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- PDB-3mgl: Crystal structure of permease family protein from Vibrio cholerae -

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Basic information

Entry
Database: PDB / ID: 3mgl
TitleCrystal structure of permease family protein from Vibrio cholerae
ComponentsSulfate permease family protein
KeywordsTRANSPORT PROTEIN / PSI2 / MCSG / structural genomics / sulfate permease family protein / Protein Structure Initiative / Midwest Center for Structural Genomics
Function / homology
Function and homology information


transmembrane transport / plasma 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
IODIDE ION / Sulfate permease family protein
Similarity search - Component
Biological speciesVibrio cholerae O1 biovar El Tor (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.25 Å
AuthorsChang, C. / Marshall, N. / Bearden, J. / Joachimiak, A. / Midwest Center for Structural Genomics (MCSG)
CitationJournal: To be Published
Title: Crystal structure of permease family protein from Vibrio cholerae
Authors: Chang, C. / Marshall, N. / Bearden, J. / Joachimiak, A.
History
DepositionApr 6, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 21, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 8, 2017Group: Refinement description / Category: software
Revision 1.3Oct 16, 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 / pdbx_struct_special_symmetry / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _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 permease family protein
B: Sulfate permease family protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,58813
Polymers29,1922
Non-polymers1,39611
Water1,22568
1
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)122,35352
Polymers116,7708
Non-polymers5,58444
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 area23990 Å2
ΔGint-119 kcal/mol
Surface area38690 Å2
MethodPISA
Unit cell
Length a, b, c (Å)90.914, 90.914, 65.210
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number90
Space group name H-MP4212
Components on special symmetry positions
IDModelComponents
11A-67-

HOH

Detailsoctamer with operator (x,y,z), (y-1/2,-x+3/2,z), (-y+3/2,x+1/2,z), (-x+1,-y+2,z)

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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 O1 biovar El Tor (bacteria)
Strain: N16961 / Gene: VC_A0077 / Plasmid: pMCSG19 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)magic / References: UniProt: Q9KN88
#2: Chemical
ChemComp-IOD / IODIDE ION


Mass: 126.904 Da / Num. of mol.: 11 / Source method: obtained synthetically / Formula: I
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 68 / 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: 2.31 Å3/Da / Density % sol: 46.7 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 0.2M Potassium iodide, 20% PEG3350, pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 298K

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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 / Date: Feb 8, 2010
RadiationMonochromator: Si(111) double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97937 Å / Relative weight: 1
ReflectionResolution: 2.25→50 Å / Num. all: 13528 / Num. obs: 13508 / % possible obs: 99.9 % / Observed criterion σ(I): -3 / Redundancy: 13.7 % / Biso Wilson estimate: 44.6 Å2 / Rmerge(I) obs: 0.096 / Net I/σ(I): 63.7
Reflection shellResolution: 2.25→2.29 Å / Redundancy: 14.5 % / Rmerge(I) obs: 0.503 / Mean I/σ(I) obs: 12.2 / Num. unique all: 656 / % possible all: 100

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Processing

Software
NameVersionClassification
SBC-Collectdata collection
HKL-3000phasing
SHELXDphasing
SHELXEmodel building
MLPHAREphasing
DMmodel building
RESOLVEmodel building
Cootmodel building
ARP/wARPmodel building
REFMAC5.5.0102refinement
HKL-3000data reduction
HKL-3000data scaling
DMphasing
RESOLVEphasing
RefinementMethod to determine structure: SAD / Resolution: 2.25→50 Å / Cor.coef. Fo:Fc: 0.958 / Cor.coef. Fo:Fc free: 0.934 / SU B: 12.864 / SU ML: 0.149 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.23 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.24745 642 4.8 %RANDOM
Rwork0.19316 ---
all0.1957 13300 --
obs0.1957 13300 98.45 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 28.258 Å2
Baniso -1Baniso -2Baniso -3
1-0.14 Å20 Å20 Å2
2--0.14 Å20 Å2
3----0.28 Å2
Refinement stepCycle: LAST / Resolution: 2.25→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1975 0 11 68 2054
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0222023
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.2781.9692734
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.0825254
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.6223.88285
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.75315362
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.4131513
X-RAY DIFFRACTIONr_chiral_restr0.0770.2315
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0211495
X-RAY DIFFRACTIONr_gen_planes_other
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_it0.7821.51266
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.43722036
X-RAY DIFFRACTIONr_scbond_it2.6653757
X-RAY DIFFRACTIONr_scangle_it4.3484.5698
X-RAY DIFFRACTIONr_rigid_bond_restr1.26832023
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.249→2.308 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.222 50 -
Rwork0.148 868 -
obs-918 95.23 %
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)
18.18891.7726-1.06994.1071-5.749914.41780.2962-0.3038-0.12190.3997-0.2542-0.2872-0.61640.097-0.0420.14580.029-0.03860.08170.01870.123652.768564.462128.545
22.9781-0.3515-0.01113.4240.82891.8111-0.08510.07280.1401-0.20240.05520.1287-0.0152-0.08640.02990.0622-0.0188-0.01030.05070.00090.046837.465473.838617.145
315.9196-7.9156-4.858316.79176.899112.3032-0.1672-0.0685-0.44450.50190.2777-0.63890.9299-0.0995-0.11050.1261-0.0092-0.0050.13120.03240.118745.346761.102324.4344
46.0414-2.2344-0.59415.95324.013519.72790.08340.0113-0.137-0.1879-0.17030.15710.09530.06220.08690.1603-0.05280.03060.0658-0.00020.089537.521464.12942.3529
54.87711.3359-0.46013.4495-0.97592.7679-0.0907-0.08110.06290.19370.0525-0.1059-0.05430.05030.03820.0790.02250.00270.04670.00540.032253.272673.847253.2484
617.64247.2799-6.5411.8326-3.091912.2228-0.42140.1321-0.70960.20310.37380.30840.7656-0.24360.04770.241-0.00780.03760.1828-0.03270.17244.788661.044646.2037
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A423 - 440
2X-RAY DIFFRACTION2A441 - 534
3X-RAY DIFFRACTION3A535 - 550
4X-RAY DIFFRACTION4B423 - 440
5X-RAY DIFFRACTION5B441 - 534
6X-RAY DIFFRACTION6B535 - 550

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