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- PDB-2f5t: Crystal Structure of the sugar binding domain of the archaeal tra... -

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Basic information

Entry
Database: PDB / ID: 2f5t
TitleCrystal Structure of the sugar binding domain of the archaeal transcriptional regulator TrmB
Componentsarchaeal transcriptional regulator TrmB
KeywordsTRANSCRIPTION / Sugar-binding
Function / homology
Function and homology information


SH3 type barrels. - #690 / 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 / SH3 type barrels. / Winged helix DNA-binding domain superfamily / Roll ...SH3 type barrels. - #690 / 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 / SH3 type barrels. / Winged helix DNA-binding domain superfamily / Roll / Winged helix-like DNA-binding domain superfamily / 2-Layer Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
alpha-maltose / IMIDAZOLE / : / HTH-type sugar sensing transcriptional regulator TrmB
Similarity search - Component
Biological speciesThermococcus litoralis (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MIRAS / Resolution: 1.45 Å
AuthorsKrug, M. / Lee, S.J. / Diederichs, K. / Boos, W. / Welte, W.
CitationJournal: J.Biol.Chem. / Year: 2006
Title: Crystal Structure of the Sugar Binding Domain of the Archaeal Transcriptional Regulator TrmB
Authors: Krug, M. / Lee, S.J. / Diederichs, K. / Boos, W. / Welte, W.
History
DepositionNov 27, 2005Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 21, 2006Provider: repository / Type: Initial release
Revision 1.1Apr 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 2.0Jul 29, 2020Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Database references / Derived calculations / Non-polymer description / Structure summary
Category: atom_site / atom_site_anisotrop ...atom_site / atom_site_anisotrop / chem_comp / database_PDB_caveat / entity / entity_name_com / pdbx_branch_scheme / pdbx_chem_comp_identifier / pdbx_entity_branch / pdbx_entity_branch_descriptor / pdbx_entity_branch_link / pdbx_entity_branch_list / pdbx_entity_nonpoly / pdbx_molecule_features / pdbx_nonpoly_scheme / pdbx_validate_chiral / struct_conn / struct_ref_seq_dif / struct_site / struct_site_gen
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_asym_id / _atom_site.auth_atom_id / _atom_site.auth_comp_id / _atom_site.auth_seq_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _atom_site_anisotrop.U[1][1] / _atom_site_anisotrop.U[1][2] / _atom_site_anisotrop.U[1][3] / _atom_site_anisotrop.U[2][2] / _atom_site_anisotrop.U[2][3] / _atom_site_anisotrop.U[3][3] / _atom_site_anisotrop.pdbx_auth_asym_id / _atom_site_anisotrop.pdbx_auth_atom_id / _atom_site_anisotrop.pdbx_auth_comp_id / _atom_site_anisotrop.pdbx_auth_seq_id / _atom_site_anisotrop.pdbx_label_atom_id / _atom_site_anisotrop.pdbx_label_comp_id / _chem_comp.formula / _chem_comp.formula_weight / _chem_comp.id / _chem_comp.mon_nstd_flag / _chem_comp.name / _chem_comp.type / _entity.formula_weight / _entity.pdbx_description / _entity.type / _pdbx_validate_chiral.auth_asym_id / _pdbx_validate_chiral.auth_atom_id / _pdbx_validate_chiral.auth_comp_id / _pdbx_validate_chiral.auth_seq_id / _struct_ref_seq_dif.details
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Feb 14, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2
Item: _chem_comp.pdbx_synonyms / _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
X: archaeal transcriptional regulator TrmB
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,0513
Polymers26,6391
Non-polymers4112
Water1,892105
1
X: archaeal transcriptional regulator TrmB
hetero molecules

X: archaeal transcriptional regulator TrmB
hetero molecules


Theoretical massNumber of molelcules
Total (without water)54,1026
Polymers53,2792
Non-polymers8234
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation6_765-x+2,-x+y+1,-z+2/31
Buried area4560 Å2
ΔGint-13 kcal/mol
Surface area18240 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)56.857, 56.857, 132.482
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Space group name H-MP3221

