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

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Basic information

Entry
Database: PDB / ID: 5bpd
TitleStructure of TrmBL2, an archaeal chromatin protein, shows a novel mode of DNA binding.
Components
  • DNA (5'-D(P*TP*AP*TP*AP*TP*CP*AP*CP*TP*AP*TP*CP*GP*AP*TP*GP*AP*TP*AP*TP*A)-3')
  • DNA (5'-D(P*TP*AP*TP*AP*TP*CP*AP*TP*CP*GP*AP*TP*AP*GP*TP*GP*AP*TP*AP*TP*A)-3')
  • TrmBL2
KeywordsDNA BINDING PROTEIN / Chromatin binding protein / Archaea
Function / homology
Function and homology information


: / Transcription regulator TrmB, C-terminal / : / Transcriptional regulator TrmB, EBD N-terminal subdomaim / 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 ...: / Transcription regulator TrmB, C-terminal / : / Transcriptional regulator TrmB, EBD N-terminal subdomaim / 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
IMIDAZOLE / DNA / DNA (> 10) / Putative HTH-type transcriptional regulator TrmBL2
Similarity search - Component
Biological speciesPyrococcus furiosus (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.4 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 28, 2015Deposition site: RCSB / Processing site: PDBE
Revision 1.0Sep 2, 2015Provider: repository / Type: Initial release
Revision 1.1Oct 7, 2015Group: Database references
Revision 1.2Oct 16, 2019Group: Data collection / Category: reflns_shell
Revision 1.3May 8, 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: TrmBL2
B: TrmBL2
C: TrmBL2
D: TrmBL2
E: DNA (5'-D(P*TP*AP*TP*AP*TP*CP*AP*TP*CP*GP*AP*TP*AP*GP*TP*GP*AP*TP*AP*TP*A)-3')
F: DNA (5'-D(P*TP*AP*TP*AP*TP*CP*AP*CP*TP*AP*TP*CP*GP*AP*TP*GP*AP*TP*AP*TP*A)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)135,90111
Polymers135,4876
Non-polymers4145
Water1,856103
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area26150 Å2
ΔGint-167 kcal/mol
Surface area52090 Å2
MethodPISA
Unit cell
Length a, b, c (Å)95.791, 58.670, 143.074
Angle α, β, γ (deg.)90.000, 92.820, 90.000
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails (eV)
11chain A and ( resseq 2:263 )
21chain B and ( resseq 2:263 )
12chain C and ( resseq 2:114 or resseq 124:262 )
22chain D and ( resseq 2:114 or resseq 124:262 )

NCS domain segments:
Dom-IDComponent-IDEns-IDSelection detailsAuth asym-IDAuth seq-ID
111chain A and ( resseq 2:263 )A0
211chain B and ( resseq 2:263 )B0
112chain C and ( resseq 2:114 or resseq 124:262 )C2 - 114
122chain C and ( resseq 2:114 or resseq 124:262 )C124 - 262
212chain D and ( resseq 2:114 or resseq 124:262 )D2 - 114
222chain D and ( resseq 2:114 or resseq 124:262 )D124 - 262

NCS ensembles :
ID
1
2

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Components

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Protein , 1 types, 4 molecules ABCD

#1: Protein
TrmBL2


Mass: 30651.584 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 BL21(DE3) (bacteria) / References: UniProt: Q8U3H1

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DNA chain , 2 types, 2 molecules EF

#2: DNA chain DNA (5'-D(P*TP*AP*TP*AP*TP*CP*AP*TP*CP*GP*AP*TP*AP*GP*TP*GP*AP*TP*AP*TP*A)-3')


Mass: 6460.221 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Pyrococcus furiosus (archaea)
#3: DNA chain DNA (5'-D(P*TP*AP*TP*AP*TP*CP*AP*CP*TP*AP*TP*CP*GP*AP*TP*GP*AP*TP*AP*TP*A)-3')


Mass: 6420.197 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Pyrococcus furiosus (archaea)

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Non-polymers , 3 types, 108 molecules

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


Mass: 92.094 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3H8O3
#5: Chemical ChemComp-IMD / IMIDAZOLE


Mass: 69.085 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H5N2
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 103 / 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: 58.67 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 8 / Details: 0.1M Imidazole HCl, pH 8.0, 30% MPD, 10% PEG4000

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Sep 12, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.4→7.13 Å / Num. obs: 62275 / % possible obs: 99.2 % / Redundancy: 6.5 % / Rmerge(I) obs: 0.1375 / Net I/σ(I): 8.23

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Processing

Software
NameVersionClassification
PHENIXrefinement
PDB_EXTRACT3.15data extraction
XDSdata reduction
Cootmodel building
PHENIXphasing
RefinementMethod to determine structure: SAD / Resolution: 2.4→7.13 Å / SU ML: 0.44 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 33.38 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2828 3030 4.87 %
Rwork0.2336 59206 -
obs0.2359 62236 99.26 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 186.78 Å2 / Biso mean: 81.9447 Å2 / Biso min: 36.36 Å2
Refinement stepCycle: final / Resolution: 2.4→7.13 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8542 861 62 103 9568
Biso mean--108.24 65.13 -
Num. residues----1087
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0059730
X-RAY DIFFRACTIONf_angle_d0.59713237
X-RAY DIFFRACTIONf_chiral_restr0.0291491
X-RAY DIFFRACTIONf_plane_restr0.0031529
X-RAY DIFFRACTIONf_dihedral_angle_d15.4863773
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A2578X-RAY DIFFRACTION10.315TORSIONAL
12B2578X-RAY DIFFRACTION10.315TORSIONAL
21C2486X-RAY DIFFRACTION10.315TORSIONAL
22D2486X-RAY DIFFRACTION10.315TORSIONAL
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 22

