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- PDB-3oiz: Crystal structure of antisigma-factor antagonist, STAS domain fro... -

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Basic information

Entry
Database: PDB / ID: 3oiz
TitleCrystal structure of antisigma-factor antagonist, STAS domain from Rhodobacter sphaeroides
ComponentsAntisigma-factor antagonist, STAS
KeywordsMEMBRANE PROTEIN / PSI-2 / Midwest Center for Structural Genomics / Protein Structure Initiative / MCSG / STAS domain
Function / homology
Function and homology information


sulfate transmembrane transporter activity / membrane => GO:0016020
Similarity search - Function
STAS domain / SLC26A/SulP transporter domain / Sulfate permease family / Transcription Regulator spoIIAA / STAS domain / STAS domain profile. / STAS domain / STAS domain superfamily / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Antisigma-factor antagonist, STAS
Similarity search - Component
Biological speciesRhodobacter sphaeroides (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.65 Å
AuthorsChang, C. / Marshall, N. / Freeman, L. / Joachimiak, A. / Midwest Center for Structural Genomics (MCSG)
CitationJournal: To be Published
Title: Crystal structure of antisigma-factor antagonist, STAS domain from Rhodobacter sphaeroides
Authors: Chang, C. / Marshall, N. / Freeman, L. / Joachimiak, A.
History
DepositionAug 20, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 8, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Antisigma-factor antagonist, STAS


Theoretical massNumber of molelcules
Total (without water)11,4421
Polymers11,4421
Non-polymers00
Water1,982110
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)72.102, 72.102, 36.429
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number96
Space group name H-MP43212

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Components

#1: Protein Antisigma-factor antagonist, STAS


Mass: 11442.281 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rhodobacter sphaeroides (bacteria) / Strain: ATCC 17023 / 2.4.1 / NCIB 8253 / DSM 158 / Gene: RHOS4_40800, RSP_4197 / Plasmid: pMCSG19 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q3IUY6
#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: 2.07 Å3/Da / Density % sol: 40.55 %
Crystal growTemperature: 297 K / Method: vapor diffusion, sitting drop / pH: 6
Details: 0.2M Calcium acetate, 0.1M MES, 10% iso-propanol, pH 6.0, VAPOR DIFFUSION, SITTING DROP, temperature 297K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.97935 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jun 7, 2010
RadiationMonochromator: Si(111) double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97935 Å / Relative weight: 1
ReflectionResolution: 1.65→50 Å / Num. all: 12087 / Num. obs: 12047 / % possible obs: 99.7 % / Observed criterion σ(I): -3 / Redundancy: 10.5 % / Biso Wilson estimate: 24.9 Å2 / Rmerge(I) obs: 0.097 / Net I/σ(I): 62.2
Reflection shellResolution: 1.65→1.68 Å / Redundancy: 4.9 % / Rmerge(I) obs: 0.507 / Mean I/σ(I) obs: 2.9 / Num. unique all: 582 / % possible all: 99.7

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Processing

Software
NameVersionClassificationNB
REFMAC5.5.0109refinement
PDB_EXTRACT3.1data extraction
SBC-Collectdata collection
HKL-3000data reduction
HKL-3000data scaling
HKL-3000phasing
SHELXDphasing
SHELXEmodel building
MLPHAREphasing
DMphasing
RESOLVEphasing
Cootmodel building
ARP/wARPmodel building
RefinementMethod to determine structure: SAD / Resolution: 1.65→50 Å / Cor.coef. Fo:Fc: 0.969 / Cor.coef. Fo:Fc free: 0.954 / Occupancy max: 1 / Occupancy min: 0.5 / SU B: 4.192 / SU ML: 0.065 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.101
Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.2156 573 4.8 %RANDOM
Rwork0.1597 ---
all0.1623 12008 --
obs0.1623 12008 99.64 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso max: 80.33 Å2 / Biso mean: 30.2107 Å2 / Biso min: 18.35 Å2
Baniso -1Baniso -2Baniso -3
1--1.39 Å20 Å20 Å2
2---1.39 Å20 Å2
3---2.78 Å2
Refinement stepCycle: LAST / Resolution: 1.65→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms731 0 0 110 841
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.022807
X-RAY DIFFRACTIONr_angle_refined_deg1.421.9391095
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.5765104
X-RAY DIFFRACTIONr_dihedral_angle_2_deg28.42323.25643
X-RAY DIFFRACTIONr_dihedral_angle_3_deg10.84815142
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.079159
X-RAY DIFFRACTIONr_chiral_restr0.1090.2119
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.02635
X-RAY DIFFRACTIONr_mcbond_it1.6231.5495
X-RAY DIFFRACTIONr_mcangle_it2.7242801
X-RAY DIFFRACTIONr_scbond_it4.2593312
X-RAY DIFFRACTIONr_scangle_it6.7824.5294
X-RAY DIFFRACTIONr_rigid_bond_restr1.8733807
LS refinement shellResolution: 1.648→1.691 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.234 44 -
Rwork0.205 783 -
all-827 -
obs-827 99.64 %
Refinement TLS params.Method: refined / Origin x: 35.8237 Å / Origin y: 17.1956 Å / Origin z: 16.8824 Å
111213212223313233
T0.0238 Å20.0004 Å2-0.002 Å2-0.0254 Å20.0007 Å2--0.0138 Å2
L0.1607 °2-0.0299 °20.0393 °2-0.1667 °20.0759 °2--0.2801 °2
S-0.0066 Å °-0.0025 Å °0.0095 Å °-0.0054 Å °-0.0008 Å °-0.0054 Å °-0.0141 Å °0.0017 Å °0.0074 Å °

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