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- PDB-1m1g: Crystal Structure of Aquifex aeolicus N-utilization substance G (... -

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Basic information

Entry
Database: PDB / ID: 1m1g
TitleCrystal Structure of Aquifex aeolicus N-utilization substance G (NusG), Space Group P2(1)
ComponentsTranscription antitermination protein nusG
KeywordsTRANSCRIPTION / Transcription termination / Antitermination / KOW domain / RNP motif / Immunoglobulin fold / Nucleic acid interaction / protein-protein interaction
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
N-utilization substance G protein NusG, insert domain / NusG, domain 2 / NusG, domain 2 superfamily / NusG domain II / mini-chromosome maintenance (MCM) complex, domain 2 / NusG, N-terminal domain / : / Transcription antitermination protein, NusG / Transcription antitermination protein, NusG, bacteria, conserved site / Transcription termination factor nusG signature. ...N-utilization substance G protein NusG, insert domain / NusG, domain 2 / NusG, domain 2 superfamily / NusG domain II / mini-chromosome maintenance (MCM) complex, domain 2 / 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 / Sandwich / 2-Layer Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
Transcription termination/antitermination protein NusG
Similarity search - Component
Biological speciesAquifex aeolicus (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsSteiner, T. / Kaiser, J.T. / Marinkovic, S. / Huber, R. / Wahl, M.C.
CitationJournal: Embo J. / Year: 2002
Title: Crystal structures of transcription factor NusG in light of its nucleic acid- and protein-binding activities
Authors: Steiner, T. / Kaiser, J.T. / Marinkovic, S. / Huber, R. / Wahl, M.C.
History
DepositionJun 19, 2002Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 4, 2003Provider: repository / Type: Initial release
Revision 1.1Apr 28, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 30, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature
Item: _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
A: Transcription antitermination protein nusG
B: Transcription antitermination protein nusG
C: Transcription antitermination protein nusG
D: Transcription antitermination protein nusG


Theoretical massNumber of molelcules
Total (without water)112,1674
Polymers112,1674
Non-polymers00
Water19,4201078
1
A: Transcription antitermination protein nusG


Theoretical massNumber of molelcules
Total (without water)28,0421
Polymers28,0421
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Transcription antitermination protein nusG


Theoretical massNumber of molelcules
Total (without water)28,0421
Polymers28,0421
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: Transcription antitermination protein nusG


Theoretical massNumber of molelcules
Total (without water)28,0421
Polymers28,0421
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
4
D: Transcription antitermination protein nusG


Theoretical massNumber of molelcules
Total (without water)28,0421
Polymers28,0421
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
5
C: Transcription antitermination protein nusG

D: Transcription antitermination protein nusG


Theoretical massNumber of molelcules
Total (without water)56,0832
Polymers56,0832
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_656-x+1,y+1/2,-z+11
Buried area2430 Å2
ΔGint-14 kcal/mol
Surface area26560 Å2
MethodPISA
6
A: Transcription antitermination protein nusG

B: Transcription antitermination protein nusG


Theoretical massNumber of molelcules
Total (without water)56,0832
Polymers56,0832
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_757-x+2,y+1/2,-z+21
Buried area2200 Å2
ΔGint-14 kcal/mol
Surface area27290 Å2
MethodPISA
Unit cell
Length a, b, c (Å)87.5, 54.4, 113.2
Angle α, β, γ (deg.)90.0, 89.3, 90.0
Int Tables number4
Space group name H-MP1211
DetailsThe biological assembly is a monomer

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Components

#1: Protein
Transcription antitermination protein nusG


Mass: 28041.703 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Aquifex aeolicus (bacteria) / Production host: Escherichia coli (E. coli) / References: UniProt: O67757
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1078 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.4 Å3/Da / Density % sol: 48.76 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 8.2
Details: PEG 3000, sodium chloride, pH 8.2, Vapor diffusion, sitting drop, temperature 291K
Crystal grow
*PLUS
Temperature: 18 ℃
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetailsChemical formula
10.1 MMES/Tris1reservoirpH8.2
215 %PEG30001reservoir
30.2 M1reservoirNaCl
420 mMTris-HCl1droppH7.0
550 mM1dropNaCl
61 MDNA1drop

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418 Å
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Details: mirrors
RadiationMonochromator: graphite / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2→30 Å / Num. obs: 69671 / % possible obs: 94.9 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Redundancy: 3.3 % / Rsym value: 0.08 / Net I/σ(I): 8.9
Reflection shellResolution: 2→2.1 Å / Mean I/σ(I) obs: 1.6 / Rsym value: 0.406 / % possible all: 79.2
Reflection
*PLUS
Rmerge(I) obs: 0.08
Reflection shell
*PLUS
% possible obs: 79.2 % / Rmerge(I) obs: 0.406

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Processing

Software
NameClassification
HKL-2000data collection
SCALEPACKdata scaling
MOLREPphasing
CNSrefinement
HKL-2000data reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2→30 Å / Isotropic thermal model: isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber / Details: Refmac 5 was also used in refinement
RfactorNum. reflection% reflectionSelection details
Rfree0.274 3484 -random
Rwork0.251 ---
all0.251 69671 --
obs0.251 69671 94.9 %-
Refinement stepCycle: LAST / Resolution: 2→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7640 0 0 1078 8718
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONRefmac50.008
X-RAY DIFFRACTIONo_angle_deg1.51
Refinement
*PLUS
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Type: o_bond_d / Dev ideal: 0.008
LS refinement shell
*PLUS
Rfactor Rfree: 0.439 / Rfactor Rwork: 0.415

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