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- PDB-2eul: Structure of the transcription factor Gfh1. -

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Basic information

Entry
Database: PDB / ID: 2eul
TitleStructure of the transcription factor Gfh1.
Componentsanti-cleavage anti-GreA transcription factor Gfh1
KeywordsTRANSCRIPTION / Gfh1 / transcription factor / RNA polymerase / RIKEN Structural Genomics/Proteomics Initiative / RSGI / Structural Genomics
Function / homology
Function and homology information


DNA-templated transcription elongation / RNA polymerase binding / regulation of DNA-templated transcription elongation / DNA binding / metal ion 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 / MIR / Resolution: 2.4 Å
AuthorsSymersky, J. / Perederina, A. / Vassylyeva, M.N. / Svetlov, V. / Artsimovitch, I. / Vassylyev, D.G. / RIKEN Structural Genomics/Proteomics Initiative (RSGI)
CitationJournal: J.Biol.Chem. / Year: 2006
Title: Regulation through the RNA Polymerase Secondary Channel: STRUCTURAL AND FUNCTIONAL VARIABILITY OF THE COILED-COIL TRANSCRIPTION FACTORS.
Authors: Symersky, J. / Perederina, A. / Vassylyeva, M.N. / Svetlov, V. / Artsimovitch, I. / Vassylyev, D.G.
History
DepositionOct 28, 2005Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 15, 2005Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Source and taxonomy / Version format compliance
Revision 1.3Oct 18, 2017Group: Refinement description / Category: software
Revision 1.4Feb 14, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.ptnr3_symmetry / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_conn.ptnr2_symmetry / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: anti-cleavage anti-GreA transcription factor Gfh1
B: anti-cleavage anti-GreA transcription factor Gfh1
C: anti-cleavage anti-GreA transcription factor Gfh1
D: anti-cleavage anti-GreA transcription factor Gfh1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)70,46129
Polymers68,8264
Non-polymers1,63525
Water6,954386
1
A: anti-cleavage anti-GreA transcription factor Gfh1
B: anti-cleavage anti-GreA transcription factor Gfh1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,19814
Polymers34,4132
Non-polymers78512
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2410 Å2
ΔGint-385 kcal/mol
Surface area17830 Å2
MethodPISA
2
C: anti-cleavage anti-GreA transcription factor Gfh1
D: anti-cleavage anti-GreA transcription factor Gfh1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,26315
Polymers34,4132
Non-polymers85013
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2550 Å2
ΔGint-369 kcal/mol
Surface area17690 Å2
MethodPISA
3


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7020 Å2
ΔGint-817 kcal/mol
Surface area33560 Å2
MethodPISA
4
B: anti-cleavage anti-GreA transcription factor Gfh1
hetero molecules

D: anti-cleavage anti-GreA transcription factor Gfh1
hetero molecules

A: anti-cleavage anti-GreA transcription factor Gfh1
C: anti-cleavage anti-GreA transcription factor Gfh1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)70,46129
Polymers68,8264
Non-polymers1,63525
Water724
TypeNameSymmetry operationNumber
crystal symmetry operation3_664-y+1,x+1,z-1/41
crystal symmetry operation4_475y-1,-x+2,z+1/41
identity operation1_555x,y,z1
Buried area6890 Å2
ΔGint-589 kcal/mol
Surface area33490 Å2
MethodPISA
5
A: anti-cleavage anti-GreA transcription factor Gfh1
hetero molecules

C: anti-cleavage anti-GreA transcription factor Gfh1
hetero molecules

B: anti-cleavage anti-GreA transcription factor Gfh1
hetero molecules

D: anti-cleavage anti-GreA transcription factor Gfh1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)70,46129
Polymers68,8264
Non-polymers1,63525
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_674-x+1,-y+2,z-1/21
crystal symmetry operation3_664-y+1,x+1,z-1/41
crystal symmetry operation3_754-y+2,x,z-1/41
Buried area6060 Å2
ΔGint-549 kcal/mol
Surface area34230 Å2
MethodPISA
6
D: anti-cleavage anti-GreA transcription factor Gfh1
hetero molecules

