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- PDB-4dgf: Structure of SulP Transporter STAS Domain from Wolinella Succinog... -

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Basic information

Entry
Database: PDB / ID: 4dgf
TitleStructure of SulP Transporter STAS Domain from Wolinella Succinogenes Refined to 1.6 Angstrom Resolution
ComponentsSULFATE TRANSPORTER SULFATE TRANSPORTER 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


transmembrane transport / membrane
Similarity search - Function
STAS domain / SLC26A/SulP transporter / Transcription Regulator spoIIAA / SLC26A/SulP transporter domain / Sulfate permease family / STAS domain / STAS domain profile. / STAS domain / STAS domain superfamily / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
FORMIC ACID / SULFATE TRANSPORTER SULFATE TRANSPORTER FAMILY PROTEIN
Similarity search - Component
Biological speciesWolinella succinogenes (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.6 Å
AuthorsKeller, J.P. / Chang, C. / Tesar, C. / Bearden, J. / Dallos, P. / Joachimiak, A. / Midwest Center for Structural Genomics (MCSG)
CitationJournal: To be Published
Title: Structure of SulP Transporter STAS Domain from Wolinella Succinogenes Refined to 1.6 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 1.1Nov 6, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: SULFATE TRANSPORTER SULFATE TRANSPORTER FAMILY PROTEIN
B: SULFATE TRANSPORTER SULFATE TRANSPORTER FAMILY PROTEIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,5996
Polymers30,4362
Non-polymers1634
Water2,918162
1
A: SULFATE TRANSPORTER SULFATE TRANSPORTER FAMILY PROTEIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)15,2993
Polymers15,2181
Non-polymers812
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: SULFATE TRANSPORTER SULFATE TRANSPORTER FAMILY PROTEIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)15,2993
Polymers15,2181
Non-polymers812
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)37.710, 71.865, 105.570
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP22121

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Components

#1: Protein SULFATE TRANSPORTER SULFATE TRANSPORTER FAMILY PROTEIN


Mass: 15217.916 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Wolinella succinogenes (bacteria) / Gene: YCHM, WS0651 / Production host: Escherichia coli (E. coli) / References: UniProt: Q7M9V0
#2: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#3: Chemical ChemComp-FMT / FORMIC ACID


Mass: 46.025 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: CH2O2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 162 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 2.35 Å3/Da / Density % sol: 47.66 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 7
Details: 60% Tacsimate pH 7, VAPOR DIFFUSION, SITTING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.97924 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97924 Å / Relative weight: 1
ReflectionResolution: 1.6→60 Å / Num. all: 38860 / Num. obs: 38860 / % possible obs: 99.8 % / Observed criterion σ(F): -1000 / Observed criterion σ(I): -1000 / Redundancy: 12.3 %
Reflection shellResolution: 1.6→1.69 Å / Redundancy: 7.1 % / Rmerge(I) obs: 1.201 / Mean I/σ(I) obs: 1.9 / Num. unique all: 5494 / % possible all: 98.5

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Processing

Software
NameVersionClassification
ADSCQuantumdata collection
PHASERphasing
REFMAC5.6.0117refinement
MOSFLMdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.6→59.41 Å / Cor.coef. Fo:Fc: 0.955 / Cor.coef. Fo:Fc free: 0.936 / SU B: 3.301 / SU ML: 0.055 / Cross valid method: THROUGHOUT / σ(F): -1000 / ESU R: 0.096 / ESU R Free: 0.099 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
RfactorNum. reflection% reflectionSelection details
Rfree0.24384 1944 5 %RANDOM
Rwork0.20578 ---
all0.20765 36859 --
obs0.20765 36859 99.61 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 20.081 Å2
Baniso -1Baniso -2Baniso -3
1--0.8 Å20 Å2-0 Å2
2--0.89 Å20 Å2
3----0.09 Å2
Refinement stepCycle: LAST / Resolution: 1.6→59.41 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1945 0 8 162 2115
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0230.0192180
X-RAY DIFFRACTIONr_angle_refined_deg2.1771.9932975
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.3235287
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.50723.93999
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.45815362
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.2121516
X-RAY DIFFRACTIONr_chiral_restr0.1550.2330
X-RAY DIFFRACTIONr_gen_planes_refined0.0140.0211696
LS refinement shellResolution: 1.597→1.639 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.348 147 -
Rwork0.33 2344 -
obs--94.97 %
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)
11.2727-0.08940.33520.1282-0.31460.86780.00070.1077-0.0140.022-0.00150.0001-0.0095-0.00220.00080.0258-0.00630.00150.0219-0.01140.0204-23.722715.1483-34.7409
20.90290.1014-0.21570.0816-0.2560.86450.0246-0.0714-0.0433-0.0053-0.0134-0.0018-0.00850.0089-0.01110.01990.01220.0070.02110.00070.0222-5.180918.1502-14.6898
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A440 - 561
2X-RAY DIFFRACTION2B438 - 562

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