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- PDB-4pur: Crystal structure of MglA from Francisella tularensis -

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Basic information

Entry
Database: PDB / ID: 4pur
TitleCrystal structure of MglA from Francisella tularensis
ComponentsMacrophage growth locus, subunit A
KeywordsTRANSCRIPTION / GST-fold / stringent starvation protein
Function / homology
Function and homology information


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 ...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
D-MALATE / Macrophage growth locus, subunit A
Similarity search - Component
Biological speciesFrancisella tularensis subsp. tularensis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.95 Å
AuthorsCuthbert, B.J. / Schumacher, M.A. / Brennan, R.G.
CitationJournal: Plos One / Year: 2015
Title: Structural and Biochemical Characterization of the Francisella tularensis Pathogenicity Regulator, Macrophage Locus Protein A (MglA).
Authors: Cuthbert, B.J. / Brennan, R.G. / Schumacher, M.A.
History
DepositionMar 13, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 24, 2015Provider: repository / Type: Initial release
Revision 1.1Jan 13, 2021Group: Database references / Derived calculations
Category: citation / citation_author ...citation / citation_author / struct_conn / struct_ref_seq_dif / struct_site
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.name / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details / _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: Macrophage growth locus, subunit A
B: Macrophage growth locus, subunit A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,5834
Polymers48,3152
Non-polymers2682
Water79344
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2830 Å2
ΔGint-10 kcal/mol
Surface area20210 Å2
MethodPISA
Unit cell
Length a, b, c (Å)104.684, 104.684, 100.045
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number169
Space group name H-MP61
DetailsAUTHORS HAVE INDICATED THAT THE BIOLOGICAL UNIT IS UNKNOWN

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Components

#1: Protein Macrophage growth locus, subunit A


Mass: 24157.391 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Francisella tularensis subsp. tularensis (bacteria)
Strain: SCHU S4 / Gene: FTT_1275, mglA / Plasmid: pMCGS9 / Production host: Escherichia coli (E. coli) / Strain (production host): C41 (DE3) / References: UniProt: Q5NFG1
#2: Chemical ChemComp-MLT / D-MALATE / (2R)-2-HYDROXYBUTANEDIOIC ACID / 2-HYDROXY-SUCCINIC ACID


Mass: 134.087 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C4H6O5
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 44 / 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: 3.28 Å3/Da / Density % sol: 62.45 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.6
Details: 0.1 M TRIS, pH 7.6, 2.55 M DL-Malic acid, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.3.1 / Wavelength: 0.979570, 0.956890, 0.979725
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jan 26, 2013
RadiationProtocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.979571
20.956891
30.9797251
ReflectionResolution: 2.95→100.044 Å / Num. all: 13182 / Num. obs: 13182 / % possible obs: 99.8 % / Observed criterion σ(I): 2 / Redundancy: 3.6 % / Biso Wilson estimate: 70.17 Å2 / Rsym value: 0.065 / Net I/σ(I): 11.2
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allRsym value% possible all
2.95-3.113.60.3472.2697919160.347100
3.11-3.33.60.2083.7656718170.208100
3.3-3.533.60.1395.5621917090.139100
3.53-3.813.60.0878.3573415840.08799.9
3.81-4.173.60.06211.4530214670.06299.8
4.17-4.663.60.05213469913150.05299.6
4.66-5.393.50.05711.4415511760.057100
5.39-6.63.40.0610.634009980.0699.6
6.6-9.333.40.0414.225727570.0498.5
9.33-100.0443.60.03912.915964430.03999.1

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Processing

Software
NameVersionClassificationNB
SCALA3.3.16data scaling
PHENIX1.8.1_1168refinement
PDB_EXTRACT3.14data extraction
ADSCQuantumdata collection
MOSFLMdata reduction
SOLVEphasing
RefinementMethod to determine structure: MAD / Resolution: 2.95→90.659 Å / FOM work R set: 0.8282 / SU ML: 0.41 / σ(F): 2 / Phase error: 24.67 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2282 1313 10.04 %Random
Rwork0.1725 ---
obs0.1782 11826 98.66 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 156.2 Å2 / Biso mean: 45.02 Å2 / Biso min: 3.87 Å2
Refinement stepCycle: LAST / Resolution: 2.95→90.659 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3240 0 18 44 3302
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0073308
X-RAY DIFFRACTIONf_angle_d1.244464
X-RAY DIFFRACTIONf_chiral_restr0.09532
X-RAY DIFFRACTIONf_plane_restr0.01556
X-RAY DIFFRACTIONf_dihedral_angle_d19.111292
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 18

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.9501-3.00680.35681460.2771301144799
3.0068-3.06820.36641320.26171259139199
3.0682-3.13490.36171510.25871310146199
3.1349-3.20790.23731330.24031227136099
3.2079-3.28810.26621550.21551332148799
3.2881-3.3770.2891390.19971258139799
3.377-3.47640.29271340.19991267140199
3.4764-3.58860.25361380.20121277141599
3.5886-3.71680.2681500.17371303145399
3.7168-3.86570.21291420.16351271141399
3.8657-4.04160.23971370.15841269140699
4.0416-4.25470.23281420.13371294143699
4.2547-4.52120.17241490.14941269141899
4.5212-4.87030.20681420.14421252139499
4.8703-5.36040.21381490.14121309145899
5.3604-6.13590.25111440.18771268141299
6.1359-7.72990.21841270.19681193132092
7.7299-90.70180.16041480.14031261140998

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