B: anti-cleavage anti-GreA transcription factor Gfh1
hetero molecules

A: anti-cleavage anti-GreA transcription factor Gfh1
C: anti-cleavage anti-GreA transcription factor Gfh1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)70,46129
Polymers68,8264
Non-polymers1,63525
Water724
TypeNameSymmetry operationNumber
crystal symmetry operation1_455x-1,y,z1
crystal symmetry operation1_565x,y+1,z1
identity operation1_555x,y,z1
Buried area5600 Å2
ΔGint-550 kcal/mol
Surface area34780 Å2
MethodPISA
7
D: anti-cleavage anti-GreA transcription factor Gfh1
hetero molecules

B: anti-cleavage anti-GreA transcription factor Gfh1
hetero molecules

A: anti-cleavage anti-GreA transcription factor Gfh1
C: anti-cleavage anti-GreA transcription factor Gfh1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)70,46129
Polymers68,8264
Non-polymers1,63525
Water724
TypeNameSymmetry operationNumber
crystal symmetry operation3_754-y+2,x,z-1/41
crystal symmetry operation4_565y,-x+1,z+1/41
identity operation1_555x,y,z1
Buried area4830 Å2
ΔGint-548 kcal/mol
Surface area35550 Å2
MethodPISA
Unit cell
Length a, b, c (Å)59.291, 59.291, 218.876
Angle α, β, γ (deg.)90, 90, 90
Int Tables number78
Space group name H-MP43

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Components

#1: Protein
anti-cleavage anti-GreA transcription factor Gfh1


Mass: 17206.482 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermus thermophilus (bacteria) / Strain: HB8 / Gene: gfhI / Plasmid: pVS26 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(lambdaDE3) / References: UniProt: Q5SJG6
#2: Chemical...
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 25 / Source method: obtained synthetically / Formula: Zn
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 386 / 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: 2.79 Å3/Da / Density % sol: 55.98 %
Crystal growTemperature: 277 K / pH: 6.5
Details: 8% PEG800, 33mM ZnAc, 17mM NaCacodylate, 0.85M NaCl, pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 277K, pH 6.50

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.5418
DetectorType: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Sep 14, 2005 / Details: MIRRORS
RadiationMonochromator: VARIMAX HR / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.4→30 Å / Num. obs: 29039 / % possible obs: 91.4 % / Observed criterion σ(I): -1 / Redundancy: 7.8 % / Biso Wilson estimate: 50 Å2 / Rmerge(I) obs: 0.04 / Net I/σ(I): 35.6
Reflection shellResolution: 2.4→2.48 Å / Redundancy: 4.2 % / Rmerge(I) obs: 0.482 / Mean I/σ(I) obs: 8.2 / % possible all: 58.8

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Processing

Software
NameVersionClassification
HKL-2000data reduction
CCP4model building
CNS1.1refinement
HKL-2000data scaling
CCP4phasing
RefinementMethod to determine structure: MIR / Resolution: 2.4→30 Å / Data cutoff high absF: 10000 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: ENGH & HUBER
RfactorNum. reflection% reflectionSelection details
Rfree0.245 1641 5.6 %RANDOM
Rwork0.206 ---
obs0.206 29039 98.9 %-
all-29361 --
Solvent computationSolvent model: FLAT MODEL / Bsol: 68.4 Å2 / ksol: 0.34 e/Å3
Displacement parametersBiso mean: 58.1 Å2
Baniso -1Baniso -2Baniso -3
1--4.382 Å20 Å20 Å2
2---4.382 Å20 Å2
3---8.765 Å2
Refinement stepCycle: LAST / Resolution: 2.4→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4808 0 25 386 5219
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.009
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.45
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it1.451.5
X-RAY DIFFRACTIONc_mcangle_it2.642
X-RAY DIFFRACTIONc_scbond_it1.592
X-RAY DIFFRACTIONc_scangle_it2.682.5
LS refinement shellResolution: 2.4→2.49 Å / Rfactor Rfree: 0.284 / Rfactor Rwork: 0.267

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