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- PDB-6alx: Structure of F. tularensis MglA-SspA solved in the presence of polyP -

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Basic information

Entry
Database: PDB / ID: 6alx
TitleStructure of F. tularensis MglA-SspA solved in the presence of polyP
Components
  • Macrophage growth locus A
  • Stringent starvation protein A
KeywordsTRANSCRIPTION / MglA / SspA / Francisella tularensis / bioweapon / ppGpp
Function / homology
Function and homology information


Glutathione S-transferase, N-terminal domain / Glutathione S-transferase, N-terminal domain / Glutathione S-transferase Yfyf (Class Pi); Chain A, domain 2 - #10 / Glutathione S-transferase Yfyf (Class Pi); Chain A, domain 2 / Soluble glutathione S-transferase N-terminal domain profile. / Glutathione S-transferase, N-terminal / Glutaredoxin / Glutaredoxin / Thioredoxin-like superfamily / Up-down Bundle ...Glutathione S-transferase, N-terminal domain / Glutathione S-transferase, N-terminal domain / Glutathione S-transferase Yfyf (Class Pi); Chain A, domain 2 - #10 / Glutathione S-transferase Yfyf (Class Pi); Chain A, domain 2 / Soluble glutathione S-transferase N-terminal domain profile. / Glutathione S-transferase, N-terminal / Glutaredoxin / Glutaredoxin / Thioredoxin-like superfamily / Up-down Bundle / 3-Layer(aba) Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
: / GST N-terminal domain-containing protein
Similarity search - Component
Biological speciesFrancisella tularensis (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 3.3 Å
AuthorsSchumacher, M.A.
CitationJournal: Genes Dev. / Year: 2017
Title: Dissection of the molecular circuitry controlling virulence in Francisella tularensis.
Authors: Cuthbert, B.J. / Ross, W. / Rohlfing, A.E. / Dove, S.L. / Gourse, R.L. / Brennan, R.G. / Schumacher, M.A.
History
DepositionAug 8, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 23, 2017Provider: repository / Type: Initial release
Revision 1.1Sep 20, 2017Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Sep 27, 2017Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.3Oct 4, 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

Downloads & links

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Assembly

Deposited unit
C: Stringent starvation protein A
A: Macrophage growth locus A
B: Stringent starvation protein A
D: Macrophage growth locus A


Theoretical massNumber of molelcules
Total (without water)95,4094
Polymers95,4094
Non-polymers00
Water0
1
C: Stringent starvation protein A
A: Macrophage growth locus A


Theoretical massNumber of molelcules
Total (without water)47,7052
Polymers47,7052
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1810 Å2
ΔGint-8 kcal/mol
Surface area19420 Å2
MethodPISA
2
B: Stringent starvation protein A
D: Macrophage growth locus A


Theoretical massNumber of molelcules
Total (without water)47,7052
Polymers47,7052
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1800 Å2
ΔGint-8 kcal/mol
Surface area19810 Å2
MethodPISA
Unit cell
Length a, b, c (Å)67.253, 114.298, 141.651
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Stringent starvation protein A / Starvation protein A


Mass: 24110.094 Da / Num. of mol.: 2 / Fragment: UNP residues 3-209
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Francisella tularensis (bacteria) / Gene: AV531_02990, DR86_1150 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A0E2ZL39
#2: Protein Macrophage growth locus A


Mass: 23594.529 Da / Num. of mol.: 2 / Fragment: UNP residues 1-201
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Francisella tularensis (bacteria) / Gene: DR86_1530 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A0E2ZLH6

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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: 2.93 Å3/Da / Density % sol: 57.97 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / Details: Peg 3350

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU FR-E SUPERBRIGHT / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS HTC / Detector: IMAGE PLATE / Date: Aug 8, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 3.3→60.754 Å / Num. obs: 16079 / % possible obs: 94.2 % / Observed criterion σ(F): 0 / Redundancy: 3.5 % / CC1/2: 0.994 / Rpim(I) all: 0.062 / Rrim(I) all: 0.117 / Rsym value: 0.098 / Net I/σ(I): 8.1
Reflection shellResolution: 3.3→3.48 Å / Redundancy: 3.3 % / Mean I/σ(I) obs: 2.5 / CC1/2: 0.843 / Rpim(I) all: 0.28 / Rrim(I) all: 0.643 / Rsym value: 0.448 / % possible all: 100

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
MOSFLMdata reduction
SCALAdata scaling
MOLREPphasing
PHENIX1.6.4_486refinement
PDB_EXTRACT3.22data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5U56

5u56


Resolution: 3.3→60.753 Å / SU ML: 0.44 / Cross valid method: FREE R-VALUE / σ(F): 0 / Phase error: 29.8
RfactorNum. reflection% reflection
Rfree0.2944 1617 10.06 %
Rwork0.2091 --
obs0.2177 16079 94.24 %
Solvent computationShrinkage radii: 0.83 Å / VDW probe radii: 1.1 Å / Bsol: 62.129 Å2 / ksol: 0.309 e/Å3
Displacement parametersBiso max: 350.4 Å2 / Biso mean: 96.9676 Å2 / Biso min: 20.46 Å2
Baniso -1Baniso -2Baniso -3
1-13.3764 Å20 Å2-0 Å2
2--4.9053 Å20 Å2
3----18.2817 Å2
Refinement stepCycle: final / Resolution: 3.3→60.753 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6230 0 0 0 6230
Num. residues----796
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 10

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
3.3001-3.41810.37351540.27981277143185
3.4181-3.55490.41571420.29751323146587
3.5549-3.71670.3921480.29791364151291
3.7167-3.91260.34841600.24691385154592
3.9126-4.15770.31580.20771401155993
4.1577-4.47860.25991650.16871495166098
4.4786-4.92910.25271650.1511502166799
4.9291-5.64190.24471710.17631535170699
5.6419-7.10650.31471710.22061547171899
7.1065-60.76360.25731830.19871633181699
Refinement TLS params.Method: refined / Origin x: 1.1972 Å / Origin y: 0.0225 Å / Origin z: 10.4491 Å
111213212223313233
T0.1573 Å2-0.0241 Å2-0.0296 Å2-0.2236 Å20.0594 Å2--0.2903 Å2
L0.1742 °20.1776 °2-0.0538 °2-0.7257 °20.9203 °2--2.1676 °2
S0.1343 Å °-0.0012 Å °0.0409 Å °-0.0862 Å °0.0102 Å °-0.0021 Å °-0.0706 Å °-0.0504 Å °-0.0001 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1allC0 - 194
2X-RAY DIFFRACTION1allA2 - 200
3X-RAY DIFFRACTION1allB0 - 194
4X-RAY DIFFRACTION1allD2 - 200

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