACTIONf_dihedral_angle_d15.973562
X-RAY DIFFRACTIONf_chiral_restr0.021216
X-RAY DIFFRACTIONf_plane_restr0.002244
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.5808-2.84050.34261440.27992699X-RAY DIFFRACTION99
2.8405-3.25130.27181470.26592776X-RAY DIFFRACTION100
3.2513-4.09530.28281420.19982738X-RAY DIFFRACTION100
4.0953-36.21970.18891420.18692748X-RAY DIFFRACTION99
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.9372.513-1.78529.0412-6.22625.431-0.19730.032-0.0713-0.6055-0.092-0.24420.19080.14490.26730.27740.0494-0.030.42830.0050.4468126.617113.9151142.616
27.4551-0.406-1.4747.05264.1454.4350.3723-0.2417-0.6144-0.39450.2448-0.3692-0.22562.2772-0.55491.02050.0486-0.05620.9769-0.33040.7829137.775351.954111.0051
30.25921.3287-0.9266.1801-5.33724.3818-0.08250.2767-0.07270.53870.3368-0.0222-0.1672-0.4085-0.35660.4312-0.040.04780.3879-0.00620.3498120.24774.7849149.0035
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'B' and (resid 52 through 139 )
2X-RAY DIFFRACTION2chain 'A' and (resid 56 through 67 )
3X-RAY DIFFRACTION3chain 'A' and (resid 68 through 140 )

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