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- PDB-3oir: Crystal structure of sulfate transporter family protein from Woli... -

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Basic information

Entry
Database: PDB / ID: 3oir
TitleCrystal structure of sulfate transporter family protein from Wolinella succinogenes
ComponentsSULFATE TRANSPORTER SULFATE TRANSPORTER FAMILY PROTEIN
KeywordsTRANSPORT PROTEIN / PSI-2 / Midwest Center for Structural Genomics / Protein Structure Initiative / MCSG / SULFATE TRANSPORTER
Function / homology
Function and homology information


inorganic anion transmembrane transport / 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
FORMIC ACID / SULFATE TRANSPORTER SULFATE TRANSPORTER FAMILY PROTEIN
Similarity search - Component
Biological speciesWolinella succinogenes (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.85 Å
AuthorsChang, C. / Tesar, C. / Bearden, J. / Joachimiak, A. / Midwest Center for Structural Genomics (MCSG)
CitationJournal: To be Published
Title: Crystal structure of sulfate transporter family protein from Wolinella succinogenes
Authors: Chang, C. / Tesar, C. / Bearden, J. / Joachimiak, A.
History
DepositionAug 19, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 8, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 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)30,6918
Polymers30,4362
Non-polymers2556
Water2,486138
1
A: SULFATE TRANSPORTER SULFATE TRANSPORTER FAMILY PROTEIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)15,3915
Polymers15,2181
Non-polymers1744
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)71.804, 105.423, 37.698
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP21212

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Components

#1: Protein SULFATE TRANSPORTER SULFATE TRANSPORTER FAMILY PROTEIN


Mass: 15217.916 Da / Num. of mol.: 2 / Fragment: sequence database residues 434-565
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Wolinella succinogenes (bacteria) / Gene: YCHM, WS0651 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)magic / References: UniProt: Q7M9V0
#2: Chemical
ChemComp-FMT / FORMIC ACID


Mass: 46.025 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: CH2O2
#3: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 138 / 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: 2.34 Å3/Da / Density % sol: 47.53 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 7
Details: 60% Tacsimate, pH 7.0, 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 / Date: Jul 28, 2010
RadiationMonochromator: Si(111)double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97924 Å / Relative weight: 1
ReflectionResolution: 1.85→50 Å / Num. all: 25303 / Num. obs: 25294 / % possible obs: 100 % / Observed criterion σ(I): -3 / Redundancy: 14 % / Biso Wilson estimate: 21.6 Å2 / Rmerge(I) obs: 0.104 / Net I/σ(I): 47.6
Reflection shellResolution: 1.85→1.88 Å / Redundancy: 14.4 % / Rmerge(I) obs: 0.52 / Mean I/σ(I) obs: 7.5 / Num. unique all: 1255 / % possible all: 100

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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: 1.85→50 Å / Cor.coef. Fo:Fc: 0.957 / Cor.coef. Fo:Fc free: 0.94 / Occupancy max: 1 / Occupancy min: 0.35 / SU B: 6.175 / SU ML: 0.087 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.278 / ESU R Free: 0.132
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
Rfree0.2278 1284 5.1 %RANDOM
Rwork0.1848 ---
all0.1871 25162 --
obs0.1871 25162 99.6 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso max: 91.92 Å2 / Biso mean: 24.7931 Å2 / Biso min: 5.22 Å2
Baniso -1Baniso -2Baniso -3
1-1.34 Å20 Å20 Å2
2---0.15 Å20 Å2
3----1.2 Å2
Refinement stepCycle: LAST / Resolution: 1.85→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1966 0 14 138 2118
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.0222171
X-RAY DIFFRACTIONr_angle_refined_deg1.3571.9812950
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.5615282
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.64924.059101
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.29115385
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.7651516
X-RAY DIFFRACTIONr_chiral_restr0.0890.2325
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.0211680
X-RAY DIFFRACTIONr_mcbond_it1.3661.51346
X-RAY DIFFRACTIONr_mcangle_it2.37522175
X-RAY DIFFRACTIONr_scbond_it3.5973825
X-RAY DIFFRACTIONr_scangle_it5.6184.5775
X-RAY DIFFRACTIONr_rigid_bond_restr1.80932171
LS refinement shellResolution: 1.847→1.895 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.278 98 -
Rwork0.194 1662 -
all-1760 -
obs-1750 98.21 %
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)
10.101-0.0023-0.02430.0980.05750.2536-0.00370.0012-0.00410.0018-0.00460.00010.0157-0.00280.00830.0117-0.00090.00080.01540.00090.002251.061518.063632.8502
20.1208-0.01840.00740.0902-0.00680.1530.00140.00060.0029-0.0013-0.00650.0008-0.0103-0.00390.0050.0122-0.00010.00030.01590.00050.003453.494438.143850.985
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A434 - 565
2X-RAY DIFFRACTION2B434 - 565

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