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- PDB-2xha: Crystal Structure of Domain 2 of Thermotoga maritima N-utilizatio... -

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Basic information

Entry
Database: PDB / ID: 2xha
TitleCrystal Structure of Domain 2 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 / Transcription antitermination protein, NusG / Transcription antitermination protein, NusG, bacteria, conserved site / Transcription termination factor nusG signature. / 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 ...NusG, additional domain / NusG additional domain / Transcription antitermination protein, NusG / Transcription antitermination protein, NusG, bacteria, conserved site / Transcription termination factor nusG signature. / 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 / KOW (Kyprides, Ouzounis, Woese) motif. / Translation protein SH3-like domain superfamily / KOW motif / KOW / Ribosomal protein L2, domain 2
Similarity search - Domain/homology
ACETATE ION / Transcription termination/antitermination protein NusG
Similarity search - Component
Biological speciesTHERMOTOGA MARITIMA (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.906 Å
AuthorsStegmann, C.M. / Mandal, A. / 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 11, 2010Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 29, 2011Provider: repository / Type: Initial release
Revision 1.1Feb 27, 2013Group: Database references / Version format compliance
Revision 1.2Apr 3, 2013Group: Database references
Revision 1.3May 8, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _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

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Assembly

Deposited unit
A: TRANSCRIPTION ANTITERMINATION PROTEIN NUSG
B: TRANSCRIPTION ANTITERMINATION PROTEIN NUSG
hetero molecules


Theoretical massNumber of molelcules
Total (without water)44,6479
Polymers44,2332
Non-polymers4137
Water3,765209
1
A: TRANSCRIPTION ANTITERMINATION PROTEIN NUSG
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,3535
Polymers22,1171
Non-polymers2364
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: TRANSCRIPTION ANTITERMINATION PROTEIN NUSG
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,2944
Polymers22,1171
Non-polymers1773
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)136.350, 42.264, 88.360
Angle α, β, γ (deg.)90.00, 106.56, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein TRANSCRIPTION ANTITERMINATION PROTEIN NUSG / NUSG


Mass: 22116.678 Da / Num. of mol.: 2 / Fragment: DOMAIN 2, RESIDUES 41-233
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) / Variant (production host): ROSETTA2 / References: UniProt: P29397
#2: Chemical
ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: C2H3O2
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 209 / 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: 2.77 Å3/Da / Density % sol: 56 %
Description: WAVELENGTH 1 WAS A CRYSTAL USED FOR NATIVE DATA COLLECTION (NON-SUBSTITUTED METHIONINES). WAVELENGTH 2 WAS USED FOR SAD DATA COLLECTION OF A SELEMETHIONINE-DERIVATIZED PROTEIN CRYSTAL. ...Description: WAVELENGTH 1 WAS A CRYSTAL USED FOR NATIVE DATA COLLECTION (NON-SUBSTITUTED METHIONINES). WAVELENGTH 2 WAS USED FOR SAD DATA COLLECTION OF A SELEMETHIONINE-DERIVATIZED PROTEIN CRYSTAL.THE STRUCTURE OF THE LATTER WAS SOLVED AND USED AS A SEARCH MODEL FOR MOLECULAR REPLACEMENT FOR THE NATIVE DATA.
Crystal growpH: 8.8
Details: 0.1 M TRIS, PH 8.8, 0.2 M SODIUM ACETATE, 20% (W/V) PEG 3350

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: MPG/DESY, HAMBURG / Beamline: BW6 / Wavelength: 0.97985, 0.97893
DetectorType: MARRESEARCH / Detector: IMAGE PLATE
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.979851
20.978931
ReflectionResolution: 1.9→50 Å / Num. obs: 37677 / % possible obs: 99.9 % / Observed criterion σ(I): 2 / Redundancy: 3.8 % / Biso Wilson estimate: 22.5 Å2 / Rmerge(I) obs: 0.09 / Net I/σ(I): 13.3
Reflection shellResolution: 1.9→1.97 Å / Redundancy: 3.7 % / Rmerge(I) obs: 0.79 / Mean I/σ(I) obs: 1.8 / % possible all: 72.7

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Processing

Software
NameVersionClassification
PHENIX(PHENIX.REFINE)refinement
DENZOdata reduction
SCALEPACKdata scaling
SHELXphasing
RefinementMethod to determine structure: SAD
Starting model: NONE

