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- PDB-5e5b: Crystal structure of Human Spt16 N-terminal domain -

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Basic information

Entry
Database: PDB / ID: 5e5b
TitleCrystal structure of Human Spt16 N-terminal domain
ComponentsFACT complex subunit SPT16FACT (biology)
KeywordsTRANSCRIPTION / pita-bread / aminopeptidase / chromatin / replication / FACT / histone binding module / Chromosomal protein / DNA damage / DNA repair / DNA replication / Nucleus / Transcription regulation
Function / homology
Function and homology information


FACT complex / nucleosome disassembly / positive regulation of DNA-templated transcription, elongation / Pausing and recovery of Tat-mediated HIV elongation / Tat-mediated HIV elongation arrest and recovery / HIV elongation arrest and recovery / Pausing and recovery of HIV elongation / nucleosome binding / Tat-mediated elongation of the HIV-1 transcript / Formation of HIV-1 elongation complex containing HIV-1 Tat ...FACT complex / nucleosome disassembly / positive regulation of DNA-templated transcription, elongation / Pausing and recovery of Tat-mediated HIV elongation / Tat-mediated HIV elongation arrest and recovery / HIV elongation arrest and recovery / Pausing and recovery of HIV elongation / nucleosome binding / Tat-mediated elongation of the HIV-1 transcript / Formation of HIV-1 elongation complex containing HIV-1 Tat / Formation of HIV elongation complex in the absence of HIV Tat / RNA Polymerase II Transcription Elongation / Formation of RNA Pol II elongation complex / RNA Polymerase II Pre-transcription Events / transcription elongation by RNA polymerase II / TP53 Regulates Transcription of DNA Repair Genes / nucleosome assembly / Regulation of TP53 Activity through Phosphorylation / DNA replication / transcription by RNA polymerase II / DNA repair / RNA binding / nucleoplasm / nucleus
Similarity search - Function
: / FACT complex subunit SPT16, C-terminal domain / FACT complex subunit Spt16, peptidase M24-like domain / FACT complex subunit Spt16 domain / FACT complex subunit (SPT16/CDC68) / FACT complex subunit (SPT16/CDC68) / FACT complex subunit Spt16, N-terminal lobe domain / FACT complex subunit Spt16 / FACT complex subunit SPT16 N-terminal lobe domain / FACT complex subunit SPT16 N-terminal lobe domain ...: / FACT complex subunit SPT16, C-terminal domain / FACT complex subunit Spt16, peptidase M24-like domain / FACT complex subunit Spt16 domain / FACT complex subunit (SPT16/CDC68) / FACT complex subunit (SPT16/CDC68) / FACT complex subunit Spt16, N-terminal lobe domain / FACT complex subunit Spt16 / FACT complex subunit SPT16 N-terminal lobe domain / FACT complex subunit SPT16 N-terminal lobe domain / Histone chaperone RTT106/FACT complex subunit SPT16-like, middle domain / Histone chaperone Rttp106-like, middle domain / Histone chaperone Rttp106-like / Creatine Amidinohydrolase; Chain A, domain 1 / Creatinase/prolidase N-terminal domain / Creatinase/Aminopeptidase P/Spt16, N-terminal / Creatine Amidinohydrolase / Creatinase/methionine aminopeptidase superfamily / Peptidase M24 / Metallopeptidase family M24 / Creatinase/aminopeptidase-like / PH-like domain superfamily / Alpha-Beta Complex / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
FACT complex subunit SPT16
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.84 Å
AuthorsMarciano, G. / Huang, D.T.
CitationJournal: Acta Crystallogr.,Sect.F / Year: 2016
Title: Structure of the human histone chaperone FACT Spt16 N-terminal domain.
Authors: Marciano, G. / Huang, D.T.
History
DepositionOct 8, 2015Deposition site: RCSB / Processing site: PDBE
Revision 1.0Feb 10, 2016Provider: repository / Type: Initial release
Revision 1.1Jul 27, 2016Group: Database references
Revision 1.2Jan 10, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / diffrn_radiation_wavelength / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: FACT complex subunit SPT16


Theoretical massNumber of molelcules
Total (without water)48,7201
Polymers48,7201
Non-polymers00
Water8,251458
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area19170 Å2
MethodPISA
Unit cell
Length a, b, c (Å)246.570, 246.570, 246.570
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number209
Space group name H-MF432

