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- PDB-3ufe: Structure of transcriptional antiterminator (BGLG-family) at 1.5 ... -

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Basic information

Entry
Database: PDB / ID: 3ufe
TitleStructure of transcriptional antiterminator (BGLG-family) at 1.5 A resolution
ComponentsTranscriptional antiterminator (BGLG family)
KeywordsTRANSCRIPTION / extended helix bundle / Arcimboldo
Function / homology
Function and homology information


positive regulation of DNA-templated transcription / RNA binding
Similarity search - Function
Methane Monooxygenase Hydroxylase; Chain G, domain 1 - #1950 / cAMP-dependent Protein Kinase, Chain A - #100 / Transcription antiterminator, conserved site / CAT RNA-binding domain / CAT RNA-binding domain superfamily / CAT RNA binding domain / PRD domain signature. / CAT RNA binding domain / PRD domain / PRD domain ...Methane Monooxygenase Hydroxylase; Chain G, domain 1 - #1950 / cAMP-dependent Protein Kinase, Chain A - #100 / Transcription antiterminator, conserved site / CAT RNA-binding domain / CAT RNA-binding domain superfamily / CAT RNA binding domain / PRD domain signature. / CAT RNA binding domain / PRD domain / PRD domain / PRD domain superfamily / PRD domain profile. / cAMP-dependent Protein Kinase, Chain A / Methane Monooxygenase Hydroxylase; Chain G, domain 1 / Up-down Bundle / Mainly Alpha
Similarity search - Domain/homology
PHOSPHATE ION / PtsGHI operon antiterminator
Similarity search - Component
Biological speciesBacillus subtilis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.5 Å
AuthorsGrosse, C. / Himmel, S. / Becker, S. / Sheldrick, G.M. / Uson, I.
CitationJournal: To be Published
Title: Structure of transcriptional antiterminator (BGLG-family) at 1.5 A resolution
Authors: Grosse, C. / Himmel, S. / Becker, S. / Sheldrick, G.M. / Uson, I.
History
DepositionNov 1, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 1, 2012Provider: repository / Type: Initial release
Revision 1.1Sep 13, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ncs_dom_lim / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id / _struct_ref_seq_dif.details / _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: Transcriptional antiterminator (BGLG family)
B: Transcriptional antiterminator (BGLG family)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,7548
Polymers26,3092
Non-polymers4456
Water1,45981
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6480 Å2
ΔGint-83 kcal/mol
Surface area11820 Å2
MethodPISA
Unit cell
Length a, b, c (Å)37.360, 65.810, 38.290
Angle α, β, γ (deg.)90.00, 109.62, 90.00
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B

NCS domain segments:

Component-ID: 1 / Ens-ID: 1 / Beg auth comp-ID: GLN / Beg label comp-ID: GLN / End auth comp-ID: GLN / End label comp-ID: GLN / Refine code: 5 / Auth seq-ID: 11 - 111 / Label seq-ID: 11 - 111

Dom-IDAuth asym-IDLabel asym-ID
1AA
2BB

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Components

#1: Protein Transcriptional antiterminator (BGLG family) / PtsGHI operon antiterminator / RNA-binding antitermination protein GlcT


Mass: 13154.480 Da / Num. of mol.: 2 / Fragment: UNP residues 171-273
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus subtilis (bacteria) / Strain: 168 / Gene: BSU13880, glcT / Plasmid: PGEX2TEV / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 / References: UniProt: O31691
#2: Chemical ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#3: Chemical ChemComp-PO4 / PHOSPHATE ION / Phosphate


Mass: 94.971 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: PO4
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 81 / 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: 1.68 Å3/Da / Density % sol: 26.83 %
Crystal growTemperature: 293 K / pH: 6
Details: 2.4 M ammonium sulfate, 0.1 M citric acid, pH 6.0, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 0.98
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Nov 22, 2008 / Details: MIRRORS
RadiationMonochromator: SI(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 1.496→36.07 Å / Num. obs: 27940 / % possible obs: 99.7 % / Observed criterion σ(I): -3 / Redundancy: 5.41 % / Rmerge(I) obs: 0.0457 / Rsym value: 0.0292 / Net I/σ(I): 18.6
Reflection shellResolution: 1.5→1.6 Å / Redundancy: 3.6 % / Rmerge(I) obs: 0.3406 / Mean I/σ(I) obs: 3.16 / Rsym value: 0.3125 / % possible all: 98.3

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Processing

Software
NameVersionClassification
MAR345dtbdata collection
PHASERphasing
REFMAC5.5.0109refinement
XDSdata reduction
SADABSdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3GWH

