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- PDB-5oho: Crystal structure of the KOWx-KOW4 domain of human DSIF -

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Basic information

Entry
Database: PDB / ID: 5oho
TitleCrystal structure of the KOWx-KOW4 domain of human DSIF
DescriptorTranscription elongation factor SPT5
KeywordsTRANSCRIPTION / RNA polymerase II / transcription elongation
Specimen sourceHomo sapiens / human
MethodX-ray diffraction (1.601 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
B: Transcription elongation factor SPT5
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,1987
Polyers25,7942
Non-polymers4045
Water4,576254
#1
A: Transcription elongation factor SPT5
hetero molecules


Theoretical massNumber of molelcules
Total (without water)13,0813
Polyers12,8971
Non-polymers1842
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
#2
B: Transcription elongation factor SPT5
hetero molecules


Theoretical massNumber of molelcules
Total (without water)13,1174
Polyers12,8971
Non-polymers2203
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
γ
α
β
Length a, b, c (Å)50.286, 54.403, 73.065
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP 21 21 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: 12896.992 Da / Num. of mol.: 2 / 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: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 4 / Formula: C3H8O3
#3: ChemicalChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Formula: Cl
#4: WaterChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 254 / 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: 1.94 / Density percent sol: 36.51
Crystal growTemp: 293 K / Method: VAPOR DIFFUSION, SITTING DROP / pH: 6.5
Details: 0.1 M sodium cacodylate pH 6.5, 1.0 M tri-sodium citrate dihydrate

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Data collection

DiffractionMean temperature: 100 kelvins
SourceSource: SYNCHROTRON / Type: SLS BEAMLINE X06SA / Synchrotron site: SLS / Beamline: X06SA / Wavelength: 1.00003056744
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Collection date: Dec 1, 2016
RadiationDiffraction protocol: SINGLE WAVELENGTH / Monochromatic or laue m l: M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.00003056744 Å / Relative weight: 1
ReflectionB iso Wilson estimate: 31.67 Å2 / D resolution high: 1.6 Å / D resolution low: 43.635 Å / Number obs: 50856 / Observed criterion sigma I: -3 / CC half: 0.999 / Rmerge I obs: 0.047 / Rrim I all: 0.051 / Chi squared: 1.273 / NetI over sigmaI: 15.88 / Redundancy: 6.76 / Percent possible obs: 99.7
Reflection shell

Diffraction ID: 1

Rmerge I obsHighest resolutionLowest resolutionMeanI over sigI obsNumber unique obsCC halfRrim I allRedundancyPercent possible all
1.3361.6001.7000.94081200.4851.4526.46698.700
0.6941.7001.8202.10077700.8100.7497.00299.900
0.3301.8201.9604.79071890.9490.3576.84599.900
0.1611.9602.1509.88066400.9880.1756.561100.000
0.1012.1502.40017.18060020.9950.1097.052100.000
0.0702.4002.77024.14052980.9970.0766.731100.000
0.0432.7703.39038.77044760.9990.0466.60999.900
0.0333.3904.78051.14034460.9990.0356.81399.900
0.0274.78043.63553.72019150.9990.0296.81099.800

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Phasing

PhasingMethod: SAD

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Processing

Software
NameVersionClassification
XDSdata scaling
SHELXphasing
PHENIXrefinement
PDB_EXTRACT3.22data extraction
XDSdata reduction
RefineMethod to determine structure: SAD / Overall SU ML: 0.22 / Cross valid method: FREE R-VALUE / Sigma F: 1.36 / Overall phase error: 24.55
Solvent computationSolvent shrinkage radii: 0.9 Å / Solvent vdw probe radii: 1.11 Å
Displacement parametersB iso max: 114.99 Å2 / B iso mean: 42.3488 Å2 / B iso min: 23.11 Å2
Least-squares processR factor R free: 0.2213 / R factor R work: 0.1745 / R factor obs: 0.1767 / Highest resolution: 1.601 Å / Lowest resolution: 43.635 Å / Number reflection R free: 2507 / Number reflection obs: 50852 / Percent reflection R free: 4.93 / Percent reflection obs: 99.73
Refine hist #finalHighest resolution: 1.601 Å / Lowest resolution: 43.635 Å / B iso mean ligand: 55 / B iso mean solvent: 54.35 / Number residues total: 226
Number of atoms included #finalProtein: 1812 / Nucleic acid: 0 / Ligand: 25 / Solvent: 254 / Total: 2091
Refine LS restraints
Refine IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0061917
X-RAY DIFFRACTIONf_angle_d0.8622586
X-RAY DIFFRACTIONf_chiral_restr0.057287
X-RAY DIFFRACTIONf_plane_restr0.005335
X-RAY DIFFRACTIONf_dihedral_angle_d18.1491158
Refine LS shell

