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- PDB-6pfv: Structure of S. venezuelae RisG-WhiG-c-di-GMP complex: orthorhomb... -

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Basic information

Entry
Database: PDB / ID: 6pfv
TitleStructure of S. venezuelae RisG-WhiG-c-di-GMP complex: orthorhombic crystal form
Components
  • AmfC protein
  • RNA polymerase sigma factor
KeywordsTRANSCRIPTION / RsiG / WhiG / c-di-GMP / sigma / anti-sigma / Streptomyces
Function / homology
Function and homology information


sigma factor activity / DNA-templated transcription initiation / DNA-directed RNA polymerase activity / nucleotide binding / DNA binding
Similarity search - Function
: / : / RsiG-like / RNA polymerase sigma factor, FliA/WhiG / Sigma-70 factors family signature 1. / RNA polymerase sigma-70 region 3 / Sigma-70 region 3 / Sigma-70 factors family signature 2. / RNA polymerase sigma-70 / RNA polymerase sigma-70 region 4 ...: / : / RsiG-like / RNA polymerase sigma factor, FliA/WhiG / Sigma-70 factors family signature 1. / RNA polymerase sigma-70 region 3 / Sigma-70 region 3 / Sigma-70 factors family signature 2. / RNA polymerase sigma-70 / RNA polymerase sigma-70 region 4 / Sigma-70, region 4 / RNA polymerase sigma-70 region 2 / RNA polymerase sigma-70 like domain / Sigma-70 region 2 / RNA polymerase sigma factor, region 2 / RNA polymerase sigma factor, region 3/4-like
Similarity search - Domain/homology
Chem-C2E / RNA polymerase sigma factor / AmfC protein
Similarity search - Component
Biological speciesStreptomyces venezuelae (bacteria)
Streptomyces sp. PanSC19 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 3 Å
AuthorsSchumacher, M.A.
CitationJournal: Mol.Cell / Year: 2020
Title: c-di-GMP Arms an Anti-sigma to Control Progression of Multicellular Differentiation in Streptomyces.
Authors: Gallagher, K.A. / Schumacher, M.A. / Bush, M.J. / Bibb, M.J. / Chandra, G. / Holmes, N.A. / Zeng, W. / Henderson, M. / Zhang, H. / Findlay, K.C. / Brennan, R.G. / Buttner, M.J.
History
DepositionJun 22, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 13, 2019Provider: repository / Type: Initial release
Revision 1.1Dec 18, 2019Group: Database references / Category: citation / citation_author
Item: _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2Feb 19, 2020Group: Database references / Structure summary / Category: chem_comp / citation
Item: _chem_comp.pdbx_synonyms / _citation.journal_volume ..._chem_comp.pdbx_synonyms / _citation.journal_volume / _citation.page_first / _citation.year
Revision 1.3Oct 11, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
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
T: AmfC protein
A: RNA polymerase sigma factor
B: AmfC protein
D: RNA polymerase sigma factor
E: AmfC protein
G: RNA polymerase sigma factor
hetero molecules


Theoretical massNumber of molelcules
Total (without water)156,54912
Polymers152,4076
Non-polymers4,1426
Water00
1
T: AmfC protein
A: RNA polymerase sigma factor
hetero molecules


Theoretical massNumber of molelcules
Total (without water)52,1834
Polymers50,8022
Non-polymers1,3812
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6890 Å2
ΔGint-20 kcal/mol
Surface area18740 Å2
MethodPISA
2
B: AmfC protein
D: RNA polymerase sigma factor
hetero molecules


Theoretical massNumber of molelcules
Total (without water)52,1834
Polymers50,8022
Non-polymers1,3812
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6950 Å2
ΔGint-20 kcal/mol
Surface area17990 Å2
MethodPISA
3
E: AmfC protein
G: RNA polymerase sigma factor
hetero molecules


Theoretical massNumber of molelcules
Total (without water)52,1834
Polymers50,8022
Non-polymers1,3812
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7040 Å2
ΔGint-23 kcal/mol
Surface area18540 Å2
MethodPISA
Unit cell
Length a, b, c (Å)79.847, 97.339, 204.580
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP22121

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Components

#1: Protein AmfC protein / RsiG


Mass: 19992.371 Da / Num. of mol.: 3 / Mutation: P91G
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptomyces venezuelae (strain ATCC 10712 / CBS 650.69 / DSM 40230 / JCM 4526 / NBRC 13096 / PD 04745) (bacteria)
Strain: ATCC 10712 / CBS 650.69 / DSM 40230 / JCM 4526 / NBRC 13096 / PD 04745
Gene: SVEN_3933 / Production host: Escherichia coli (E. coli) / References: UniProt: F2RFR7
#2: Protein RNA polymerase sigma factor / WhiG