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Components

#1: Protein FACT complex subunit SPT16 / FACT (biology) / Chromatin-specific transcription elongation factor 140 kDa subunit / FACT 140 kDa subunit / ...Chromatin-specific transcription elongation factor 140 kDa subunit / FACT 140 kDa subunit / FACTp140 / Facilitates chromatin transcription complex subunit SPT16 / hSPT16


Mass: 48720.102 Da / Num. of mol.: 1 / Fragment: N-terminal fragment, residues 1-510
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: SUPT16H, FACT140, FACTP140 / Plasmid: pGEX 4-T-1 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q9Y5B9
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 458 / 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: 3.21 Å3/Da / Density % sol: 61.62 %
Crystal growTemperature: 292 K / Method: vapor diffusion, hanging drop
Details: 17% (w/v) PEG 3350, 0.1 M ammonium iodide and 0.1 M sodium acetate pH 5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I02 / Wavelength: 0.979493 Å
DetectorType: PSI PILATUS 6M / Detector: PIXEL / Date: Sep 19, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979493 Å / Relative weight: 1
ReflectionResolution: 1.84→87.18 Å / Num. obs: 56315 / % possible obs: 100 % / Redundancy: 20 % / Biso Wilson estimate: 22.67 Å2 / Rmerge(I) obs: 0.082 / Rpim(I) all: 0.019 / Net I/σ(I): 28.1 / Num. measured all: 1124024
Reflection shell

Diffraction-ID: 1 / Rejects: 0

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allRpim(I) all% possible all
1.84-1.8817.80.7794.27285940940.193100
8.21-87.1817.60.02977.1134557630.00799.1

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Phasing

PhasingMethod: molecular replacement
Phasing MR
Highest resolutionLowest resolution
Rotation2.5 Å87.18 Å
Translation2.5 Å87.18 Å

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Processing

Software
NameVersionClassification
Aimless3.3.16data scaling
PHASER2.3.0phasing
PHENIXrefinement
PDB_EXTRACT3.15data extraction
xia2data reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3biq

3biq


Resolution: 1.84→61.642 Å / SU ML: 0.15 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 16.03 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1756 2857 5.07 %
Rwork0.1564 53453 -
obs0.1574 56310 99.96 %
Solvent computationShrinkage radii: 1.2 Å / VDW probe radii: 1.3 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 81.22 Å2 / Biso mean: 29.9188 Å2 / Biso min: 11.12 Å2
Refinement stepCycle: final / Resolution: 1.84→61.642 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3367 0 0 458 3825
Biso mean---40.5 -
Num. residues----431
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0083485
X-RAY DIFFRACTIONf_angle_d1.2164707
X-RAY DIFFRACTIONf_chiral_restr0.058533
X-RAY DIFFRACTIONf_plane_restr0.008603
X-RAY DIFFRACTIONf_dihedral_angle_d11.771313
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20 / % reflection obs: 100 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all
1.8356-1.86730.21471300.203326342764
1.8673-1.90120.21561420.184626122754
1.9012-1.93780.21411480.190726322780
1.9378-1.97740.20071330.182826152748
1.9774-2.02040.22121300.166826432773
2.0204-2.06740.18891400.165726242764
2.0674-2.11910.1771480.161526272775
2.1191-2.17640.20621520.156426492801
2.1764-2.24040.19171230.159626522775
2.2404-2.31270.16971510.160926152766
2.3127-2.39540.19691540.164626492803
2.3954-2.49130.18951690.161726402809
2.4913-2.60470.23051410.161226682809
2.6047-2.7420.17731410.1626452786
2.742-2.91380.1741590.156426552814
2.9138-3.13880.17771420.156526862828
3.1388-3.45460.17331320.152427282860
3.4546-3.95440.15021480.139127272875
3.9544-4.98180.12411200.130327982918
4.9818-61.67730.16911540.167229543108
Refinement TLS params.Method: refined / Origin x: 82.681 Å / Origin y: 53.8889 Å / Origin z: 107.2956 Å
111213212223313233
T0.1743 Å20.0059 Å20.0113 Å2-0.1436 Å2-0.0267 Å2--0.0815 Å2
L1.9876 °20.5763 °2-0.5602 °2-0.9768 °2-0.1986 °2--0.7782 °2
S0.0651 Å °-0.0734 Å °0.0925 Å °-0.0162 Å °-0.0068 Å °-0.0807 Å °-0.0579 Å °0.1467 Å °-0.0514 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1allA2 - 432
2X-RAY DIFFRACTION1allS1 - 508

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