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- PDB-4dgh: Structure of SulP Transporter STAS Domain from Vibrio Cholerae Re... -

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Basic information

Entry
Database: PDB / ID: 4dgh
TitleStructure of SulP Transporter STAS Domain from Vibrio Cholerae Refined to 1.9 Angstrom Resolution
ComponentsSulfate permease family protein
KeywordsTRANSPORT PROTEIN / STAS Domain / Anion Exchange / Membrane / Structural Genomics / PSI-Biology / Midwest Center for Structural Genomics / MCSG
Function / homology
Function and homology information


inorganic anion transmembrane transport / fumarate transmembrane transporter activity / fumarate transport / succinate transmembrane transport / succinate transmembrane transporter activity / L-aspartate transmembrane transporter activity / monoatomic anion transmembrane transporter activity / membrane
Similarity search - Function
STAS domain / SLC26A/SulP transporter / 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
IODIDE ION / : / Sulfate permease family protein
Similarity search - Component
Biological speciesVibrio cholerae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsKeller, J.P. / Chang, C. / Marshall, N. / Bearden, J. / Dallos, P. / Joachimiak, A. / Midwest Center for Structural Genomics (MCSG)
CitationJournal: To be Published
Title: Structure of SulP Transporter STAS Domain from Vibrio Cholerae Refined to 1.9 Angstrom Resolution
Authors: Keller, J.P. / Chang, C. / Dallos, P. / Joachimiak, A.
History
DepositionJan 25, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 8, 2012Provider: repository / Type: Initial release
Revision 1.1Feb 15, 2012Group: Other

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Sulfate permease family protein
B: Sulfate permease family protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,41121
Polymers29,1922
Non-polymers2,21919
Water1,78399
1
A: Sulfate permease family protein
hetero molecules

A: Sulfate permease family protein
hetero molecules

A: Sulfate permease family protein
hetero molecules

A: Sulfate permease family protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)62,32440
Polymers58,3854
Non-polymers3,93936
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_675-x+1,-y+2,z1
crystal symmetry operation3_655-y+3/2,x+1/2,z1
crystal symmetry operation4_465y-1/2,-x+3/2,z1
Buried area10420 Å2
ΔGint-43 kcal/mol
Surface area21650 Å2
MethodPISA
2
B: Sulfate permease family protein
hetero molecules

B: Sulfate permease family protein
hetero molecules

B: Sulfate permease family protein
hetero molecules

B: Sulfate permease family protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)63,32244
Polymers58,3854
Non-polymers4,93740
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_675-x+1,-y+2,z1
crystal symmetry operation3_655-y+3/2,x+1/2,z1
crystal symmetry operation4_465y-1/2,-x+3/2,z1
Buried area10340 Å2
ΔGint-42 kcal/mol
Surface area22730 Å2
MethodPISA
3
A: Sulfate permease family protein
B: Sulfate permease family protein
hetero molecules

A: Sulfate permease family protein
B: Sulfate permease family protein
hetero molecules

A: Sulfate permease family protein
B: Sulfate permease family protein
hetero molecules

A: Sulfate permease family protein
B: Sulfate permease family protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)125,64584
Polymers116,7708
Non-polymers8,87676
Water1448
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_675-x+1,-y+2,z1
crystal symmetry operation3_655-y+3/2,x+1/2,z1
crystal symmetry operation4_465y-1/2,-x+3/2,z1
Buried area25440 Å2
ΔGint-111 kcal/mol
Surface area40280 Å2
MethodPISA
Unit cell
Length a, b, c (Å)90.850, 90.850, 65.180
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number90
Space group name H-MP4212

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Components

#1: Protein Sulfate permease family protein


Mass: 14596.197 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Vibrio cholerae (bacteria) / Gene: VC_A0077 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9KN88
#2: Chemical ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: K
#3: Chemical
ChemComp-IOD / IODIDE ION / Iodide


Mass: 126.904 Da / Num. of mol.: 15 / Source method: obtained synthetically / Formula: I
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3H8O3
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 99 / 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: 2.3 Å3/Da / Density % sol: 46.6 %
Crystal growTemperature: 292 K / Method: vapor diffusion, sitting drop / pH: 6
Details: 200 mM KI, 20% PEG 3350, pH 6, VAPOR DIFFUSION, SITTING DROP, temperature 292K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.97937 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97937 Å / Relative weight: 1
ReflectionResolution: 1.9→65.18 Å / Num. all: 22098 / Num. obs: 22098 / % possible obs: 100 % / Observed criterion σ(F): -1000 / Observed criterion σ(I): -1000
Reflection shellResolution: 1.9→2 Å / % possible all: 100

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Processing

Software
NameVersionClassification
ADSCQuantumdata collection
PHASERphasing
REFMAC5.6.0117refinement
MOSFLMdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.9→65.18 Å / Cor.coef. Fo:Fc: 0.962 / Cor.coef. Fo:Fc free: 0.946 / SU B: 6.965 / SU ML: 0.087 / Cross valid method: THROUGHOUT / ESU R: 0.165 / ESU R Free: 0.15 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
RfactorNum. reflection% reflectionSelection details
Rfree0.23601 1131 5.1 %RANDOM
Rwork0.19629 ---
obs0.19822 20943 99.93 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 30.749 Å2
Baniso -1Baniso -2Baniso -3
1-0.03 Å20 Å20 Å2
2--0.03 Å20 Å2
3----0.06 Å2
Refinement stepCycle: LAST / Resolution: 1.9→65.18 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1989 0 34 99 2122
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0190.0192191
X-RAY DIFFRACTIONr_angle_refined_deg2.1191.9892978
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.8215288
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.49323.8394
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.715374
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.5541516
X-RAY DIFFRACTIONr_chiral_restr0.1510.2341
X-RAY DIFFRACTIONr_gen_planes_refined0.010.0211646
LS refinement shellResolution: 1.9→1.949 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.311 80 -
Rwork0.282 1359 -
obs--100 %
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)
10.91580.10470.29661.11350.00550.1018-0.0465-0.05380.0114-0.05250.02670.04930.005-0.01790.01990.10940.00840.02190.0734-0.00960.077140.61770.992419.5473
21.1750.14010.22090.8235-0.2830.1825-0.11140.0307-0.05450.02890.0664-0.10770.0129-0.01940.04490.12660.0130.03550.08380.00150.057950.190270.937350.803
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A423 - 550
2X-RAY DIFFRACTION1A702 - 758
3X-RAY DIFFRACTION2B423 - 550
4X-RAY DIFFRACTION2B701 - 741

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