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- PDB-4nq0: Structural insights into yeast histone chaperone Hif1: a scaffold... -

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Basic information

Entry
Database: PDB / ID: 4nq0
TitleStructural insights into yeast histone chaperone Hif1: a scaffold protein recruiting protein complexes to core histones
ComponentsHAT1-interacting factor 1
KeywordsCHAPERONE / TPR / NASP homologue / SHNi-TPR / mediating protein-protein interactions / histone chaperone / Nucleus
Function / homology
Function and homology information


histone acetyltransferase complex / subtelomeric heterochromatin formation / nucleosome assembly / histone binding / chromosome, telomeric region / protein homodimerization activity / nucleus
Similarity search - Function
Tetratricopeptide repeat domain / Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat / Alpha Horseshoe / Tetratricopeptide-like helical domain superfamily / Mainly Alpha
Similarity search - Domain/homology
HAT1-interacting factor 1
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.1 Å
AuthorsLiu, H. / Zhang, M. / He, W. / Zhu, Z. / Teng, M. / Gao, Y. / Niu, L.
CitationJournal: Biochem.J. / Year: 2014
Title: Structural insights into yeast histone chaperone Hif1: a scaffold protein recruiting protein complexes to core histones
Authors: Liu, H. / Zhang, M. / He, W. / Zhu, Z. / Teng, M. / Gao, Y. / Niu, L.
History
DepositionNov 23, 2013Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Jul 16, 2014Provider: repository / Type: Initial release
Revision 1.1Dec 10, 2014Group: Database references
Revision 1.2Mar 20, 2024Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: HAT1-interacting factor 1


Theoretical massNumber of molelcules
Total (without water)44,5531
Polymers44,5531
Non-polymers00
Water1,20767
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)48.308, 78.280, 82.689
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein HAT1-interacting factor 1


Mass: 44553.188 Da / Num. of mol.: 1 / Fragment: HAT1-interacting factor 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Strain: ATCC 204508 / S288c / Gene: HIF1, YLL022C, L1205 / Production host: Escherichia coli (E. coli) / References: UniProt: Q12373
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 67 / 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: 1.75 Å3/Da / Density % sol: 29.9 %
Crystal growTemperature: 287 K / Method: vapor diffusion, hanging drop / pH: 6
Details: 0.1M sodium cacodylate, 15% PEG4000, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 287K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 0.97915 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Sep 20, 2011
RadiationMonochromator: Si 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97915 Å / Relative weight: 1
ReflectionResolution: 2.1→50 Å / Num. all: 18938 / Num. obs: 18861 / % possible obs: 99.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 2 / Redundancy: 4.5 % / Rmerge(I) obs: 0.083
Reflection shellResolution: 2.1→2.14 Å / Redundancy: 4.5 % / Rmerge(I) obs: 0.656 / Mean I/σ(I) obs: 2.1 / Num. unique all: 917 / % possible all: 99

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Processing

Software
NameVersionClassification
Blu-Icedata collection
PHENIXmodel building
REFMAC5.5.0109refinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing
RefinementMethod to determine structure: SAD / Resolution: 2.1→41.3 Å / Cor.coef. Fo:Fc: 0.952 / Cor.coef. Fo:Fc free: 0.93 / SU B: 11.71 / SU ML: 0.139 / Cross valid method: THROUGHOUT / σ(F): 2 / ESU R: 0.214 / ESU R Free: 0.179 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.24304 965 5.2 %RANDOM
Rwork0.2111 ---
all0.2256 18819 --
obs0.21269 17758 99.09 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 39.268 Å2
Baniso -1Baniso -2Baniso -3
1--1.52 Å20 Å20 Å2
2--2.75 Å20 Å2
3----1.23 Å2
Refinement stepCycle: LAST / Resolution: 2.1→41.3 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2022 0 0 67 2089
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0222055
X-RAY DIFFRACTIONr_bond_other_d0.0010.021383
X-RAY DIFFRACTIONr_angle_refined_deg1.0011.9622776
X-RAY DIFFRACTIONr_angle_other_deg0.83433383
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.6555252
X-RAY DIFFRACTIONr_dihedral_angle_2_deg39.15225.14107
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.64315372
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.3431513
X-RAY DIFFRACTIONr_chiral_restr0.0570.2312
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.022292
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02392
X-RAY DIFFRACTIONr_mcbond_it0.5871.51269
X-RAY DIFFRACTIONr_mcbond_other0.0911.5506
X-RAY DIFFRACTIONr_mcangle_it1.11722033
X-RAY DIFFRACTIONr_scbond_it1.5173786
X-RAY DIFFRACTIONr_scangle_it2.624.5743
LS refinement shellResolution: 2.1→2.155 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.276 75 -
Rwork0.276 1254 -
obs--98.74 %
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)
11.43990.57170.93730.27430.54341.2828-0.03280.0946-0.0032-0.0050.02190.01150.00270.06580.01090.01310.00560.01040.0656-0.00810.0478-4.3852.106-11.743
21.39260.69371.29950.46480.64871.43040.0876-0.015-0.1157-0.01630.0011-0.10030.0417-0.0596-0.08870.0430.01470.01620.0436-0.00980.077-4.8260.798-9.368
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A13 - 346
2X-RAY DIFFRACTION2A401 - 467

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