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- PDB-2etn: Crystal structure of Thermus aquaticus Gfh1 -

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Basic information

Entry
Database: PDB / ID: 2etn
TitleCrystal structure of Thermus aquaticus Gfh1
Componentsanti-cleavage anti-GreA transcription factor Gfh1
KeywordsTRANSCRIPTION / anti Gre-factor / RNA polymerase / transcript cleavage
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 aquaticus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 3.3 Å
AuthorsLamour, V. / Hogan, B.P. / Erie, D.A. / Darst, S.A.
CitationJournal: J.Mol.Biol. / Year: 2006
Title: Crystal structure of Thermus aquaticus Gfh1, a Gre-factor paralog that inhibits rather than stimulates transcript cleavage.
Authors: Lamour, V. / Hogan, B.P. / Erie, D.A. / Darst, S.A.
History
DepositionOct 27, 2005Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 14, 2006Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: 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

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


Theoretical massNumber of molelcules
Total (without water)51,7553
Polymers51,7553
Non-polymers00
Water0
1
A: anti-cleavage anti-GreA transcription factor Gfh1


Theoretical massNumber of molelcules
Total (without water)17,2521
Polymers17,2521
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: anti-cleavage anti-GreA transcription factor Gfh1


Theoretical massNumber of molelcules
Total (without water)17,2521
Polymers17,2521
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: anti-cleavage anti-GreA transcription factor Gfh1


Theoretical massNumber of molelcules
Total (without water)17,2521
Polymers17,2521
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
4
B: anti-cleavage anti-GreA transcription factor Gfh1
C: anti-cleavage anti-GreA transcription factor Gfh1


Theoretical massNumber of molelcules
Total (without water)34,5032
Polymers34,5032
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1390 Å2
ΔGint-17 kcal/mol
Surface area18190 Å2
MethodPISA
Unit cell
Length a, b, c (Å)191.200, 76.400, 53.100
Angle α, β, γ (deg.)90.00, 101.90, 90.00
Int Tables number5
Space group name H-MC121

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Components

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


Mass: 17251.580 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermus aquaticus (bacteria) / Gene: gfh1 / Plasmid: pET11 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: GenBank: 18034643, UniProt: Q8VQD7*PLUS

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 2

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Sample preparation

CrystalDensity Matthews: 3.67 Å3/Da / Density % sol: 66.44 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 6
Details: 50mM sodium Cacodylate pH 6.0, 10 mM magnesium sulfate, 1.9 M lithium sulfate 1% ethylene glycol, VAPOR DIFFUSION, HANGING DROP, temperature 295K

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
1771
2771
Diffraction source
SourceSiteBeamlineIDWavelength (Å)
SYNCHROTRONNSLS X9A10.9795
SYNCHROTRONNSLS X2520.97857,0.97885,0.96486
Detector
IDDetectorDate
1CCDJun 30, 2003
2CCDOct 23, 2003
Radiation
IDProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1SINGLE WAVELENGTHMx-ray1
2MADMx-ray1
Radiation wavelength
IDWavelength (Å)Relative weight
10.97951
20.978571
30.978851
40.964861
ReflectionResolution: 3.2→30 Å / Num. obs: 12359 / % possible obs: 99.2 % / Observed criterion σ(I): 2 / Rsym value: 0.064 / Net I/σ(I): 18.5
Reflection shellResolution: 3.2→3.31 Å / Mean I/σ(I) obs: 2.2 / % possible all: 99

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Processing

Software
NameVersionClassification
REFMAC5.1.24refinement
HKL-2000data reduction
SCALEPACKdata scaling
MLPHAREphasing
RefinementMethod to determine structure: MAD / Resolution: 3.3→30 Å / Cor.coef. Fo:Fc: 0.909 / Cor.coef. Fo:Fc free: 0.838 / SU B: 40.102 / SU ML: 0.629 / Cross valid method: THROUGHOUT / ESU R Free: 0.696
Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES
RfactorNum. reflection% reflectionSelection details
Rfree0.32464 1020 9.7 %RANDOM
Rwork0.25026 ---
obs0.25742 9498 92.47 %-
all-11394 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 42.835 Å2
Baniso -1Baniso -2Baniso -3
1--3.46 Å20 Å22.22 Å2
2--0.36 Å20 Å2
3---4.01 Å2
Refinement stepCycle: LAST / Resolution: 3.3→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3550 0 0 0 3550
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0330.0213580
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg3.0092.0054808
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg8.5315461
X-RAY DIFFRACTIONr_dihedral_angle_2_deg
X-RAY DIFFRACTIONr_dihedral_angle_3_deg
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.1740.2560
X-RAY DIFFRACTIONr_gen_planes_refined0.0120.022627
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.3770.22039
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.3020.2228
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.410.251
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.3690.24
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.3631.52299
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it2.54623680
X-RAY DIFFRACTIONr_scbond_it3.53331281
X-RAY DIFFRACTIONr_scangle_it6.0014.51128
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 3.3→3.386 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.377 47
Rwork0.404 635
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
132.2403-0.5947-18.33478.5294-1.853520.32910.494-0.75362.54370.5226-0.09160.5613-0.6365-0.1922-0.40240.4140.0592-0.23810.1066-0.02980.54960.659422.696543.6965
213.463-5.3702-0.61623.6889-3.10237.7470.02580.68151.5066-0.1845-0.2198-0.7183-0.2124-0.00060.1940.3199-0.05960.04010.73090.19430.487983.378313.080140.2067
311.2248.57595.858924.109710.364812.98370.4655-0.5516-1.51981.27480.11260.06061.6871-0.5897-0.57810.29990.11470.25010.36920.24090.4351-2.143522.056834.6951
414.048-2.7901-2.83747.98682.82814.91910.1194-0.1481-0.59340.2693-0.1402-0.029-0.0583-0.07330.02080.3287-0.0112-0.01330.33270.29340.258819.936432.931232.6985
59.92631.80955.38813.273313.347227.66610.4664-1.2124-0.56570.9204-0.52520.08370.7666-0.2830.05880.1290.07540.07060.4234-0.04810.261449.30718.506742.5627
611.472-7.79362.871311.3368-2.17155.38990.73070.6272-0.0767-0.9668-0.54150.98760.6610.393-0.18920.48040.2085-0.13090.3230.03110.505335.023915.703323.4911
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA3 - 733 - 73
2X-RAY DIFFRACTION2AA74 - 15574 - 155
3X-RAY DIFFRACTION3BB2 - 732 - 73
4X-RAY DIFFRACTION4BB74 - 15574 - 155
5X-RAY DIFFRACTION5CC2 - 732 - 73
6X-RAY DIFFRACTION6CC74 - 15574 - 155

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