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- PDB-6drq: The crystal structure of SatS c-terminal domain in complex with b... -

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Basic information

Entry
Database: PDB / ID: 6drq
TitleThe crystal structure of SatS c-terminal domain in complex with bromine
ComponentsPrimosomal protein
KeywordsCHAPERONE / SecA2 / protein export / Structural Genomics / PSI-2 / Protein Structure Initiative / TB Structural Genomics Consortium / TBSGC
Function / homologyBROMIDE ION / :
Function and homology information
Biological speciesMycobacterium tuberculosis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.3 Å
AuthorsHughes, R.C. / Sacchettini, J.C. / TB Structural Genomics Consortium (TBSGC)
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Human Genome Research Institute (NIH/NHGRI)PO1AI095208 United States
CitationJournal: Elife / Year: 2019
Title: Mycobacterium tuberculosisSatS is a chaperone for the SecA2 protein export pathway.
Authors: Miller, B.K. / Hughes, R. / Ligon, L.S. / Rigel, N.W. / Malik, S. / Anjuwon-Foster, B.R. / Sacchettini, J.C. / Braunstein, M.
History
DepositionJun 12, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 23, 2019Provider: repository / Type: Initial release
Revision 1.1Dec 18, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.2Mar 13, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
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: Primosomal protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)20,8614
Polymers20,6211
Non-polymers2403
Water23413
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area430 Å2
ΔGint-2 kcal/mol
Surface area9750 Å2
MethodPISA
Unit cell
Length a, b, c (Å)48.796, 50.596, 76.075
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Primosomal protein


Mass: 20620.805 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium tuberculosis (bacteria) / Strain: ATCC 25618 / H37Rv / Gene: LH57_18085 / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 / References: UniProt: A0A089QXD1
#2: Chemical ChemComp-BR / BROMIDE ION


Mass: 79.904 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Br
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 13 / 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: 2.28 Å3/Da / Density % sol: 45.98 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / Details: 3.5M ammonium citrate

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Data collection

DiffractionMean temperature: 129 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-B / Wavelength: 0.902 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Mar 26, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.902 Å / Relative weight: 1
ReflectionResolution: 2.3→99 Å / Num. obs: 8721 / % possible obs: 99.2 % / Redundancy: 3.8 % / Rmerge(I) obs: 0.05 / Rsym value: 0.053 / Net I/σ(I): 27.4
Reflection shellResolution: 2.3→2.34 Å / Rmerge(I) obs: 0.105 / Num. unique all: 806

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Processing

Software
NameVersionClassification
PHENIX(1.11.1_2575: ???)refinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXHySSphasing
RefinementMethod to determine structure: SAD / Resolution: 2.3→42.129 Å / SU ML: 0.25 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 28.32
RfactorNum. reflection% reflection
Rfree0.2973 444 5.09 %
Rwork0.2095 --
obs0.2137 8721 99.01 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.3→42.129 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1447 0 3 13 1463
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0071474
X-RAY DIFFRACTIONf_angle_d0.8222007
X-RAY DIFFRACTIONf_dihedral_angle_d10.94879
X-RAY DIFFRACTIONf_chiral_restr0.048227
X-RAY DIFFRACTIONf_plane_restr0.006267
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.2996-2.63230.30951580.22292692X-RAY DIFFRACTION100
2.6323-3.31630.33291490.24272753X-RAY DIFFRACTION100
3.3163-42.13630.27581370.19212832X-RAY DIFFRACTION98

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