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- PDB-2xhc: Crystal Structure of Thermotoga maritima N-utilization Substance ... -

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Basic information

Entry
Database: PDB / ID: 2xhc
TitleCrystal Structure of Thermotoga maritima N-utilization Substance G (NusG)
ComponentsTRANSCRIPTION ANTITERMINATION PROTEIN NUSG
KeywordsTRANSCRIPTION
Function / homology
Function and homology information


transcription elongation-coupled chromatin remodeling / regulation of DNA-templated transcription elongation / transcription antitermination / DNA-templated transcription termination / cytosol
Similarity search - Function
NusG, additional domain / NusG additional domain / NusG, N-terminal domain / Transcription antitermination protein, NusG / Transcription antitermination protein, NusG, bacteria, conserved site / Transcription termination factor nusG signature. / SH3 type barrels. - #30 / NusG-like / Transcription termination factor nusG / NusG, N-terminal ...NusG, additional domain / NusG additional domain / NusG, N-terminal domain / Transcription antitermination protein, NusG / Transcription antitermination protein, NusG, bacteria, conserved site / Transcription termination factor nusG signature. / SH3 type barrels. - #30 / NusG-like / Transcription termination factor nusG / NusG, N-terminal / In Spt5p, this domain may confer affinity for Spt4p. It possesses a RNP-like fold. / NusG, N-terminal domain superfamily / SH3 type barrels. / KOW (Kyprides, Ouzounis, Woese) motif. / Translation protein SH3-like domain superfamily / KOW motif / KOW / Ribosomal protein L2, domain 2 / Roll / Alpha-Beta Plaits / 2-Layer Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
Transcription termination/antitermination protein NusG
Similarity search - Component
Biological speciesTHERMOTOGA MARITIMA (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.45 Å
AuthorsStegmann, C.M. / Wahl, M.C.
CitationJournal: Structure / Year: 2013
Title: An Autoinhibited State in the Structure of Thermotoga Maritima Nusg.
Authors: Drogemuller, J. / Stegmann, C.M. / Mandal, A. / Steiner, T. / Burmann, B.M. / Gottesman, M.E. / Wohrl, B.M. / Rosch, P. / Wahl, M.C. / Schweimer, K.
History
DepositionJun 14, 2010Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 29, 2011Provider: repository / Type: Initial release
Revision 1.1Feb 27, 2013Group: Database references / Refinement description / Version format compliance
Revision 1.2Apr 3, 2013Group: Database references
Revision 1.3Dec 20, 2023Group: Data collection / Database references ...Data collection / Database references / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: TRANSCRIPTION ANTITERMINATION PROTEIN NUSG


Theoretical massNumber of molelcules
Total (without water)40,2641
Polymers40,2641
Non-polymers00
Water48627
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)59.750, 59.750, 310.135
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number95
Space group name H-MP4322

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Components

#1: Protein TRANSCRIPTION ANTITERMINATION PROTEIN NUSG


Mass: 40263.934 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) THERMOTOGA MARITIMA (bacteria) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P29397
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 27 / 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: 3.61 Å3/Da / Density % sol: 66 % / Description: NONE

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: MPG/DESY, HAMBURG / Beamline: BW6 / Wavelength: 1.05
DetectorType: MARRESEARCH / Detector: IMAGE PLATE
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.05 Å / Relative weight: 1
ReflectionResolution: 2.4→50 Å / Num. obs: 23437 / % possible obs: 99.2 % / Observed criterion σ(I): 2 / Redundancy: 4.9 % / Biso Wilson estimate: 56.1 Å2 / Rmerge(I) obs: 0.07 / Net I/σ(I): 16.6
Reflection shellResolution: 2.4→2.44 Å / Redundancy: 4.7 % / Rmerge(I) obs: 0.57 / Mean I/σ(I) obs: 2 / % possible all: 99.6

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Processing

Software
NameVersionClassification
PHENIX(PHENIX.REFINE)refinement
DENZOdata reduction
SCALEPACKdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2XHA

2xha


Resolution: 2.45→32.712 Å / SU ML: 0.31 / σ(F): 1.99 / Phase error: 24.82 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2767 1059 5.1 %
Rwork0.2175 --
obs0.2204 20844 95.37 %
Solvent computationShrinkage radii: 0.8 Å / VDW probe radii: 0.8 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 67.43 Å2 / ksol: 0.377 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-4.6444 Å20 Å20 Å2
2--4.6444 Å20 Å2
3----11.5511 Å2
Refinement stepCycle: LAST / Resolution: 2.45→32.712 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2736 0 0 27 2763
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0062782
X-RAY DIFFRACTIONf_angle_d1.0363744
X-RAY DIFFRACTIONf_dihedral_angle_d16.0131099
X-RAY DIFFRACTIONf_chiral_restr0.067421
X-RAY DIFFRACTIONf_plane_restr0.004478
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.4501-2.56150.34021370.26042237X-RAY DIFFRACTION89
2.5615-2.69650.34031230.25472316X-RAY DIFFRACTION92
2.6965-2.86540.31821240.26062359X-RAY DIFFRACTION93
2.8654-3.08650.30851310.2512404X-RAY DIFFRACTION95
3.0865-3.39680.28881420.23632496X-RAY DIFFRACTION97
3.3968-3.88760.2651230.21542581X-RAY DIFFRACTION99
3.8876-4.89540.23841470.17442613X-RAY DIFFRACTION99
4.8954-32.71520.26391320.20812779X-RAY DIFFRACTION98
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)
10.06140.25240.04430.56281.34183.51330.12680.4106-0.17350.03250.0155-0.1270.046-0.6094-0.17240.55240.0493-0.05350.3987-0.09870.446710.708633.638644.1568
23.0326-0.37020.69220.4331.13472.421-0.13410.4728-0.0692-0.19330.3837-0.1044-0.55420.3027-0.32220.2385-0.16630.01950.7052-0.00920.2941-12.950719.552913.871
30.89290.48860.62890.27140.34230.643-1.24730.4909-0.804-0.78480.08540.05290.44510.47320.5010.7238-0.04560.11031.18140.22761.1289-4.507815.9204-3.1596
40.74020.15550.61360.7726-0.08961.14950.07241.1111-1.2280.354-0.1480.20330.1508-0.4199-0.0770.13050.03230.01851.0943-0.1910.7619-13.70612.61753.873
50.35390.37752.04441.90610.76812.447-0.1950.302-0.40220.19660.36830.1728-1.147-0.1801-0.2795-0.5388-0.16470.10260.6271-0.09110.1418-20.2418.17813.2944
61.57380.1183-0.56041.53930.21692.30310.22110.17220.06180.4794-0.0627-0.166-0.52910.2608-0.14770.48260.0601-0.03130.2779-0.07480.320115.21839.844440.5866
73.9974-0.8495-1.47280.6042-0.84543.05370.19930.38560.0889-0.04720.0564-0.1791-1.0798-0.1028-0.1360.43330.0563-0.01340.6228-0.04720.391916.453937.020116.0334
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(CHAIN A AND RESID 3:42)
2X-RAY DIFFRACTION2(CHAIN A AND RESID 43:104)
3X-RAY DIFFRACTION3(CHAIN A AND RESID 105:109)
4X-RAY DIFFRACTION4(CHAIN A AND RESID 110:156)
5X-RAY DIFFRACTION5(CHAIN A AND RESID 157:229)
6X-RAY DIFFRACTION6(CHAIN A AND RESID 230:283)
7X-RAY DIFFRACTION7(CHAIN A AND RESID 284:352)

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