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.4-2.43750.39681160.36572470258690
2.4375-2.47750.38981210.3662607272899
2.4775-2.52020.36941610.349526602821100
2.5202-2.5660.40711340.353527102844100
2.566-2.61540.34051230.336126792802100
2.6154-2.66880.3891470.305327172864100
2.6688-2.72680.36631420.315126102752100
2.7268-2.79020.35811510.307626942845100
2.7902-2.860.37021330.30242680281399
2.86-2.93730.33421450.284926912836100
2.9373-3.02370.31441340.282826992833100
3.0237-3.12130.32551550.287726632818100
3.1213-3.23280.31141390.27527082847100
3.2328-3.36220.30271350.253427022837100
3.3622-3.51520.29171090.236227342843100
3.5152-3.70050.30351320.228327242856100
3.7005-3.93220.26561340.215326992833100
3.9322-4.23570.24071470.201627102857100
4.2357-4.66160.23871560.185327152871100
4.6616-5.33540.22751540.187527392893100
5.3354-6.7190.29661450.223427252870100
6.719-47.84690.25521170.20882870298799
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)
17.57311.5534-2.07313.4130.70325.46380.04610.31790.2465-0.3941-0.0780.24730.0417-0.22160.06520.44520.04580.01930.44670.05510.5023.618233.7503128.9978
27.23861.6962-6.2556-0.208-0.66956.27570.0269-0.65220.0939-0.16320.1198-0.12850.08980.655-0.21070.43030.05730.04690.4525-0.02370.530822.937935.0886130.7191
33.11311.6574-1.68513.1176-4.5646.7875-0.1298-0.4350.70230.21220.29130.4769-0.3064-0.5513-0.13710.79440.0830.01730.5865-0.04190.501753.125132.557184.691
47.0611-3.8246-3.4456.52225.54069.5063-0.23170.57320.3964-0.7759-0.3003-0.4494-0.25930.26650.47461.1132-0.06240.25680.72680.2030.772968.568239.157473.9354
54.1734-0.84251.82896.1165-0.05254.866-0.25420.34120.1186-0.61570.0145-0.93940.18660.61450.22210.85570.09470.22580.64480.0830.593768.263227.990678.5769
61.3849-0.4332-1.8620.6242-0.96055.7913-0.01130.05510.0195-0.22060.00560.06790.07650.10290.00650.7371-0.03310.01050.4191-0.02960.366338.37439.699594.5184
76.59165.1535-4.86033.8012-4.3245.37420.1790.31070.131-0.5066-0.0117-0.17410.30.3037-0.05940.5460.00520.05450.59-0.05760.46858.208511.5816146.975
83.4532-3.0649-3.27227.93874.09148.73910.2829-0.3526-0.6660.2111-0.29320.59520.4529-0.55770.070.7274-0.11820.08830.67770.05890.63243.00934.9899165.1013
94.95110.94740.27885.79960.16523.72690.2719-0.4056-0.02370.6772-0.17780.4056-0.13520.0035-0.07340.5297-0.06110.07920.5186-0.09770.45467.179816.2897163.1624
104.8023-0.8382-4.65460.36561.56215.40120.4203-0.09670.3012-0.45510.0379-0.0487-0.51970.1591-0.65280.70970.05670.08910.41420.00060.53933.267636.5137107.4653
112.80121.27721.53861.94750.14453.3999-0.0132-0.22230.53120.1829-0.1205-0.039-0.48720.23680.13770.5073-0.03270.10860.558-0.09210.599819.309836.0098153.4544
123.6088-1.5264-4.60411.09671.51647.4744-0.37640.0228-0.2171-0.0703-0.07790.42030.6572-0.13650.50710.5778-0.01720.03140.4284-0.07740.407323.69217.6896120.605
134.9315-0.43730.57711.9883-0.84151.816-0.0223-0.3064-0.5053-0.07450.0018-0.29580.45180.29380.02420.91520.10940.13460.62010.03550.455662.7428.151692.9986
141.46130.5425-2.9451-1.6381-0.21952.57480.13960.89910.665-0.59550.06170.1601-0.4044-1.6998-0.22470.96430.05130.04451.1301-0.01970.837415.087222.2946103.7186
150.4060.5781-3.3279-0.5513-0.93283.9214-0.40941.3462-0.3965-0.24710.31830.77151.0364-1.23230.05761.0146-0.0748-0.00770.9826-0.01530.827714.338921.8009104.8489
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 2 through 59 )A0
2X-RAY DIFFRACTION2chain 'A' and (resid 60 through 111 )A0
3X-RAY DIFFRACTION3chain 'A' and (resid 112 through 145 )A0
4X-RAY DIFFRACTION4chain 'A' and (resid 146 through 198 )A0
5X-RAY DIFFRACTION5chain 'A' and (resid 199 through 264 )A0
6X-RAY DIFFRACTION6chain 'B' and (resid 2 through 111 )B0
7X-RAY DIFFRACTION7chain 'B' and (resid 112 through 145 )B0
8X-RAY DIFFRACTION8chain 'B' and (resid 146 through 198 )B0
9X-RAY DIFFRACTION9chain 'B' and (resid 199 through 263 )B0
10X-RAY DIFFRACTION10chain 'C' and (resid 2 through 109 )C0
11X-RAY DIFFRACTION11chain 'C' and (resid 110 through 264 )C0
12X-RAY DIFFRACTION12chain 'D' and (resid 1 through 110 )D0
13X-RAY DIFFRACTION13chain 'D' and (resid 111 through 262 )D0
14X-RAY DIFFRACTION14chain 'E' and (resid 1 through 21 )E0
15X-RAY DIFFRACTION15chain 'F' and (resid 1 through 21 )F0

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