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Components

#1: Protein archaeal transcriptional regulator TrmB


Mass: 26639.393 Da / Num. of mol.: 1 / Fragment: residues 110-338
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermococcus litoralis (archaea) / Plasmid: pSL152 / Production host: Escherichia coli (E. coli) / Strain (production host): SF120 / References: GenBank: 12018064, UniProt: Q7LYW4*PLUS
#2: Polysaccharide alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose / alpha-maltose


Type: oligosaccharide, Oligosaccharide / Class: Nutrient / Mass: 342.297 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: oligosaccharide / References: alpha-maltose
DescriptorTypeProgram
DGlcpa1-4DGlcpa1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/1,2,1/[a2122h-1a_1-5]/1-1/a4-b1WURCSPDB2Glycan 1.1.0
[][b-D-Glcp]{[(4+1)][a-D-Glcp]{}}LINUCSPDB-CARE
#3: Chemical ChemComp-IMD / IMIDAZOLE


Mass: 69.085 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H5N2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 105 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.32 Å3/Da / Density % sol: 46.98 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 4.6
Details: 100mM sodium acetate, 8%(w/v) PEG 4000, pH 4.6, VAPOR DIFFUSION, SITTING DROP, temperature 291K

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Data collection

Diffraction
IDCrystal-ID
11
21
31
41
51
61
71
81
91
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 0.85, 0.978, 0.979, 1.699
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.851
20.9781
30.9791
41.6991
Reflection
IDAv σ(I) over netINumberRmerge(I) obsD res high (Å)Num. obs% possible obs
18.873471912.32.081646357.9
28.36826012.82.082649893.3
39.6210238413.22.082701195.1
411.2313666112.72.082713195.5
513.6817071212.12.082742896.5
615.9420532011.52.082754497
717.66239715112.082757197
819.1127436010.72.082762697.2
920.5930867210.32.082764497.3
Diffraction reflection shell
Highest resolution (Å)Lowest resolution (Å)Num. obs% possible obs (%)IDRmerge(I) obs
6.239.5385079110.5
4.416.2141873110.5
3.64.41169667.9110.6
3.123.6186763.8110.4
2.793.12202859.8111.7
2.552.79206756.2114.1
2.362.55216654.1116.5
2.212.36223551.6121.6
2.082.21213646.8127.6
6.239.53105998.429.3
4.416.2193399.529.9
3.64.41246698.829.8
3.123.6286898210.4
2.793.12327896.7212.5
2.552.79349194.9216.4
2.362.55371792.8220.1
2.212.36393090.7226.7
2.082.21375682.4236.5
6.239.53106899.339.4
4.416.2193699.739.4
3.64.4124739939.7
3.123.6288198.4310.4
2.793.12330597.5313
2.552.79354996.5317.3
2.362.55381695.3321.4
2.212.36403793.1329.6
2.082.21394686.5340.8
6.239.53106999.349.1
4.416.2194099.949.3
3.64.41247999.349.4
3.123.6288698.6410
2.793.12331197.7412.3
2.552.79356296.8416.3
2.362.55382695.6420
2.212.36405993.6427.7
2.082.21399987.7438.1
6.239.53106999.358.9
4.416.2193999.859
3.64.41248399.459.1
3.123.6289798.959.6
2.793.12333498.4511.7
2.552.79358197.4515.2
2.362.55386096.4518.7
2.212.36411094.8526.1
2.082.21415591.1536.2
6.239.53106999.368.7
4.416.2194099.968.8
3.64.41248599.568.8
3.123.628989969.3
2.793.12333798.5611.1
2.552.79358797.5614.2
2.362.55387696.8617.3
2.212.36414695.6624.3
2.082.21420692.2633.5
6.239.53107099.478.4
4.416.2194099.978.4
3.64.41248399.478.5
3.123.6290199.178.9
2.793.12333898.5710.6
2.552.79359297.7713.5
2.362.55388297716.4
2.212.36415495.8723
2.082.21421192.3731.2
6.239.53107099.488.1
4.416.2194099.988.2
3.64.41248699.688.4
3.123.6290299.188.7
2.793.12334298.6810.4
2.552.79359497.7813.1
2.362.55389097.2815.9
2.212.36416396822.2
2.082.21423992.9830
6.239.53107099.498
4.416.2194099.998
3.64.41248499.598.2
3.123.6290299.198.5
2.793.12334398.6910.1
2.552.79359997.9912.7
2.362.55388697.1915.3
2.212.36416696.1921.4
2.082.21425493.3928.8
ReflectionResolution: 1.45→39.53 Å / Num. obs: 44046 / % possible obs: 97.2 % / Rmerge(I) obs: 0.049 / Net I/σ(I): 36.1
Reflection shell
Resolution (Å)Rmerge(I) obsMean I/σ(I) obsNum. unique allNum. unique obsDiffraction-ID% possible all
1.45-1.540.298.12558236390187.5
1.54-1.60.2914.07425943890197.4
1.6-20.2926.4120751115922198.7
2-30.2955.6421833012120199.9
3-40.2969.22526013020199.9
4-60.2973.39263201603199.9
6-100.2969.186585661100
10-39.530.2956.681896173193