Mass: 30809.855 Da / Num. of mol.: 3 / Mutation: D38E, I97V, R144G, S150T, T159S, E162D
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptomyces sp. PanSC19 (bacteria) / Gene: EDD98_3685 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A3N1Q704
#3: Chemical
ChemComp-C2E / 9,9'-[(2R,3R,3aS,5S,7aR,9R,10R,10aS,12S,14aR)-3,5,10,12-tetrahydroxy-5,12-dioxidooctahydro-2H,7H-difuro[3,2-d:3',2'-j][1,3,7,9,2,8]tetraoxadiphosphacyclododecine-2,9-diyl]bis(2-amino-1,9-dihydro-6H-purin-6-one) / c-di-GMP / Cyclic diguanosine monophosphate


Mass: 690.411 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C20H24N10O14P2 / Feature type: SUBJECT OF INVESTIGATION
Has ligand of interestY

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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: 2.6 Å3/Da / Density % sol: 52.74 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop
Details: 0.1 M Tris Bicine pH 8.5, 0.03 M sodium nitrate, 0.03 M sodium phosphate, 0.03 M ammonium sulfate, 9% MPD, 10% PEG 1000 and 15% PEG 3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.3.1 / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Oct 14, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.99→87.897 Å / Num. obs: 59828 / % possible obs: 99.1 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4 % / CC1/2: 0.997 / Rmerge(I) obs: 0.098 / Rpim(I) all: 0.053 / Net I/σ(I): 8.9
Reflection shellResolution: 2.99→3.04 Å / Redundancy: 3.2 % / Rmerge(I) obs: 0.998 / Mean I/σ(I) obs: 1.2 / Num. unique obs: 2129 / CC1/2: 0.447 / Rpim(I) all: 0.653 / % possible all: 99.1

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
MOSFLMdata reduction
SCALAdata scaling
PHASERphasing
PHENIX1.12_2829refinement
PDB_EXTRACT3.25data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6PFJ

6pfj


Resolution: 3→87.897 Å / SU ML: 0.55 / Cross valid method: THROUGHOUT / σ(F): 0.23 / Phase error: 33.04
RfactorNum. reflection% reflection
Rfree0.2784 3613 6.04 %
Rwork0.2139 --
obs0.2178 59828 97.01 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 256.36 Å2 / Biso mean: 112.7061 Å2 / Biso min: 32.82 Å2
Refinement stepCycle: final / Resolution: 3→87.897 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9026 0 276 0 9302
Biso mean--76.67 --
Num. residues----1146
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0079458
X-RAY DIFFRACTIONf_angle_d0.97512864
X-RAY DIFFRACTIONf_chiral_restr0.0511486
X-RAY DIFFRACTIONf_plane_restr0.0051632
X-RAY DIFFRACTIONf_dihedral_angle_d21.1885761
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 26

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
3-3.03950.47251350.37482129226496
3.0395-3.08110.32191420.34062181232397
3.0811-3.12510.42631420.33332157229997
3.1251-3.17180.37851390.34382149228897
3.1718-3.22140.39411440.35362190233498
3.2214-3.27420.37491320.33022131226397
3.2742-3.33060.41631440.33142228237297
3.3306-3.39120.42011410.31712142228398
3.3912-3.45640.41111340.28622165229996
3.4564-3.5270.33521390.2722058219793
3.527-3.60370.36661360.25922159229596
3.6037-3.68750.38431420.25492151229398
3.6875-3.77970.32551370.22892176231398
3.7797-3.88190.31691360.23072189232598
3.8819-3.99610.291340.22062184231897
3.9961-4.12510.27081380.19342122226097
4.1251-4.27260.28151360.18792164230097
4.2726-4.44360.22741400.16832165230596
4.4436-4.64580.20511430.1622200234399
4.6458-4.89080.21891390.16892176231598
4.8908-5.19720.26621430.17142151229498
5.1972-5.59840.27951370.19592159229697
5.5984-6.16160.23651460.20042178232497
6.1616-7.05290.27581390.21152194233398
7.0529-8.88460.19791380.16122162230096
8.8846-87.93460.22221370.18592155229297
Refinement TLS params.Method: refined / Origin x: 54.1987 Å / Origin y: 32.2717 Å / Origin z: 15.9632 Å
111213212223313233
T0.2005 Å2-0.0381 Å20.003 Å2-0.181 Å2-0.3193 Å2--0.1653 Å2
L0.043 °20.0081 °20.0827 °2--0.0139 °20.0778 °2--0.0671 °2
S0.18 Å °0.0086 Å °0.0186 Å °0.0966 Å °-0.0315 Å °0.054 Å °0.0627 Å °0.0715 Å °-0 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1allT36 - 199
2X-RAY DIFFRACTION1allR203 - 201
3X-RAY DIFFRACTION1allA24 - 275
4X-RAY DIFFRACTION1allB40 - 199
5X-RAY DIFFRACTION1allC203 - 201
6X-RAY DIFFRACTION1allD24 - 275
7X-RAY DIFFRACTION1allE41 - 199
8X-RAY DIFFRACTION1allF203 - 201
9X-RAY DIFFRACTION1allG21 - 275

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