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- PDB-6dnm: The crystal structure of SatS c-terminal domain -

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Basic information

Entry
Database: PDB / ID: 6dnm
TitleThe crystal structure of SatS c-terminal domain
ComponentsExport chaperone SatS
KeywordsCHAPERONE / SecA2 / protein export / Structural Genomics / PSI-2 / Protein Structure Initiative / TB Structural Genomics Consortium / TBSGC
Function / homology:
Function and homology information
Biological speciesMycobacterium tuberculosis H37Rv (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 1.397 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 7, 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

Downloads & links

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Assembly

Deposited unit
A: Export chaperone SatS


Theoretical massNumber of molelcules
Total (without water)21,1751
Polymers21,1751
Non-polymers00
Water1,982110
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area9780 Å2
MethodPISA
Unit cell
Length a, b, c (Å)48.867, 50.580, 76.465
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 Export chaperone SatS


Mass: 21175.488 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium tuberculosis H37Rv (bacteria)
Strain: ATCC 25618 / H37Rv / Gene: LH57_18085 / Production host: Escherichia coli BL21 (bacteria) / References: UniProt: A0A089QXD1
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 110 / 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: 2.23 Å3/Da / Density % sol: 44.88 %
Crystal growTemperature: 289 K / Method: vapor diffusion, hanging drop / Details: 3.5M ammonium citrate

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Data collection

DiffractionMean temperature: 120 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-D / Wavelength: 0.979 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Apr 14, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 1.4→99 Å / Num. obs: 35457 / % possible obs: 92.6 % / Redundancy: 5.9 % / Rmerge(I) obs: 0.081 / Rsym value: 0.079 / Net I/σ(I): 14.4
Reflection shellResolution: 1.4→1.42 Å / Rmerge(I) obs: 0.254 / Rsym value: 0.297

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Processing

Software
NameVersionClassification
PHENIX(1.11.1_2575: ???)refinement
HKL-3000data reduction
HKL-3000data scaling
PHENIXphasing
RefinementResolution: 1.397→42.186 Å / SU ML: 0.14 / Cross valid method: FREE R-VALUE / σ(F): 1.38 / Phase error: 21.34 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2307 1702 4.85 %
Rwork0.1928 --
obs0.1947 35079 91.62 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.397→42.186 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1467 0 0 110 1577
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0051494
X-RAY DIFFRACTIONf_angle_d0.7362034
X-RAY DIFFRACTIONf_dihedral_angle_d17.499544
X-RAY DIFFRACTIONf_chiral_restr0.069231
X-RAY DIFFRACTIONf_plane_restr0.005270
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.3971-1.43820.2382950.17752145X-RAY DIFFRACTION71
1.4382-1.48460.21741300.14642616X-RAY DIFFRACTION88
1.4846-1.53770.19851490.14122879X-RAY DIFFRACTION96
1.5377-1.59930.21721530.14982931X-RAY DIFFRACTION98
1.5993-1.67210.24031320.15562952X-RAY DIFFRACTION98
1.6721-1.76020.20331620.16832931X-RAY DIFFRACTION98
1.7602-1.87050.22661590.16812928X-RAY DIFFRACTION98
1.8705-2.01490.22521660.17882897X-RAY DIFFRACTION96
2.0149-2.21770.21351420.18792882X-RAY DIFFRACTION94
2.2177-2.53850.21851540.20212812X-RAY DIFFRACTION93
2.5385-3.19810.24411210.23222761X-RAY DIFFRACTION89
3.1981-42.20510.25031390.20372643X-RAY DIFFRACTION82
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)
10.6637-0.2458-0.25160.2434-0.00930.15510.2132-0.24980.2313-0.1112-0.0942-0.263-0.15280.11050.00430.1918-0.01450.03380.138-0.00690.20853.885942.7998.2137
20.2306-0.1037-0.29620.47330.27260.39520.06180.0045-0.02820.0339-0.03620.0361-0.0459-0.0771-0.00010.14430.0078-0.00440.1290.01510.1432-4.968835.530121.7795
30.23740.057-0.12620.24190.13520.67920.0520.12620.0071-0.00860.0190.1385-0.3376-0.55040.00070.19070.0403-0.00550.2297-0.0020.1537-14.963136.80314.4413
40.55660.1014-0.24060.5444-0.4090.4082-0.02860.1059-0.1111-0.1718-0.0409-0.01290.13520.0569-0.00010.17740.007-0.01990.1554-0.02310.1475-4.850130.071710.6435
50.04530.01370.05660.01980.00280.0676-0.04030.2332-0.0936-0.5256-0.06540.07980.1026-0.1996-0.00880.22740.03680.02760.1665-0.00610.1990.535733.58133.5375
60.3727-0.09780.26410.3833-0.07630.26130.0482-0.06770.0040.0385-0.0361-0.1026-0.18950.1372-00.1487-0.00540.00580.14550.00570.15230.180438.296622.4641
70.0371-0.0019-0.08020.10660.05590.15080.0252-0.1015-0.01220.12940.0839-0.2465-0.03060.485-00.18310.01890.0060.26120.00550.1876-9.619939.659543.2337
80.2807-0.2047-0.28830.17160.16110.28250.04860.10140.1233-0.1603-0.0048-0.0628-0.3942-0.072-0.00050.15020.01260.02650.1578-0.00840.1716-11.860442.188927.3242
90.0708-0.12350.06390.163-0.10480.08130.06320.2082-0.0450.0394-0.14310.0052-0.0586-0.3673-0.00020.15290.00760.00860.2429-0.00350.1976-23.964141.265630.0712
100.01980.0484-0.03330.0848-0.04340.02660.1192-0.2091-0.0581-0.0692-0.0770.048-0.2306-0.13530.00050.1754-0.02130.02680.1492-0.0060.1565-16.675946.324839.7703
110.11310.04090.14220.0149-0.01560.15980.0841-0.0650.18660.23720.0770.0359-0.1273-0.09680.01430.2181-0.01360.07240.175-0.02220.176-15.556849.429645.6871
120.4447-0.19930.26850.3683-0.15280.2228-0.11790.1304-0.18620.1081-0.0620.20690.244-0.1445-0.00580.1605-0.00150.01610.188-0.00170.1823-16.49531.008331.0431
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 234 through 248 )
2X-RAY DIFFRACTION2chain 'A' and (resid 249 through 267 )
3X-RAY DIFFRACTION3chain 'A' and (resid 268 through 279 )
4X-RAY DIFFRACTION4chain 'A' and (resid 280 through 306 )
5X-RAY DIFFRACTION5chain 'A' and (resid 307 through 316 )
6X-RAY DIFFRACTION6chain 'A' and (resid 317 through 333 )
7X-RAY DIFFRACTION7chain 'A' and (resid 334 through 346 )
8X-RAY DIFFRACTION8chain 'A' and (resid 347 through 364 )
9X-RAY DIFFRACTION9chain 'A' and (resid 365 through 377 )
10X-RAY DIFFRACTION10chain 'A' and (resid 378 through 387 )
11X-RAY DIFFRACTION11chain 'A' and (resid 388 through 399 )
12X-RAY DIFFRACTION12chain 'A' and (resid 400 through 420 )

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