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- PDB-3gxx: Structure of the SH2 domain of the Candida glabrata transcription... -

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Basic information

Entry
Database: PDB / ID: 3gxx
TitleStructure of the SH2 domain of the Candida glabrata transcription elongation factor Spt6, crystal form B
ComponentsTranscription elongation factor SPT6
KeywordsTRANSCRIPTION / SH2-fold / three stranded anti-parallel beta sheet / N-terminal alpha helix / C-terminal alpha helix / Nucleus / SH2 domain / Transcription regulation
Function / homology
Function and homology information


carbon catabolite repression of transcription from RNA polymerase II promoter by glucose / regulation of transcriptional start site selection at RNA polymerase II promoter / transcription antitermination factor activity, DNA binding / regulation of mRNA 3'-end processing / poly(A)+ mRNA export from nucleus / transcription elongation-coupled chromatin remodeling / nucleosome binding / positive regulation of transcription elongation by RNA polymerase II / euchromatin / nucleosome assembly ...carbon catabolite repression of transcription from RNA polymerase II promoter by glucose / regulation of transcriptional start site selection at RNA polymerase II promoter / transcription antitermination factor activity, DNA binding / regulation of mRNA 3'-end processing / poly(A)+ mRNA export from nucleus / transcription elongation-coupled chromatin remodeling / nucleosome binding / positive regulation of transcription elongation by RNA polymerase II / euchromatin / nucleosome assembly / histone binding / negative regulation of transcription by RNA polymerase II / DNA binding / nucleus
Similarity search - Function
: / Spt6, S1/OB domain / YqgF/RNase H-like domain / Likely ribonuclease with RNase H fold. / Spt6 acidic, N-terminal domain / Helix-turn-helix DNA-binding domain of Spt6 / Transcription elongation factor Spt6, YqgF domain / Transcription elongation factor Spt6, helix-hairpin-helix motif / Spt6, SH2 domain, C terminus / Acidic N-terminal SPT6 ...: / Spt6, S1/OB domain / YqgF/RNase H-like domain / Likely ribonuclease with RNase H fold. / Spt6 acidic, N-terminal domain / Helix-turn-helix DNA-binding domain of Spt6 / Transcription elongation factor Spt6, YqgF domain / Transcription elongation factor Spt6, helix-hairpin-helix motif / Spt6, SH2 domain, C terminus / Acidic N-terminal SPT6 / Helix-hairpin-helix motif / Holliday-junction resolvase-like of SPT6 / Helix-turn-helix DNA-binding domain of SPT6 / Tex-like protein, HTH domain superfamily / Tex-like domain superfamily / Spt6, Death-like domain / Tex central region-like / Transcription elongation factor Spt6 / Spt6, SH2 domain, N terminus / Spt6, SH2 domain / SH2 domain / YqgF/RNase H-like domain superfamily / RuvA domain 2-like / SH2 domain / SHC Adaptor Protein / Src homology 2 (SH2) domain profile. / Src homology 2 domains / SH2 domain / SH2 domain superfamily / Ribonuclease H-like superfamily / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Transcription elongation factor SPT6
Similarity search - Component
Biological speciesCandida glabrata (fungus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.4 Å
AuthorsDengl, S. / Mayer, A. / Sun, M. / Cramer, P.
CitationJournal: J.Mol.Biol. / Year: 2009
Title: Structure and in vivo requirement of the yeast Spt6 SH2 domain
Authors: Dengl, S. / Mayer, A. / Sun, M. / Cramer, P.
History
DepositionApr 3, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 26, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Oct 13, 2021Group: Database references / Derived calculations / Category: database_2 / struct_conn / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details
Revision 1.3Sep 6, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.4Nov 22, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond / Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_2

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Transcription elongation factor SPT6
B: Transcription elongation factor SPT6
C: Transcription elongation factor SPT6
D: Transcription elongation factor SPT6


Theoretical massNumber of molelcules
Total (without water)49,7064
Polymers49,7064
Non-polymers00
Water1,31573
1
A: Transcription elongation factor SPT6


Theoretical massNumber of molelcules
Total (without water)12,4271
Polymers12,4271
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Transcription elongation factor SPT6


Theoretical massNumber of molelcules
Total (without water)12,4271
Polymers12,4271
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Transcription elongation factor SPT6


Theoretical massNumber of molelcules
Total (without water)12,4271
Polymers12,4271
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: Transcription elongation factor SPT6


Theoretical massNumber of molelcules
Total (without water)12,4271
Polymers12,4271
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)71.600, 71.600, 87.600
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number145
Space group name H-MP32

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Components

#1: Protein
Transcription elongation factor SPT6 / Chromatin elongation factor SPT6


Mass: 12426.574 Da / Num. of mol.: 4 / Fragment: SH2 domain / Mutation: L1309M, L1317M
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Candida glabrata (fungus) / Gene: CAGL0L04774g, SPT6 / Plasmid: pET28b / Production host: Escherichia coli (E. coli) / Strain (production host): BL23 (DE3) CodonPlus RIL / References: UniProt: Q6FLB1
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 73 / 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: 2.64 Å3/Da / Density % sol: 53.37 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8
Details: 100 mM bicine pH 8.0, 4,3 M NaCl and 5 mM Tris(2-Carboxyethyl) phosphine Hydro-chloride, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.1 / Wavelength: 0.97971 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Aug 15, 2007
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97971 Å / Relative weight: 1
ReflectionResolution: 2.4→20 Å / Num. all: 18513 / Num. obs: 18513 / % possible obs: 99.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.9 % / Rsym value: 0.062 / Net I/σ(I): 45.1
Reflection shellResolution: 2.4→2.49 Å / Redundancy: 3.7 % / Mean I/σ(I) obs: 7.7 / Rsym value: 0.19 / % possible all: 95.4

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Processing

Software
NameVersionClassification
PHASERphasing
REFMAC5.5refinement
HKL-2000data reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 3GXW

3gxw


Resolution: 2.4→18.7 Å / Stereochemistry target values: Engh & Huber
RfactorNum. reflectionSelection details
Rfree0.285 999 random
Rwork0.253 --
all-18513 -
obs-18513 -
Refinement stepCycle: LAST / Resolution: 2.4→18.7 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3146 0 0 73 3219

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