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Phasing

PhasingMethod: MIRAS
Phasing dmFOM : 0.8 / FOM acentric: 0.81 / FOM centric: 0.79 / Reflection: 5368 / Reflection acentric: 4277 / Reflection centric: 1091
Phasing dm shell
Resolution (Å)FOM FOM acentricFOM centricReflectionReflection acentricReflection centric
8.6-19.8420.890.910.87250144106
5.4-8.60.840.850.82752537215
4.3-5.40.870.870.87906712194
3.8-4.30.840.850.82913741172
3.2-3.80.770.790.7215871329258
3-3.20.70.70.68960814146

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Processing

Software
NameVersionClassificationNB
XSCALEdata scaling
SOLVE2.08phasing
RESOLVE2.08phasing
REFMACrefinement
PDB_EXTRACT1.701data extraction
RefinementMethod to determine structure: MIRAS / Resolution: 1.45→39.53 Å / Cor.coef. Fo:Fc: 0.966 / Cor.coef. Fo:Fc free: 0.953 / SU B: 1.755 / SU ML: 0.032 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.071 / ESU R Free: 0.064 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.195 2224 5.1 %RANDOM
Rwork0.162 ---
all0.164 ---
obs-43989 98.7 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 16.215 Å2
Baniso -1Baniso -2Baniso -3
1-0.05 Å20.02 Å20 Å2
2--0.05 Å20 Å2
3----0.07 Å2
Refinement stepCycle: LAST / Resolution: 1.45→39.53 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1878 0 28 105 2011
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0170.0221965
X-RAY DIFFRACTIONr_angle_refined_deg1.8221.9722654
X-RAY DIFFRACTIONr_dihedral_angle_1_deg11.8655240
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.57824.02292
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.48315356
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.8261512
X-RAY DIFFRACTIONr_chiral_restr0.2980.2304
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.021453
X-RAY DIFFRACTIONr_nbd_refined0.2210.2879
X-RAY DIFFRACTIONr_nbtor_refined0.320.21383
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1160.2102
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1940.245
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1280.29
X-RAY DIFFRACTIONr_mcbond_it1.9561.51206
X-RAY DIFFRACTIONr_mcangle_it2.70321903
X-RAY DIFFRACTIONr_scbond_it3.7453854
X-RAY DIFFRACTIONr_scangle_it5.1694.5747
X-RAY DIFFRACTIONr_rigid_bond_restr2.19732060
X-RAY DIFFRACTIONr_sphericity_free9.9773105
X-RAY DIFFRACTIONr_sphericity_bonded5.65931922
LS refinement shellResolution: 1.453→1.491 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.283 150 -
Rwork0.172 2743 -
obs-2893 89.21 %

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