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- PDB-5box: Structure of TrmBL2, an archaeal chromatin protein, shows a novel... -

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Basic information

Entry
Database: PDB / ID: 5box
TitleStructure of TrmBL2, an archaeal chromatin protein, shows a novel mode of DNA binding.
Components
  • DNA (25-MER)
  • DNA TGM (25-MER)
  • Putative HTH-type transcriptional regulator TrmBL2
KeywordsDNA BINDING PROTEIN / Chromatin binding protein
Function / homology
Function and homology information


Transcription regulator TrmB, C-terminal / Archaeal transcriptional regulator TrmB / Transcription regulator TrmB, N-terminal / Sugar-specific transcriptional regulator TrmB / Endonuclease Chain A / Endonuclease; Chain A / Winged helix-like DNA-binding domain superfamily/Winged helix DNA-binding domain / Arc Repressor Mutant, subunit A / Winged helix DNA-binding domain superfamily / Winged helix-like DNA-binding domain superfamily ...Transcription regulator TrmB, C-terminal / Archaeal transcriptional regulator TrmB / Transcription regulator TrmB, N-terminal / Sugar-specific transcriptional regulator TrmB / Endonuclease Chain A / Endonuclease; Chain A / Winged helix-like DNA-binding domain superfamily/Winged helix DNA-binding domain / Arc Repressor Mutant, subunit A / Winged helix DNA-binding domain superfamily / Winged helix-like DNA-binding domain superfamily / 2-Layer Sandwich / Orthogonal Bundle / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
DNA / DNA (> 10) / Putative HTH-type transcriptional regulator TrmBL2
Similarity search - Component
Biological speciesPyrococcus furiosus (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 Å
AuthorsAhmad, M.U. / Diederichs, K. / Welte, W.
CitationJournal: J.Mol.Biol. / Year: 2015
Title: Structural Insights into Nonspecific Binding of DNA by TrmBL2, an Archaeal Chromatin Protein.
Authors: Ahmad, M.U. / Waege, I. / Hausner, W. / Thomm, M. / Boos, W. / Diederichs, K. / Welte, W.
History
DepositionMay 27, 2015Deposition site: RCSB / Processing site: PDBE
Revision 1.0Sep 2, 2015Provider: repository / Type: Initial release
Revision 1.1Oct 7, 2015Group: Database references
Revision 1.2Sep 21, 2016Group: Data collection
Revision 1.3Jan 10, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
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: Putative HTH-type transcriptional regulator TrmBL2
B: Putative HTH-type transcriptional regulator TrmBL2
C: Putative HTH-type transcriptional regulator TrmBL2
D: Putative HTH-type transcriptional regulator TrmBL2
E: DNA TGM (25-MER)
F: DNA (25-MER)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)138,43516
Polymers137,4366
Non-polymers99910
Water2,234124
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area28520 Å2
ΔGint-217 kcal/mol
Surface area53170 Å2
MethodPISA
Unit cell
Length a, b, c (Å)83.619, 105.790, 93.235
Angle α, β, γ (deg.)90.000, 96.750, 90.000
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11chain A and ( resseq 2:264 )
21chain B and ( resseq 2:264 )
12chain C and ( resseq 2:264 )
22chain D and ( resseq 2:264 )

NCS domain segments:
Dom-IDComponent-IDEns-IDSelection detailsAuth asym-IDAuth seq-ID
111chain A and ( resseq 2:264 )A0
211chain B and ( resseq 2:264 )B0
112chain C and ( resseq 2:264 )C0
212chain D and ( resseq 2:264 )D0

NCS ensembles :
ID
1
2

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Components

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Protein , 1 types, 4 molecules ABCD

#1: Protein
Putative HTH-type transcriptional regulator TrmBL2


Mass: 30520.393 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pyrococcus furiosus (archaea) / Gene: trmBL2, PF0496 / Plasmid: pET24d / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q8U3H1

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DNA chain , 2 types, 2 molecules EF

#2: DNA chain DNA TGM (25-MER)


Mass: 7696.997 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Pyrococcus furiosus (archaea)
#3: DNA chain DNA (25-MER)


Mass: 7656.972 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Pyrococcus furiosus (archaea)

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Non-polymers , 3 types, 134 molecules

#4: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: C3H8O3
#5: Chemical ChemComp-MPD / (4S)-2-METHYL-2,4-PENTANEDIOL / 2-Methyl-2,4-pentanediol


Mass: 118.174 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C6H14O2 / Comment: precipitant*YM
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 124 / 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: 2.98 Å3/Da / Density % sol: 58.72 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / Details: 60% MPD, 0.1M HEPES pH 6.5 / PH range: 6.2-7.2