Refine ID: X-RAY DIFFRACTION / R factor R free error: 0 / Total number of bins used: 18

Highest resolutionR factor R freeR factor R workLowest resolutionNumber reflection R freeNumber reflection R workNumber reflection allPercent reflection obs
1.60120.39220.33711.63201582559271796.0000
1.63200.35980.32521.665314426752819100.0000
1.66530.29840.28991.701513627202856100.0000
1.70150.28830.26431.741114226982840100.0000
1.74110.32040.25761.784612826882816100.0000
1.78460.27690.24441.832914126712812100.0000
1.83290.32580.23281.886813727092846100.0000
1.88680.28630.20741.947716426492813100.0000
1.94770.22960.19072.017314427162860100.0000
2.01730.20390.18422.098112827102838100.0000
2.09810.20240.18402.193612726902817100.0000
2.19360.25250.19432.309211427092823100.0000
2.30920.25070.20392.453916226762838100.0000
2.45390.26910.20922.643314326942837100.0000
2.64330.24410.18602.909311926982817100.0000
2.90930.20300.16273.330115726862843100.0000
3.33010.16950.12864.195112227192841100.0000
4.19510.19490.153843.651814126782819100.0000
Refine TLS

Method: refined / Refine ID: X-RAY DIFFRACTION

IDL11L12L13L22L23L33S11S12S13S21S22S23S31S32S33T11T12T13T22T23T33Origin xOrigin yOrigin z
11.69931.2923-0.71622.39030.54131.20870.08020.0951-0.2758-0.26170.1182-0.1443-0.26080.03680.00000.29110.0289-0.07160.2818-0.02880.297315.702764.725622.8543
20.9783-0.0767-0.48051.3642-0.81001.29000.04340.67800.1180-0.2106-0.0015-0.3255-0.25100.6816-0.00020.27410.0052-0.01080.4026-0.01900.316222.563566.238921.3771
30.12500.2612-0.03580.3080-0.18400.07160.1964-0.26610.66390.5720-0.13150.46110.21780.0194-0.00210.4309-0.0430-0.01980.3961-0.02450.44126.016464.498027.3113
41.67410.22510.15172.86201.15141.78150.09800.2670-0.39700.32490.1067-0.26010.54720.1426-0.00090.44460.0353-0.06780.2984-0.01150.31174.460249.757717.2323
52.11312.01120.02201.97080.68782.27730.18380.3737-0.30800.18450.1699-0.68310.49010.50370.02950.35920.1019-0.10800.3117-0.05630.389610.417252.634217.1767
64.21442.0111-0.38004.33062.34113.0584-0.06290.01880.2825-0.5283-0.1017-0.0401-0.1468-0.0014-0.00430.1765-0.01210.00290.3280-0.07780.2834-6.704860.133037.7925
71.0031-0.7903-0.36820.46620.27400.06680.35350.2975-0.6039-0.02280.2500-0.77591.17010.25890.00220.7475-0.0486-0.14470.3813-0.02850.4442-3.790446.859430.3823
83.60011.9657-0.15593.07352.56083.8996-0.18260.1194-0.25890.0218-0.04410.10460.2537-0.1433-0.00030.2753-0.0277-0.00360.23330.00890.2148-18.607544.297636.7247
90.0291-0.0077-0.05620.0502-0.00610.1466-0.1413-0.5745-0.9396-0.31550.80410.6355-0.1998-0.58580.00330.43780.0024-0.19740.35400.04340.6655-26.307157.075432.1734
101.87390.1344-0.49041.01830.84720.8414-0.3398-0.09580.2461-0.23860.06770.14470.1212-0.4423-0.00020.3206-0.0178-0.04890.2821-0.01600.3271-19.828648.684239.0040
Refine TLS group

Refine ID: X-RAY DIFFRACTION

IDBeg auth asym IDBeg auth seq IDEnd auth asym IDEnd auth seq IDRefine TLS IDSelection details
1A534A5531chain 'A' and (resid 534 through 553 )
2A554A5742chain 'A' and (resid 554 through 574 )
3A575A5843chain 'A' and (resid 575 through 584 )
4A585A6174chain 'A' and (resid 585 through 617 )
5A618A6465chain 'A' and (resid 618 through 646 )
6B534B5746chain 'B' and (resid 534 through 574 )
7B575B5847chain 'B' and (resid 575 through 584 )
8B585B6258chain 'B' and (resid 585 through 625 )
9B626B6309chain 'B' and (resid 626 through 630 )
10B631B64610chain 'B' and (resid 631 through 646 )

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