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- PDB-7ekn: Crystal structure of AF10-ipep complex -

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Basic information

Entry
Database: PDB / ID: 7ekn
TitleCrystal structure of AF10-ipep complex
Components
  • Protein AF-10
  • ipep
KeywordsPROTEIN BINDING / inhibitor
Function / homologynucleoplasm / cytosol / Protein AF-10
Function and homology information
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.14 Å
AuthorsChen, S. / Zhou, Z.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)31770801 China
CitationJournal: J Leukoc Biol / Year: 2021
Title: Structural characteristics of coiled-coil regions in AF10-DOT1L and AF10-inhibitory peptide complex.
Authors: Zhou, Z. / Kang, S. / Huang, Z. / Zhou, Z. / Chen, S.
History
DepositionApr 5, 2021Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Apr 28, 2021Provider: repository / Type: Initial release
Revision 1.1Nov 10, 2021Group: Database references / Structure summary
Category: citation / citation_author ...citation / citation_author / database_2 / struct
Item: _citation.journal_abbrev / _citation.journal_id_CSD ..._citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct.title
Revision 1.2Feb 16, 2022Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.3Nov 29, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
B: ipep
A: Protein AF-10
D: ipep
C: Protein AF-10
F: ipep
E: Protein AF-10
H: ipep
G: Protein AF-10


Theoretical massNumber of molelcules
Total (without water)40,1068
Polymers40,1068
Non-polymers00
Water5,405300
1
B: ipep
A: Protein AF-10


Theoretical massNumber of molelcules
Total (without water)10,0272
Polymers10,0272
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2310 Å2
ΔGint-20 kcal/mol
Surface area6300 Å2
MethodPISA
2
D: ipep
C: Protein AF-10


Theoretical massNumber of molelcules
Total (without water)10,0272
Polymers10,0272
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2280 Å2
ΔGint-18 kcal/mol
Surface area6100 Å2
MethodPISA
3
F: ipep
E: Protein AF-10


Theoretical massNumber of molelcules
Total (without water)10,0272
Polymers10,0272
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2220 Å2
ΔGint-18 kcal/mol
Surface area6510 Å2
MethodPISA
4
H: ipep
G: Protein AF-10


Theoretical massNumber of molelcules
Total (without water)10,0272
Polymers10,0272
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2110 Å2
ΔGint-18 kcal/mol
Surface area6420 Å2
MethodPISA
Unit cell
Length a, b, c (Å)42.626, 46.389, 49.170
Angle α, β, γ (deg.)76.669, 67.700, 74.673
Int Tables number1
Space group name H-MP1
Space group name HallP1

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Components

#1: Protein/peptide
ipep


Mass: 5018.727 Da / Num. of mol.: 4 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human)
#2: Protein/peptide
Protein AF-10


Mass: 5007.853 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: MLLT10 / Production host: Escherichia coli (E. coli) / References: UniProt: Q5JT35
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 300 / 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: 2.14 Å3/Da / Density % sol: 42.52 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / Details: PEG4000, Tris8.5, Sodium acetate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL18U1 / Wavelength: 0.9788 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Mar 1, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9788 Å / Relative weight: 1
ReflectionResolution: 2.14→50 Å / Num. obs: 17862 / % possible obs: 97.5 % / Redundancy: 3.8 % / Biso Wilson estimate: 19.38 Å2 / Rmerge(I) obs: 0.129 / Rpim(I) all: 0.129 / Rrim(I) all: 0.182 / Net I/σ(I): 10.2
Reflection shellResolution: 2.14→2.31 Å / Num. unique obs: 30000 / CC1/2: 0.648

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Processing

Software
NameVersionClassification
PHENIX1.17.1_3660refinement
PHENIX1.17.1_3660refinement
PDB_EXTRACT3.27data extraction
HKL-3000data reduction
HKL-3000data scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 7EDP

7edp


Resolution: 2.14→45.01 Å / SU ML: 0.2943 / Cross valid method: FREE R-VALUE / σ(F): 1.98 / Phase error: 26.5325
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2605 1785 10 %
Rwork0.1865 16066 -
obs0.1936 17851 97.47 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 23.98 Å2
Refinement stepCycle: LAST / Resolution: 2.14→45.01 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2659 0 0 300 2959
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00692661
X-RAY DIFFRACTIONf_angle_d0.74693542
X-RAY DIFFRACTIONf_chiral_restr0.0405419
X-RAY DIFFRACTIONf_plane_restr0.0034454
X-RAY DIFFRACTIONf_dihedral_angle_d23.757352
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.14-2.20.33081310.25171188X-RAY DIFFRACTION95.58
2.2-2.260.3141320.24581187X-RAY DIFFRACTION94.42
2.26-2.340.28441380.21591246X-RAY DIFFRACTION96.72
2.34-2.420.29481370.19621233X-RAY DIFFRACTION97.23
2.42-2.520.28851380.20081232X-RAY DIFFRACTION97.72
2.52-2.630.27411360.1871228X-RAY DIFFRACTION97.64
2.63-2.770.28811400.19271260X-RAY DIFFRACTION98.31
2.77-2.940.24571380.20351245X-RAY DIFFRACTION98.09
2.94-3.170.30131390.19531250X-RAY DIFFRACTION98.23
3.17-3.490.25121400.17671262X-RAY DIFFRACTION98.39
3.49-3.990.22961350.1511213X-RAY DIFFRACTION97.05
3.99-5.030.18931410.15891266X-RAY DIFFRACTION98.81
5.03-45.010.26541400.18211256X-RAY DIFFRACTION99.01

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