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- PDB-5ohq: Crystal structure of the KOW6-KOW7 domain of human DSIF -

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Basic information

Entry
Database: PDB / ID: 5ohq
TitleCrystal structure of the KOW6-KOW7 domain of human DSIF
DescriptorTranscription elongation factor SPT5
KeywordsTRANSCRIPTION / RNA polymerase II / transcription elongation
Specimen sourceHomo sapiens / human
MethodX-ray diffraction (1.098 Å resolution / SAD)
AuthorsBernecky, C. / Plitzko, J.M. / Cramer, P.
CitationNat. Struct. Mol. Biol., 2017, 24, 809-815

Nat. Struct. Mol. Biol., 2017, 24, 809-815 Yorodumi Papers
Structure of a transcribing RNA polymerase II-DSIF complex reveals a multidentate DNA-RNA clamp.
Bernecky, C. / Plitzko, J.M. / Cramer, P.

Validation Report
SummaryFull reportAbout validation report
DateDeposition: Jul 17, 2017 / Release: Sep 13, 2017
RevisionDateData content typeGroupCategoryItemProviderType
1.0Sep 13, 2017Structure modelrepositoryInitial release
1.1Sep 20, 2017Structure modelDatabase referencescitation_citation.journal_abbrev / _citation.pdbx_database_id_PubMed / _citation.title
1.2Oct 18, 2017Structure modelDatabase referencescitation_citation.journal_volume / _citation.page_first / _citation.page_last

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Structure visualization

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Assembly

Deposited unit
A: Transcription elongation factor SPT5
hetero molecules


Theoretical massNumber of molelcules
Total (without water)12,2703
Polyers12,2121
Non-polymers582
Water4,288238
#1


TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area (Å2)220
ΔGint (kcal/M)-16
Surface area (Å2)6460
MethodPISA
Unit cell
γ
α
β
Length a, b, c (Å)35.091, 75.657, 96.749
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number20
Space group name H-MC 2 2 21

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Components

#1: Polypeptide(L)Transcription elongation factor SPT5 / hSPT5 / DRB sensitivity-inducing factor 160 kDa subunit / DSIF p160 / DRB sensitivity-inducing factor large subunit / DSIF large subunit / Tat-cotransactivator 1 protein / Tat-CT1 protein


Mass: 12211.998 Da / Num. of mol.: 1 / Source: (gene. exp.) Homo sapiens / human / References: UniProt: O00267

Cellular component

Molecular function

Biological process

  • 7-methylguanosine mRNA capping (GO: 0006370)
  • cell cycle (GO: 0007049)
  • chromatin remodeling (GO: 0006338)
  • DNA-templated transcription, elongation (GO: 0006354)
  • negative regulation of DNA-templated transcription, elongation (GO: 0032785)
  • negative regulation of mRNA polyadenylation (GO: 1900364)
  • negative regulation of transcription from RNA polymerase II promoter (GO: 0000122)
  • positive regulation of DNA-templated transcription, elongation (GO: 0032786)
  • positive regulation of macroautophagy (GO: 0016239)
  • positive regulation of transcription from RNA polymerase II promoter (GO: 0045944)
  • positive regulation of viral transcription (GO: 0050434)
  • response to organic substance (GO: 0010033)
  • single stranded viral RNA replication via double stranded DNA intermediate (GO: 0039692)
  • transcription elongation from RNA polymerase II promoter (GO: 0006368)
  • transcription from RNA polymerase II promoter (GO: 0006366)
#2: ChemicalChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Formula: Cl
#3: ChemicalChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Formula: Na
#4: WaterChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 238 / 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: 2.63 / Density percent sol: 53.22
Crystal growTemp: 293 K / Method: VAPOR DIFFUSION, HANGING DROP / pH: 7 / Details: 0.1 M bis-tris propane pH 7, 3 M sodium formate

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Data collection

DiffractionMean temperature: 100 kelvins
SourceSource: SYNCHROTRON / Type: SLS BEAMLINE X06SA / Synchrotron site: SLS / Beamline: X06SA / Wavelength: 0.999987357022
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Collection date: Jun 3, 2016
RadiationDiffraction protocol: SINGLE WAVELENGTH / Monochromatic or laue m l: M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.999987357022 Å / Relative weight: 1
ReflectionB iso Wilson estimate: 12.93 Å2 / D resolution high: 1.098 Å / D resolution low: 48.375 Å / Number obs: 93250 / Observed criterion sigma I: -3 / CC half: 0.999 / Rmerge I obs: 0.032 / Rrim I all: 0.035 / Chi squared: 1.033 / NetI over sigmaI: 27.7 / Number measured all: 574723 / Redundancy: 6.163 / Percent possible obs: 91.7
Reflection shell

