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- PDB-6ckn: Crystal structure of an AF10 fragment -

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Basic information

Entry
Database: PDB / ID: 6ckn
TitleCrystal structure of an AF10 fragment
ComponentsProtein AF-10
KeywordsDNA BINDING PROTEIN / Structural Genomics / Structural Genomics Consortium / SGC
Function / homology
Function and homology information


nucleosome binding / histone binding / chromatin binding / regulation of transcription by RNA polymerase II / positive regulation of transcription by RNA polymerase II / protein-containing complex / DNA binding / nucleoplasm / metal ion binding / nucleus
Similarity search - Function
: / : / : / PHD-finger / PHD-zinc-finger like domain / Extended PHD (ePHD) domain / Extended PHD (ePHD) domain profile. / Zinc finger, PHD-type, conserved site / Zinc finger PHD-type signature. / Zinc finger PHD-type profile. ...: / : / : / PHD-finger / PHD-zinc-finger like domain / Extended PHD (ePHD) domain / Extended PHD (ePHD) domain profile. / Zinc finger, PHD-type, conserved site / Zinc finger PHD-type signature. / Zinc finger PHD-type profile. / Zinc finger, PHD-finger / Zinc finger, PHD-type / PHD zinc finger / Zinc finger, FYVE/PHD-type / Zinc finger, RING/FYVE/PHD-type
Similarity search - Domain/homology
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.49 Å
AuthorsQin, S. / Tempel, W. / Li, Y. / Bountra, C. / Arrowsmith, C.H. / Edwards, A.M. / Min, J. / Structural Genomics Consortium (SGC)
CitationJournal: Genes Dev. / Year: 2018
Title: Structural and functional analysis of the DOT1L-AF10 complex reveals mechanistic insights into MLL-AF10-associated leukemogenesis.
Authors: Zhang, H. / Zhou, B. / Qin, S. / Xu, J. / Harding, R. / Tempel, W. / Nayak, V. / Li, Y. / Loppnau, P. / Dou, Y. / Min, J.
History
DepositionFeb 28, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 21, 2018Provider: repository / Type: Initial release
Revision 1.1Apr 18, 2018Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Protein AF-10
B: Protein AF-10


Theoretical massNumber of molelcules
Total (without water)17,5844
Polymers17,5842
Non-polymers02
Water0
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1340 Å2
ΔGint-12 kcal/mol
Surface area9740 Å2
MethodPISA
Unit cell
Length a, b, c (Å)40.058, 40.058, 205.570
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number96
Space group name H-MP43212

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Components

#1: Protein Protein AF-10 / ALL1-fused gene from chromosome 10 protein


Mass: 8791.813 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: MLLT10, AF10 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)-V2R-pRARE2 / References: UniProt: P55197
#2: Chemical ChemComp-UNX / UNKNOWN ATOM OR ION


Num. of mol.: 2 / Source method: obtained synthetically

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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: 2.36 Å3/Da / Density % sol: 47.83 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop
Details: This crystal's crystallization record is incomplete. We attempted to reconstruct the condition through reference to records from related crystals: 20% PEG-3350, 0.2 M magnesium nitrate. Additive: 1,6-hexanediol

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.97918 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Jun 20, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97918 Å / Relative weight: 1
ReflectionResolution: 2.49→41.11 Å / Num. obs: 6558 / % possible obs: 99.9 % / Redundancy: 13.1 % / Biso Wilson estimate: 66.04 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.087 / Rpim(I) all: 0.025 / Rrim(I) all: 0.091 / Net I/σ(I): 20.6 / Num. measured all: 85873 / Scaling rejects: 2
Reflection shellResolution: 2.49→2.59 Å / Redundancy: 13.7 % / Rmerge(I) obs: 1.272 / Num. unique obs: 696 / CC1/2: 0.963 / Rpim(I) all: 0.354 / Rrim(I) all: 1.322 / % possible all: 99.8

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Processing

Software
NameVersionClassification
BUSTER2.10.2refinement
Aimless0.5.32data scaling
PDB_EXTRACT3.22data extraction
XDSdata reduction
PHASERphasing
SHELXDphasing
PARROTphasing
BUCCANEERmodel building
RefinementMethod to determine structure: SAD / Resolution: 2.49→39.32 Å / Cor.coef. Fo:Fc: 0.888 / Cor.coef. Fo:Fc free: 0.901 / Rfactor Rfree error: 0 / SU R Cruickshank DPI: 0.377 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.407 / SU Rfree Blow DPI: 0.257 / SU Rfree Cruickshank DPI: 0.253
Details: Se-Met SAD phasing with shelx/phaser/parrot. Autotracing with BUCCANEER. Refinement with REFMAC and autobuster.
RfactorNum. reflection% reflection
Rfree0.262 652 10.05 %
Rwork0.247 --
obs0.249 6488 99.9 %
Displacement parametersBiso max: 150.5 Å2 / Biso mean: 79.69 Å2 / Biso min: 55.09 Å2
Baniso -1Baniso -2Baniso -3
1--18.15 Å20 Å20 Å2
2---18.15 Å20 Å2
3---36.2999 Å2
Refine analyzeLuzzati coordinate error obs: 0.44 Å
Refinement stepCycle: final / Resolution: 2.49→39.32 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms973 0 2 0 975
Biso mean--61.64 --
Num. residues----132
Refine LS restraints
Refine-IDTypeNumberRestraint functionWeightDev ideal
X-RAY DIFFRACTIONt_dihedral_angle_d353SINUSOIDAL2
X-RAY DIFFRACTIONt_trig_c_planes31HARMONIC2
X-RAY DIFFRACTIONt_gen_planes140HARMONIC5
X-RAY DIFFRACTIONt_it980HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_chiral_improper_torsion133SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact1163SEMIHARMONIC4
X-RAY DIFFRACTIONt_bond_d980HARMONIC20.01
X-RAY DIFFRACTIONt_angle_deg1323HARMONIC21.1
X-RAY DIFFRACTIONt_omega_torsion2.3
X-RAY DIFFRACTIONt_other_torsion14.95
LS refinement shellResolution: 2.49→2.78 Å / Total num. of bins used: 5
RfactorNum. reflection% reflection
Rfree0.28 183 10.45 %
Rwork0.278 1569 -
all-1752 -
obs--99.89 %
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)
12.11180.5835-2.50720-0.65082.91720.0368-0.05140.17860.24530.0407-0.073-0.1833-0.5199-0.07750.0613-0.1598-0.05530.0031-0.0002-0.1825-31.559633.0791109.74
21.02811.7485-0.26881.8838-2.85342.97160.02170.3008-0.0916-0.12160.0511-0.0047-0.5056-0.1979-0.07270.0863-0.095-0.0073-0.0924-0.0493-0.2007-36.704125.478395.1806
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1{ A|* }A730 - 795
2X-RAY DIFFRACTION2{ B|* }B730 - 795

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