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- PDB-3t6o: The Structure of an Anti-sigma-factor antagonist (STAS) domain pr... -

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Basic information

Entry
Database: PDB / ID: 3t6o
TitleThe Structure of an Anti-sigma-factor antagonist (STAS) domain protein from Planctomyces limnophilus.
ComponentsSulfate transporter/antisigma-factor antagonist STAS
KeywordsTRANSPORT PROTEIN / Structural Genomics / PSI-Biology / Midwest Center for Structural Genomics / MCSG / Sulfate transporter/antisigma-factor antagonist STAS / anti sigma factor / regulatory phosphorylation
Function / homologySTAS domain / STAS domain / Transcription Regulator spoIIAA / STAS domain profile. / STAS domain / STAS domain superfamily / 2-Layer Sandwich / Alpha Beta / Sulfate transporter/antisigma-factor antagonist STAS
Function and homology information
Biological speciesPlanctomyces limnophilus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.1 Å
AuthorsCuff, M.E. / Moser, C. / Hatzos-Skintges, C. / Bearden, J. / Joachimiak, A. / Midwest Center for Structural Genomics (MCSG)
CitationJournal: TO BE PUBLISHED
Title: The Structure of an Anti-sigma-factor antagonist (STAS) domain protein from Planctomyces limnophilus.
Authors: Cuff, M.E. / Moser, C. / Hatzos-Skintges, C. / Bearden, J. / Joachimiak, A.
History
DepositionJul 28, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 7, 2011Provider: repository / Type: Initial release
Revision 1.1Nov 8, 2017Group: Refinement description / Category: software

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Sulfate transporter/antisigma-factor antagonist STAS
B: Sulfate transporter/antisigma-factor antagonist STAS
C: Sulfate transporter/antisigma-factor antagonist STAS
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,3074
Polymers41,2723
Non-polymers351
Water4,936274
1
A: Sulfate transporter/antisigma-factor antagonist STAS
B: Sulfate transporter/antisigma-factor antagonist STAS
C: Sulfate transporter/antisigma-factor antagonist STAS
hetero molecules

A: Sulfate transporter/antisigma-factor antagonist STAS
B: Sulfate transporter/antisigma-factor antagonist STAS
C: Sulfate transporter/antisigma-factor antagonist STAS
hetero molecules


Theoretical massNumber of molelcules
Total (without water)82,6158
Polymers82,5446
Non-polymers712
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_565-x,-y+1,z1
Buried area8150 Å2
ΔGint-48 kcal/mol
Surface area31680 Å2
MethodPISA
2


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3010 Å2
ΔGint-20 kcal/mol
Surface area16900 Å2
MethodPISA
Unit cell
Length a, b, c (Å)73.038, 92.453, 142.753
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number23
Space group name H-MI222

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Components

#1: Protein Sulfate transporter/antisigma-factor antagonist STAS


Mass: 13757.277 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Planctomyces limnophilus (bacteria) / Strain: DSM 3776 / Gene: Plim_2399 / Plasmid: pMCSG7 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 (DE3) Magic / References: UniProt: D5SP81
#2: Chemical ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 274 / 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: 2.92 Å3/Da / Density % sol: 57.87 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: 0.8M LiCl2, 0.1 Tris:HCl pH8.5, 32% PEG 4K, VAPOR DIFFUSION, SITTING DROP, temperature 289K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.97935, 0.97945
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jun 9, 2011
RadiationMonochromator: SAGITALLY FOCUSED Si(111) / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.979351
20.979451
ReflectionResolution: 2.1→50 Å / Num. all: 27534 / Num. obs: 27534 / % possible obs: 97.1 % / Observed criterion σ(I): -3 / Redundancy: 8.7 % / Rmerge(I) obs: 0.101 / Net I/σ(I): 7.2
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsDiffraction-ID% possible all
2.1-2.146.90.452183.4
2.14-2.187.10.432186.1
2.18-2.227.40.387189
2.22-2.267.70.378191.6
2.26-2.317.90.343194.8
2.31-2.378.20.305197.9
2.37-2.428.70.28199.9
2.42-2.499.30.2961100
2.49-2.569.40.2691100
2.56-2.659.40.2181100
2.65-2.749.40.1831100
2.74-2.859.40.151100
2.85-2.989.40.1311100
2.98-3.149.40.1151100
3.14-3.339.30.0941100
3.33-3.599.30.0891100
3.59-3.959.20.091100
3.95-4.529.10.081100
4.52-5.78.90.0821100
5.7-508.40.085197.7

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
REFMACrefinement
PDB_EXTRACT3.1data extraction
SBC-Collectdata collection
HKL-3000data reduction
HKL-3000data scaling
HKL-3000phasing
SHELXDphasing
SHELXEmodel building
MLPHAREphasing
DMphasing
SOLVEphasing
RESOLVEphasing
ARP/wARPmodel building
CCP4phasing
Omodel building
Cootmodel building
RefinementMethod to determine structure: MAD / Resolution: 2.1→50 Å / Cor.coef. Fo:Fc: 0.956 / Cor.coef. Fo:Fc free: 0.925 / Occupancy max: 1 / Occupancy min: 0.5 / SU B: 9.446 / SU ML: 0.114 / SU R Cruickshank DPI: 0.2159 / Cross valid method: THROUGHOUT / ESU R: 0.216 / ESU R Free: 0.186
Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.22322 1216 5 %RANDOM
Rwork0.17406 ---
obs0.17645 23115 85.45 %-
all-24331 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 27.955 Å2
Baniso -1Baniso -2Baniso -3
1--0.93 Å20 Å20 Å2
2---0.75 Å20 Å2
3---1.69 Å2
Refinement stepCycle: LAST / Resolution: 2.1→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2786 0 1 274 3061
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0170.0222963
X-RAY DIFFRACTIONr_bond_other_d0.0010.022017
X-RAY DIFFRACTIONr_angle_refined_deg1.5361.9434038
X-RAY DIFFRACTIONr_angle_other_deg0.9534905
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.615375
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.77723.427143
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.19315515
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.0911525
X-RAY DIFFRACTIONr_chiral_restr0.0990.2461
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.023310
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02640
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.8741.51799
X-RAY DIFFRACTIONr_mcbond_other0.2031.5719
X-RAY DIFFRACTIONr_mcangle_it1.63622932
X-RAY DIFFRACTIONr_scbond_it2.36731164
X-RAY DIFFRACTIONr_scangle_it3.9954.51095
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.103→2.158 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.246 55 -
Rwork0.188 937 -
obs--48.23 %
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)
13.7726-0.0498-0.10073.5722-0.95672.03830.0778-0.0553-0.21210.012-0.07840.1017-0.1083-0.04340.00060.01440.0047-0.03170.0389-0.02590.126118.977946.930634.4292
22.29250.2136-0.92252.0621-0.03485.676-0.0644-0.0378-0.20770.0079-0.0325-0.05410.49310.44670.09690.08220.0738-0.00760.0731-0.00350.02794.033132.285815.667
32.960.7631-0.07865.6069-0.67621.4028-0.1068-0.19220.12720.1010.0613-0.0675-0.00580.03490.04550.0154-0.00170.00020.04580.0190.11511.079124.491146.023
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A-10 - 9999
2X-RAY DIFFRACTION2B-10 - 9999
3X-RAY DIFFRACTION3C-10 - 9999

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