Resolution: 1.906→29.113 Å / SU ML: 0.25 / σ(F): 0.03 / Phase error: 22.25 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2299 1766 5 %
Rwork0.181 --
obs0.1835 35358 92.67 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 46.989 Å2 / ksol: 0.395 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-2.7471 Å20 Å2-3.6206 Å2
2--0.1728 Å20 Å2
3----2.92 Å2
Refinement stepCycle: LAST / Resolution: 1.906→29.113 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3108 0 28 209 3345
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0093304
X-RAY DIFFRACTIONf_angle_d1.1484457
X-RAY DIFFRACTIONf_dihedral_angle_d13.5911340
X-RAY DIFFRACTIONf_chiral_restr0.089495
X-RAY DIFFRACTIONf_plane_restr0.005584
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.9057-1.95720.30931030.22861896X-RAY DIFFRACTION69
1.9572-2.01480.2711010.20572385X-RAY DIFFRACTION85
2.0148-2.07980.22961220.1922397X-RAY DIFFRACTION87
2.0798-2.15410.25771120.17942531X-RAY DIFFRACTION91
2.1541-2.24030.25141190.17372596X-RAY DIFFRACTION93
2.2403-2.34220.22441510.17862603X-RAY DIFFRACTION95
2.3422-2.46560.22751300.1812663X-RAY DIFFRACTION95
2.4656-2.620.2451350.18242681X-RAY DIFFRACTION96
2.62-2.82220.23991530.1752691X-RAY DIFFRACTION97
2.8222-3.10590.22341550.17822726X-RAY DIFFRACTION98
3.1059-3.55460.20721650.16772765X-RAY DIFFRACTION99
3.5546-4.47580.2281470.15282786X-RAY DIFFRACTION99
4.4758-29.11650.20871730.19092872X-RAY DIFFRACTION99
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)
10.6979-0.17170.2970.81750.07321.05580.06080.1188-0.0021-0.0869-0.06710.264-0.155-0.16510.03540.18880.0059-0.02020.18080.02310.1979-43.933315.2572-48.5394
20.7167-0.123-0.03381.20920.90642.07350.0445-0.0283-0.1239-0.0014-0.07050.08520.0874-0.13240.00750.1202-0.0212-0.00230.10590.02720.1316-31.714-2.3084-38.1013
31.4773-0.3030.65080.49560.08190.39070.0216-0.14920.00290.10020.0483-0.004-0.0411-0.0607-0.04190.1506-0.04570.00840.085-0.01710.0839-25.52787.2138-27.2489
41.1744-0.2511.14870.9945-0.89532.8477-0.0271-0.0354-0.0216-0.04640.08840.1599-0.2164-0.1726-0.05470.11030.01530.01980.1029-0.00360.1453-38.299814.2171-41.6174
50.6988-0.05140.68320.5082-0.63041.28650.0315-0.075-0.0747-0.0370.0272-0.01470.0391-0.0210.03380.2147-0.0273-0.02140.34090.02640.1784-23.9238-6.77598.7248
61.0005-0.17341.14082.0201-0.01333.369-0.10560.1343-0.09510.04430.1035-0.53620.00420.777-0.08810.1863-0.04020.0030.33980.00960.2515-18.1632-4.6229-12.5734
70.8540.0579-0.20370.3287-0.25971.31520.0272-0.1204-0.0954-0.05810.01360.00280.103-0.1392-0.02290.1879-0.0471-0.01330.1550.02480.1559-32.7642-7.9294-18.5485
80.39610.15960.6583-0.1839-0.20121.35160.0838-0.1667-0.13460.04290.056-0.0757-0.04930.0214-0.0480.2316-0.018-0.05410.2520.01840.1601-27.4546-7.36031.9245
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(CHAIN A AND RESID 42:80)
2X-RAY DIFFRACTION2(CHAIN A AND RESID 81:155)
3X-RAY DIFFRACTION3(CHAIN A AND RESID 156:183)
4X-RAY DIFFRACTION4(CHAIN A AND RESID 184:234)
5X-RAY DIFFRACTION5(CHAIN B AND RESID 42:80)
6X-RAY DIFFRACTION6(CHAIN B AND RESID 81:155)
7X-RAY DIFFRACTION7(CHAIN B AND RESID 156:183)
8X-RAY DIFFRACTION8(CHAIN B AND RESID 184:234)

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