3gwh


Resolution: 1.5→36.07 Å / Cor.coef. Fo:Fc: 0.971 / Cor.coef. Fo:Fc free: 0.955 / Occupancy max: 1 / Occupancy min: 0.5 / SU B: 3.122 / SU ML: 0.052 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.106 / ESU R Free: 0.081 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: THE FRAMES WERE INDEXED AND INTEGRATED WITH XDS AND SCALED WITH SADABS STRUCTURE WAS SOLVED WITH PHASER AND REFINED WITH REFMAC HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.19961 1401 5 %RANDOM
Rwork0.15671 ---
obs0.15892 26515 99.73 %-
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: 8.445 Å2
Baniso -1Baniso -2Baniso -3
1--0.4 Å20 Å2-0.69 Å2
2--0.14 Å20 Å2
3----0.2 Å2
Refinement stepCycle: LAST / Resolution: 1.5→36.07 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1701 0 24 81 1806
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0221835
X-RAY DIFFRACTIONr_bond_other_d0.0010.021254
X-RAY DIFFRACTIONr_angle_refined_deg1.4721.992497
X-RAY DIFFRACTIONr_angle_other_deg0.92233099
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.0965226
X-RAY DIFFRACTIONr_dihedral_angle_2_deg39.04624.7580
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.87915354
X-RAY DIFFRACTIONr_dihedral_angle_4_deg22.0051510
X-RAY DIFFRACTIONr_chiral_restr0.0850.2288
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0211982
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02330
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.2151.51105
X-RAY DIFFRACTIONr_mcbond_other0.3771.5422
X-RAY DIFFRACTIONr_mcangle_it1.95721815
X-RAY DIFFRACTIONr_scbond_it3.4133730
X-RAY DIFFRACTIONr_scangle_it4.944.5679
X-RAY DIFFRACTIONr_rigid_bond_restr1.34533089
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Dom-ID: 1 / Auth asym-ID: A / Ens-ID: 1 / Refine-ID: X-RAY DIFFRACTION

NumberTypeRms dev position (Å)Weight position
564MEDIUM POSITIONAL0.810.5
707LOOSE POSITIONAL1.175
564MEDIUM THERMAL1.952
707LOOSE THERMAL2.6410
LS refinement shellResolution: 1.5→1.539 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.29 103 -
Rwork0.228 1867 -
obs--96.62 %
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)
132.608321.3625-4.147743.566916.287717.51080.6002-0.0221-0.17910.4674-0.19440.4338-0.3307-0.3376-0.40580.2212-0.00490.11220.13640.09220.251517.27116.46718.322
21.94172.15730.627314.10143.22933.31980.0769-0.14520.19340.504-0.17740.4883-0.2033-0.17240.10050.14890.01090.02820.0839-0.03790.1254134.71.817
34.24881.62851.61371.37660.3561.5950.1596-0.2978-0.11870.2289-0.15370.02510.0792-0.1064-0.00590.1255-0.0116-0.00580.10240.01090.092918.318-5.673.634
41.3324-1.63620.18099.3165-4.23182.3903-0.1069-0.1270.20280.3946-0.0112-0.289-0.19290.00440.11810.17260.0188-0.05310.102-0.02780.137724.81710.5330.65
519.6742-20.89546.027245.0755-5.12421.91791.04890.55073.8435-3.0522-2.2778-3.75780.20580.07551.22890.53440.13940.2620.4605-0.06921.007935.5796.722-6.122
63.8713-0.1865-0.62370.6948-0.25061.758-0.0161-0.23990.0154-0.01560.017-0.01680.00460.0006-0.00090.0589-0.0145-0.00530.1227-0.02810.115344.639-8.371-9.187
75.26030.8014-2.18513.3865-2.27154.2553-0.0007-0.3042-0.10680.02850.04630.11850.0629-0.0587-0.04560.0684-0.009-0.00490.1272-0.01050.104634.782-10.036-10.126
86.63942.396-5.52447.2346-4.550817.11120.0288-0.1231-0.3937-0.18490.0004-0.37910.28760.0857-0.02930.0985-0.0061-0.04560.0626-0.01140.143543.61-20.668-12.805
92.9298-1.49172.539714.7714-13.727913.23750.8542-0.6604-0.25010.5251-0.38340.4329-0.11150.0651-0.47080.4951-0.2631-0.05160.3079-0.00280.244833.286-23.079-15.501
105.40844.05430.04847.51850.30393.2681-0.0320.0438-0.0752-0.1303-0.07470.02050.1347-0.09860.10670.0923-0.0071-0.02110.1071-0.00170.109640.15-10.865-21.857
1132.9172-19.2439-18.774613.18019.846111.38160.5940.50970.9593-0.0482-0.276-0.8193-0.5083-0.2796-0.31790.1748-0.04070.01580.19960.06610.492341.0630.982-21.48
129.18651.0903-3.59316.6329-0.95744.8341-0.00530.30810.0895-0.2544-0.0157-0.0716-0.1259-0.03820.02110.0846-0.00340.00290.0966-0.01540.091828.215-3.284-16.47
131.953-1.2849-0.05147.11011.04250.41450.05050.12910.1134-0.0943-0.15370.1584-0.1377-0.08820.10320.12810.0186-0.00860.0941-0.00170.116518.397.317-9.629
146.02452.4854-0.64866.92930.14994.408-0.0931-0.1122-0.0518-0.05810.0298-0.2274-0.02380.11720.06330.0815-0.00710.00270.1023-0.01280.090225.447-1.396-5.23
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A3 - 10
2X-RAY DIFFRACTION2A11 - 24
3X-RAY DIFFRACTION3A25 - 39
4X-RAY DIFFRACTION4A40 - 55
5X-RAY DIFFRACTION5A56 - 67
6X-RAY DIFFRACTION6A68 - 95
7X-RAY DIFFRACTION7A96 - 111
8X-RAY DIFFRACTION8B11 - 28
9X-RAY DIFFRACTION9B29 - 42
10X-RAY DIFFRACTION10B43 - 53
11X-RAY DIFFRACTION11B54 - 61
12X-RAY DIFFRACTION12B62 - 72
13X-RAY DIFFRACTION13B73 - 96
14X-RAY DIFFRACTION14B97 - 111

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