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06DA / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Aug 23, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.5→7.41 Å / Num. obs: 55688 / % possible obs: 99.5 % / Redundancy: 3.4 % / Rmerge(I) obs: 0.1503 / Net I/σ(I): 7.84
Reflection shellResolution: 2.5→2.59 Å / Redundancy: 3.4 % / Rmerge(I) obs: 3.064 / Mean I/σ(I) obs: 0.41 / % possible all: 100

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Processing

Software
NameVersionClassification
XDSdata reduction
PHENIXrefinement
PDB_EXTRACT3.15data extraction
PHENIXphasing
Cootmodel building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5BPD

5bpd


Resolution: 2.5→7.41 Å / SU ML: 0.53 / Cross valid method: FREE R-VALUE / σ(F): 1.04 / Phase error: 34.56 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.272 5314 4.98 %
Rwork0.2242 101331 -
obs0.2265 55688 97.18 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 303.92 Å2 / Biso mean: 89.0938 Å2 / Biso min: 31.95 Å2
Refinement stepCycle: final / Resolution: 2.5→7.41 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8596 1022 164 124 9906
Biso mean--123.38 71.86 -
Num. residues----1102
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00710022
X-RAY DIFFRACTIONf_angle_d0.78113654
X-RAY DIFFRACTIONf_chiral_restr0.0361535
X-RAY DIFFRACTIONf_plane_restr0.0041548
X-RAY DIFFRACTIONf_dihedral_angle_d16.5213893
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A2613X-RAY DIFFRACTION11.505TORSIONAL
12B2613X-RAY DIFFRACTION11.505TORSIONAL
21C2635X-RAY DIFFRACTION11.505TORSIONAL
22D2635X-RAY DIFFRACTION11.505TORSIONAL
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 30

