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- PDB-2f23: Crystal structure of GreA factor homolog 1 (Gfh1) protein of Ther... -

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Basic information

Entry
Database: PDB / ID: 2f23
TitleCrystal structure of GreA factor homolog 1 (Gfh1) protein of Thermus thermophilus
ComponentsAnti-cleavage anti-greA transcription factor gfh1
KeywordsTRANSCRIPTION / crystal structure anti-grea gfh1 Thermus thermophilus
Function / homology
Function and homology information


RNA polymerase binding / regulation of DNA-templated transcription elongation / DNA binding
Similarity search - Function
Transcription elongation factor, GreA/GreB, N-terminal domain / Transcription elongation factor, GreA/GreB, C-terminal domain / Transcription elongation factor, GreA/GreB, conserved site / Transcription elongation factor, GreA/GreB, N-terminal / Transcription elongation factor, GreA/GreB, N-terminal domain superfamily / Transcription elongation factor, N-terminal / Prokaryotic transcription elongation factors signature 2. / Transcription elongation factor, GreA/GreB, C-terminal / Transcription elongation factor GreA/GreB family / Transcription elongation factor, GreA/GreB, C-term ...Transcription elongation factor, GreA/GreB, N-terminal domain / Transcription elongation factor, GreA/GreB, C-terminal domain / Transcription elongation factor, GreA/GreB, conserved site / Transcription elongation factor, GreA/GreB, N-terminal / Transcription elongation factor, GreA/GreB, N-terminal domain superfamily / Transcription elongation factor, N-terminal / Prokaryotic transcription elongation factors signature 2. / Transcription elongation factor, GreA/GreB, C-terminal / Transcription elongation factor GreA/GreB family / Transcription elongation factor, GreA/GreB, C-term / Transcription elongation factor GreA/GreB, C-terminal domain superfamily / Chitinase A; domain 3 / Helix Hairpins / Roll / Orthogonal Bundle / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
Transcription inhibitor protein Gfh1
Similarity search - Component
Biological speciesThermus thermophilus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.6 Å
AuthorsKong, X.P. / Kim, S.-S.
CitationJournal: Embo J. / Year: 2006
Title: pH-dependent conformational switch activates the inhibitor of transcription elongation.
Authors: Laptenko, O. / Kim, S.-S. / Lee, J. / Starodubtseva, M. / Cava, F. / Berenguer, J. / Kong, X.P. / Borukhov, S.
History
DepositionNov 15, 2005Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 30, 2006Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Source and taxonomy / Version format compliance
Revision 1.3Feb 14, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Anti-cleavage anti-greA transcription factor gfh1
B: Anti-cleavage anti-greA transcription factor gfh1


Theoretical massNumber of molelcules
Total (without water)34,3572
Polymers34,3572
Non-polymers00
Water5,260292
1
A: Anti-cleavage anti-greA transcription factor gfh1


Theoretical massNumber of molelcules
Total (without water)17,1781
Polymers17,1781
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Anti-cleavage anti-greA transcription factor gfh1


Theoretical massNumber of molelcules
Total (without water)17,1781
Polymers17,1781
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)28.412, 152.662, 32.375
Angle α, β, γ (deg.)90.00, 102.65, 90.00
Int Tables number4
Space group name H-MP1211
DetailsBiological assembly is a monomer. The asymetric unit of the crystal contains two monomers.

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Components

#1: Protein Anti-cleavage anti-greA transcription factor gfh1


Mass: 17178.469 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermus thermophilus (bacteria) / Strain: HB27 / Gene: gfh1 / Plasmid: pET19C / Species (production host): Escherichia coli / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 / References: UniProt: Q72JT8
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 292 / 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: 2.02 Å3/Da / Density % sol: 39.02 %
Crystal growTemperature: 296 K / Method: vapor diffusion, hanging drop / pH: 6
Details: 29% PEG 3350, 0.1M MES, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 296K

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
21
31
Diffraction source
SourceSiteBeamlineIDWavelength (Å)
SYNCHROTRONNSLS X4A10.97917, 0.97939, 0.97853
SYNCHROTRONNSLS X2521.1
SYNCHROTRONNSLS X6A31.07
Detector
TypeIDDetectorDate
ADSC QUANTUM 4r1CCDAug 26, 2003
ADSC QUANTUM 3152CCDFeb 9, 2004
ADSC QUANTUM 2103CCDJan 20, 2004
RadiationProtocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.979171
20.979391
30.978531
41.11
51.071
ReflectionResolution: 1.52→38.17 Å / Num. obs: 39911 / % possible obs: 96.7 % / Observed criterion σ(F): 0 / Redundancy: 7.1 % / Biso Wilson estimate: 17 Å2 / Rmerge(I) obs: 0.098
Reflection shellResolution: 1.52→1.57 Å / Redundancy: 5.1 % / Rmerge(I) obs: 0.312 / Num. unique all: 3624 / % possible all: 87.5

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Processing

Software
NameVersionClassification
CNS1.1refinement
DENZOdata reduction
SCALEPACKdata scaling
PHASESphasing
RefinementMethod to determine structure: MAD / Resolution: 1.6→27.72 Å / Rfactor Rfree error: 0.006 / Data cutoff high absF: 276484.58 / Data cutoff high rms absF: 276484.58 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.254 1728 5.1 %RANDOM
Rwork0.206 ---
all-35323 --
obs-34114 96.6 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 39.8802 Å2 / ksol: 0.372025 e/Å3
Displacement parametersBiso mean: 18.6 Å2
Baniso -1Baniso -2Baniso -3
1-4.93 Å20 Å20.57 Å2
2---3.01 Å20 Å2
3----1.92 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.22 Å0.18 Å
Luzzati d res low-5 Å
Luzzati sigma a0.11 Å0.08 Å
Refinement stepCycle: LAST / Resolution: 1.6→27.72 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2374 0 0 292 2666
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.005
X-RAY DIFFRACTIONc_angle_deg1.2
X-RAY DIFFRACTIONc_dihedral_angle_d21.4
X-RAY DIFFRACTIONc_improper_angle_d0.63
X-RAY DIFFRACTIONc_mcbond_it1.311.5
X-RAY DIFFRACTIONc_mcangle_it2.052
X-RAY DIFFRACTIONc_scbond_it2.562
X-RAY DIFFRACTIONc_scangle_it3.772.5
LS refinement shellResolution: 1.6→1.7 Å / Rfactor Rfree error: 0.016 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.268 278 5.2 %
Rwork0.235 5063 -
obs--90.8 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2water_rep.paramwater.top

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