Diffraction ID: 1

Rmerge I obsHighest resolutionLowest resolutionMeanI over sigI obsNumber measured obsNumber possibleNumber unique obsCC halfRrim I allRedundancyPercent possible all
0.1631.1001.1604.320255121636693100.9770.2032.74056.900
0.1441.1601.2408.3907463715461142820.9900.1605.22692.400
0.1091.2401.34013.3809685114422144090.9960.1186.72299.900
0.0701.3401.47020.2508596513231131690.9970.0776.52899.500
0.0491.4701.65031.2608470911967119690.9990.0537.077100.000
0.0371.6501.90042.2007215210575105490.9990.0406.84099.800
0.0311.9002.33054.93061125893289070.9990.0346.86399.700
0.0282.3303.29061.03048914689368920.9990.0307.097100.000
0.0293.29048.37562.25024858379937630.9980.0326.60699.100

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Phasing

PhasingMethod: SAD

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Processing

Software
NameVersionClassification
PHENIXrefinement
XDSdata scaling
SHELXDEphasing
PDB_EXTRACT3.22data extraction
XDSdata reduction
RefineMethod to determine structure: SAD / Overall SU ML: 0.07 / Cross valid method: FREE R-VALUE / Sigma F: 1.36 / Overall phase error: 12.81 / Stereochemistry target values: ML
Solvent computationSolvent shrinkage radii: 0.9 Å / Solvent vdw probe radii: 1.11 Å / Solvent model details: FLAT BULK SOLVENT MODEL
Displacement parametersB iso max: 60.6 Å2 / B iso mean: 20.851 Å2 / B iso min: 9.75 Å2
Least-squares processR factor R free: 0.1401 / R factor R work: 0.1224 / R factor obs: 0.1233 / Highest resolution: 1.098 Å / Lowest resolution: 48.374 Å / Number reflection R free: 4760 / Number reflection R work: 88464 / Number reflection obs: 93224 / Percent reflection R free: 5.11 / Percent reflection obs: 91.72
Refine hist #finalHighest resolution: 1.098 Å / Lowest resolution: 48.374 Å / B iso mean ligand: 26.74 / B iso mean solvent: 38.38 / Number residues total: 110
Number of atoms included #finalProtein: 849 / Nucleic acid: 0 / Ligand: 2 / Solvent: 243 / Total: 1094
Refine LS restraints
Refine IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0101015
X-RAY DIFFRACTIONf_angle_d1.1631413
X-RAY DIFFRACTIONf_chiral_restr0.092179
X-RAY DIFFRACTIONf_plane_restr0.006180
X-RAY DIFFRACTIONf_dihedral_angle_d20.082422
Refine LS shell

Refine ID: X-RAY DIFFRACTION / R factor R free error: 0 / Total number of bins used: 30

Highest resolutionR factor R freeR factor R workLowest resolutionNumber reflection R freeNumber reflection R workNumber reflection allPercent reflection obs
1.09750.20590.20851.1100671175124238.0000
1.11000.21580.17281.1230871530161747.0000
1.12300.20810.14841.13671061798190456.0000
1.13670.14050.14221.15111292125225467.0000
1.15110.14190.13541.16631202571269178.0000
1.16630.15610.12531.18221752651282683.0000
1.18220.15980.12941.19911442875301990.0000
1.19910.15460.11951.21701743044321895.0000
1.21700.14460.11591.236117132163387100.0000
1.23610.16300.10591.256317532073382100.0000
1.25630.14270.10181.278015732163373100.0000
1.27800.12740.11041.301223231943426100.0000
1.30120.11850.10291.326314732023349100.0000
1.32630.12990.10041.353319232353427100.0000
1.35330.11600.09901.382816631923358100.0000
1.38280.14250.09581.414917232023374100.0000
1.41490.11300.09711.45031563226338299.0000
1.45030.12660.09791.489514732543401100.0000
1.48950.12140.09311.533414332463389100.0000
1.53340.11870.08881.582918831673355100.0000
1.58290.11720.09861.639416432283392100.0000
1.63940.12130.10471.705116432343398100.0000
1.70510.14530.11511.782718931793368100.0000
1.78270.13030.11441.876715632373393100.0000
1.87670.12030.11081.99431523219337199.0000
1.99430.12000.10832.148217732133390100.0000
2.14820.12310.11142.364420131793380100.0000
2.36440.14340.13902.706516032553415100.0000
2.70650.15330.13933.409818931953384100.0000
3.40980.16430.148248.42151603199335999.0000

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