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.5-2.52840.39131670.40053341350896
2.5284-2.55820.42441960.40863324352097
2.5582-2.58940.37672030.41123347355097
2.5894-2.62210.39341840.40813303348796
2.6221-2.65660.41111970.39993351354897
2.6566-2.6930.36721840.38443398358297
2.693-2.73150.37781980.38433282348096
2.7315-2.77220.40081630.37353363352696
2.7722-2.81560.41191710.37913329350096
2.8156-2.86170.41281620.36093339350196
2.8617-2.91110.38261680.36583320348895
2.9111-2.9640.36181690.33483392356198
2.964-3.0210.36411760.33143431360798
3.021-3.08260.30411550.3033454360998
3.0826-3.14960.34191810.28633389357098
3.1496-3.22290.3311780.27133430360898
3.2229-3.30350.29432000.26583410361098
3.3035-3.39280.31661990.24653365356498
3.3928-3.49260.32291770.24493410358798
3.4926-3.60530.33581850.21693399358498
3.6053-3.73410.25091550.18943382353797
3.7341-3.88350.21041620.18353391355397
3.8835-4.06010.22931710.17093335350695
4.0601-4.27410.24781360.16853369350596
4.2741-4.54160.22132060.14393391359798
4.5416-4.89190.1921870.14893432361999
4.8919-5.38360.21151480.15443455360399
5.3836-6.1610.25181850.18593422360798
6.161-7.75630.21651780.20163347352596
7.7563-46.30230.23251730.19333430360398
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)
14.53241.28882.1470.98140.46632.2425-0.00090.0425-0.0405-0.16330.1120.10340.19660.0753-0.11230.62520.1059-0.12960.4228-0.04740.407920.1781-0.7765136.4344
22.5689-0.67494.02481.59640.50136.76110.4447-0.2015-0.77080.76020.2169-0.98270.00240.1666-0.98380.6745-0.122-0.30050.69530.00670.8401-20.3523-12.204299.509
33.18974.1795-3.96398.8926-3.59036.45570.75380.1144-2.22320.0514-0.4569-1.83450.04570.3729-0.27510.72520.0305-0.15660.7133-0.12840.9661-29.6087-20.345786.8342
46.56280.14262.24968.3290.4154.99040.52950.3496-1.5783-0.38270.0466-0.46930.96270.2676-0.51310.6879-0.0518-0.24410.5432-0.03920.9317-39.4194-27.771285.068
54.72341.10850.61288.4784-0.3786.1265-0.19050.52380.1536-0.43610.02490.3014-0.1614-0.18440.08390.44660.0259-0.20490.67850.02990.5153-36.5214-11.577987.7204
62.20320.24841.84350.92311.33026.5823-0.09750.2132-0.01770.1468-0.0058-0.10870.00450.03560.12850.3403-0.0495-0.12410.40290.10190.5384-9.778710.550897.8999
70.51640.7920.88612.35771.90522.7784-0.00790.0925-0.0003-0.56150.2191-0.0493-0.6674-0.2652-0.04210.9023-0.0031-0.04250.57870.04440.483720.293224.4754148.6624
86.8197-0.7771-2.2922.8178-1.42092.08530.6338-0.1277-0.1099-1.3961-0.58070.1918-1.12050.86340.16410.9339-0.0782-0.11030.8017-0.06480.519424.779430.8009162.4711
96.12141.11520.38046.99971.07063.36720.0366-0.25410.6693-0.6165-0.1339-0.1258-1.42450.27650.14371.10450.0851-0.1080.6054-0.09280.507325.483435.4643169.049
107.5265-0.21912.63266.36390.94666.7269-0.14610.05550.00960.00430.08950.0139-0.3260.27270.07440.51280.0793-0.10090.5143-0.01840.325722.868521.3481163.7522
115.70610.53054.58110.1304-0.05244.46350.5911-0.1082-0.55460.06370.12360.04391.064-0.0922-0.77710.86290.0549-0.32110.4659-0.00580.7618-0.2135-11.9183116.6975
120.44781.40451.68364.35775.5597.5234-1.1008-0.25230.47142.44520.6724-0.91141.23252.10610.02861.09980.245-0.26061.03990.10050.840634.5887-2.1645151.1913
132.87161.4106-2.12322.8798-0.08527.5502-0.24090.0225-0.28360.2188-0.06510.19261.2349-0.58370.26030.7591-0.0449-0.12570.5111-0.00030.534112.3251.2004160.5089
142.9557-1.4593.4490.6299-1.51837.2283-0.753-0.17220.820.02730.0490.0252-0.8118-0.14080.70110.85830.0254-0.34390.4498-0.02420.78874.29821.7094122.6809
157.48135.51311.60914.22751.31220.3768-0.73551.80772.2719-1.22010.81221.96520.5667-0.1244-0.09141.0357-0.1296-0.48130.88520.21491.1113-20.171712.304980.2424
164.86911.2143-1.39013.65750.78551.76080.177-0.54861.61530.3946-0.06590.4028-0.3917-0.1233-0.07170.6840.0961-0.22960.6362-0.17291.0135-32.613112.342598.4504
171.34461.58040.89862.63092.52543.52020.5691-0.9613.46270.2543-0.71631.8373-1.3863-1.16750.24971.06240.0979-0.03081.0656-0.55972.0054-41.949322.7132104.664
188.6544-1.3993-0.56844.2811-0.28172.543-0.2786-0.62110.59240.36310.04020.46740.0049-0.140.18680.48440.0109-0.16120.5056-0.04710.5823-35.6652.137999.4836
194.54395.04496.67453.68697.12687.935-0.15460.1739-0.7538-0.60220.3853-0.5499-0.50320.6086-0.27360.8883-0.0357-0.21350.6964-0.04390.822215.51325.3239107.9836
200.84522.74642.5911-1.03743.21390.94780.28550.3867-0.7509-0.13480.3417-0.6235-0.82610.3774-0.57530.8876-0.0271-0.31550.9409-0.14040.999416.66984.9365109.5816
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 2 through 109 )A0
2X-RAY DIFFRACTION2chain 'A' and (resid 110 through 132 )A0
3X-RAY DIFFRACTION3chain 'A' and (resid 133 through 161 )A0
4X-RAY DIFFRACTION4chain 'A' and (resid 162 through 207 )A0
5X-RAY DIFFRACTION5chain 'A' and (resid 208 through 264 )A0
6X-RAY DIFFRACTION6chain 'B' and (resid 2 through 109 )B0
7X-RAY DIFFRACTION7chain 'B' and (resid 110 through 144 )B0
8X-RAY DIFFRACTION8chain 'B' and (resid 145 through 162 )B0
9X-RAY DIFFRACTION9chain 'B' and (resid 163 through 213 )B0
10X-RAY DIFFRACTION10chain 'B' and (resid 214 through 264 )B0
11X-RAY DIFFRACTION11chain 'C' and (resid 2 through 111 )C0
12X-RAY DIFFRACTION12chain 'C' and (resid 112 through 125 )C0
13X-RAY DIFFRACTION13chain 'C' and (resid 126 through 264 )C0
14X-RAY DIFFRACTION14chain 'D' and (resid 2 through 110 )D0
15X-RAY DIFFRACTION15chain 'D' and (resid 111 through 125 )D0
16X-RAY DIFFRACTION16chain 'D' and (resid 126 through 187 )D0
17X-RAY DIFFRACTION17chain 'D' and (resid 188 through 202 )D0
18X-RAY DIFFRACTION18chain 'D' and (resid 203 through 264 )D0
19X-RAY DIFFRACTION19chain 'E' and (resid 1 through 25 )E0
20X-RAY DIFFRACTION20chain 'F' and (resid 1 through 25 )F0

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