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- PDB-4mtn: Crystal structure of transcription termination factor NusA from P... -

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Basic information

Entry
Database: PDB / ID: 4mtn
TitleCrystal structure of transcription termination factor NusA from Planctomyces limnophilus DSM 3776
ComponentsTranscription termination factor NusA
KeywordsTRANSCRIPTION REGULATOR / transcription termination factor NusA / PSI-BIOLOGY / MCSG / Midwest Center for Structural Genomics
Function / homology
Function and homology information


transcription antitermination / DNA-templated transcription termination / DNA-binding transcription factor activity / nucleotide binding / RNA binding / cytoplasm
Similarity search - Function
N Utilization Substance Protein A; Chain:P; domain 4 / NusA, N-terminal domain / Transcription termination factor NusA / Transcription factor NusA, N-terminal / KH domain, NusA-like / NusA, N-terminal domain superfamily / NusA N-terminal domain / NusA-like KH domain / Transcription termination/antitermination protein NusA, bacterial / K homology (KH) domain ...N Utilization Substance Protein A; Chain:P; domain 4 / NusA, N-terminal domain / Transcription termination factor NusA / Transcription factor NusA, N-terminal / KH domain, NusA-like / NusA, N-terminal domain superfamily / NusA N-terminal domain / NusA-like KH domain / Transcription termination/antitermination protein NusA, bacterial / K homology (KH) domain / RNA-binding domain, S1 / DNA repair Rad51/transcription factor NusA, alpha-helical / Helix-hairpin-helix domain / GMP Synthetase; Chain A, domain 3 / S1 domain profile. / Ribosomal protein S1-like RNA-binding domain / S1 RNA binding domain / S1 domain / Nucleic acid-binding proteins / K homology domain superfamily, prokaryotic type / OB fold (Dihydrolipoamide Acetyltransferase, E2P) / K homology domain-like, alpha/beta / Nucleic acid-binding, OB-fold / Beta Barrel / 2-Layer Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
Transcription termination/antitermination protein NusA
Similarity search - Component
Biological speciesPlanctomyces limnophilus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.579 Å
AuthorsChang, C. / Hatzos-Skintges, C. / Clancy, S. / Joachimiak, A. / Midwest Center for Structural Genomics (MCSG)
CitationJournal: TO BE PUBLISHED
Title: Crystal structure of transcription termination factor NusA from Planctomyces limnophilus DSM 3776
Authors: Chang, C. / Hatzos-Skintges, C. / Clancy, S. / Joachimiak, A.
History
DepositionSep 19, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 2, 2013Provider: repository / Type: Initial release
Revision 1.1Nov 15, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 1.2Jul 17, 2019Group: Data collection / Derived calculations / Refinement description
Category: software / struct_conn
Item: _software.contact_author / _software.contact_author_email ..._software.contact_author / _software.contact_author_email / _software.language / _software.location / _software.name / _software.type / _software.version / _struct_conn.pdbx_leaving_atom_flag

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Transcription termination factor NusA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,2243
Polymers46,0321
Non-polymers1922
Water45025
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)162.026, 54.065, 62.859
Angle α, β, γ (deg.)90.000, 110.690, 90.000
Int Tables number5
Space group name H-MC121

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Components

#1: Protein Transcription termination factor NusA


Mass: 46031.609 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Planctomyces limnophilus (bacteria) / Strain: DSM 3776 / Gene: Plim_2559 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) magic / References: UniProt: D5SQ09
#2: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 25 / 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: 2.8 Å3/Da / Density % sol: 56.03 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 0.2M Ammonium sulfate, 22% PEG 4000, 0.1M sodium acetate, pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 289K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.97931 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Mar 25, 2012
RadiationMonochromator: Si(111) double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97931 Å / Relative weight: 1
ReflectionResolution: 2.6→50 Å / Num. all: 16108 / Num. obs: 16040 / % possible obs: 99.6 % / Observed criterion σ(I): -3 / Redundancy: 4.6 % / Rmerge(I) obs: 0.092 / Net I/σ(I): 23
Reflection shellResolution: 2.6→2.64 Å / Redundancy: 4.8 % / Rmerge(I) obs: 0.476 / Mean I/σ(I) obs: 2.1 / Num. unique all: 761 / % possible all: 96.6

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Processing

Software
NameVersionClassificationNB
PHENIX1.8.3_1479refinement
PDB_EXTRACT3.11data extraction
SBC-CollectCOLLECTdata collection
HKL-3000data reduction
HKL-3000data scaling
HKL-3000phasing
MLPHAREphasing
DMphasing
SHELXDEphasing
ARP/wARPmodel building
RESOLVEphasing
Cootmodel building
REFMACrefinement
RefinementMethod to determine structure: SAD / Resolution: 2.579→38.677 Å / Occupancy max: 1 / Occupancy min: 0.5 / SU ML: 0.39 / σ(F): 1.35 / Phase error: 30.62 / Stereochemistry target values: MLHL
RfactorNum. reflection% reflectionSelection details
Rfree0.2509 802 5 %RANDOM
Rwork0.222 ---
obs0.2235 16027 98.52 %-
all-16027 --
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 222.13 Å2 / Biso mean: 73.3413 Å2 / Biso min: 29.55 Å2
Refinement stepCycle: LAST / Resolution: 2.579→38.677 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3073 0 10 25 3108
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONf_bond_d0.002
X-RAY DIFFRACTIONf_angle_deg0.575
X-RAY DIFFRACTIONf_dihedral_angle_d10.43
LS refinement shellResolution: 2.5794→2.741 Å
RfactorNum. reflection
Rfree0.3797 133
Rwork0.3145 -
obs-2456
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)
13.6093-1.6682.33838.4417-3.07998.6024-0.1281-0.64350.08060.65280.01030.72220.2231-0.12380.13570.66780.0013-0.0660.7895-0.04720.55538.598470.2179-11.2495
23.8188-2.98541.24023.1-1.32181.83790.00450.08970.0161-0.2092-0.04530.257-0.0236-0.27710.04130.5335-0.0382-0.12020.3507-0.00780.35428.275650.3873-6.8843
30.7081-0.1313-1.66330.00460.25964.0275-0.0838-0.1219-0.0655-0.08670.06140.00320.39820.7241-0.00840.76050.0639-0.08030.6850.01460.420761.507835.1622-20.1171
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 3 through 56 )A0
2X-RAY DIFFRACTION2chain 'A' and (resid 57 through 228 )A0
3X-RAY DIFFRACTION3chain 'A' and (resid 229 through 404 )A0

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