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- PDB-3uif: CRYSTAL STRUCTURE OF putative sulfonate ABC transporter, periplas... -

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Basic information

Entry
Database: PDB / ID: 3uif
TitleCRYSTAL STRUCTURE OF putative sulfonate ABC transporter, periplasmic sulfonate-binding protein SsuA from Methylobacillus flagellatus KT
ComponentsSulfonate ABC transporter, periplasmic sulfonate-binding protein SsuA
KeywordsTRANSPORT PROTEIN / STRUCTURAL GENOMICS / PROTEIN STRUCTURE INITIATIVE / NEW YORK STRUCTURAL GENOMIX RESEARCH CONSORTIUM / NYSGRC / sulfonate ABC transporter / PSI-Biology / New York Structural Genomics Research Consortium
Function / homologySsuA/THI5-like / NMT1/THI5 like / Periplasmic binding protein-like II / D-Maltodextrin-Binding Protein; domain 2 / 3-Layer(aba) Sandwich / Alpha Beta / Sulfonate ABC transporter, periplasmic sulfonate-binding protein SsuA
Function and homology information
Biological speciesMethylobacillus flagellatus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.6 Å
AuthorsMalashkevich, V.N. / Bonanno, J.B. / Bhosle, R. / Toro, R. / Seidel, R. / Almo, S.C. / New York Structural Genomics Research Consortium (NYSGRC)
CitationJournal: To be Published
Title: CRYSTAL STRUCTURE OF putative sulfonate ABC transporter, periplasmic sulfonate-binding protein SsuA from Methylobacillus flagellatus KT
Authors: Malashkevich, V.N. / Bonanno, J.B. / Bhosle, R. / Toro, R. / Seidel, R. / Almo, S.C.
History
DepositionNov 4, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 23, 2011Provider: 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

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Assembly

Deposited unit
A: Sulfonate ABC transporter, periplasmic sulfonate-binding protein SsuA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,5044
Polymers39,2201
Non-polymers2843
Water1,06359
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)101.097, 101.097, 66.897
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number96
Space group name H-MP43212
Detailsbiological unit is the same as asym.

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Components

#1: Protein Sulfonate ABC transporter, periplasmic sulfonate-binding protein SsuA


Mass: 39219.766 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Methylobacillus flagellatus (bacteria) / Strain: KT / Gene: 4000324, Mfla_1563 / Plasmid: BC-PSGX3(BC) / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)CODON+RIL / References: UniProt: Q1H106
#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 59 / 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: 2.18 Å3/Da / Density % sol: 43.56 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 5.5
Details: 0.2 M Li-sulfate, 0.1 M Bis-Tris, 25% PEG 3350, pH 5.5, VAPOR DIFFUSION, SITTING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X29A / Wavelength: 0.979 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Apr 15, 2011
RadiationProtocol: SINGLE WAVELENGTH / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 2.5→50 Å / Num. obs: 22865 / % possible obs: 100 % / Redundancy: 7 % / Rmerge(I) obs: 0.11 / Χ2: 1.18 / Net I/σ(I): 7.7
Reflection shell
Resolution (Å)Redundancy (%)Χ2Diffraction-IDRmerge(I) obsNum. unique all% possible all
0.9611
0.9651
2.59-2.647.10.96810.6991124100
2.64-2.697.10.94210.5991139100
2.69-2.757.20.95610.611146100
2.75-2.827.20.96810.5061155100
2.82-2.897.10.96910.4091149100
2.89-2.9670.99410.323113699.9
2.96-3.0571.02610.2711135100
3.05-3.156.90.97810.221133100
3.15-3.2671.00510.1871146100
3.26-3.396.90.97610.13113899.9
3.39-3.556.91.1310.1141137100
3.55-3.736.91.22910.095115999.9
3.73-3.976.91.38210.0781125100
3.97-4.276.81.50910.0681137100
4.27-4.771.66810.0631149100
4.7-5.3871.56910.0611142100
5.38-6.7871.410.0591152100
6.78-5072.03410.048115899.8

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Phasing

PhasingMethod: SAD

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Processing

Software
NameVersionClassificationNB
SCALEPACKdata scaling
SHELXphasing
REFMACrefinement
PDB_EXTRACT3.1data extraction
CBASSdata collection
HKL-3000data reduction
SHELXDphasing
RefinementMethod to determine structure: SAD / Resolution: 2.6→19.78 Å / Cor.coef. Fo:Fc: 0.949 / Cor.coef. Fo:Fc free: 0.905 / WRfactor Rfree: 0.245 / WRfactor Rwork: 0.1717 / Occupancy max: 1 / Occupancy min: 0.3 / FOM work R set: 0.8081 / SU B: 24.775 / SU ML: 0.254 / SU R Cruickshank DPI: 0.2609 / SU Rfree: 0.3719 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.372 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT U VALUES : RESIDUAL ONLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2783 528 4.8 %RANDOM
Rwork0.1951 ---
obs0.1989 11101 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 max: 85.57 Å2 / Biso mean: 49.1495 Å2 / Biso min: 35.27 Å2
Baniso -1Baniso -2Baniso -3
1--0.01 Å20 Å20 Å2
2---0.01 Å20 Å2
3---0.02 Å2
Refinement stepCycle: LAST / Resolution: 2.6→19.78 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2593 0 16 59 2668
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.022704
X-RAY DIFFRACTIONr_angle_refined_deg1.3021.9513685
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.6165337
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.79224.38121
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.38515437
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.3391514
X-RAY DIFFRACTIONr_chiral_restr0.0930.2407
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0212054
LS refinement shellResolution: 2.6→2.666 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.318 34 -
Rwork0.242 652 -
all-686 -
obs--100 %
Refinement TLS params.Method: refined / Origin x: 1.8947 Å / Origin y: 26.8726 Å / Origin z: 3.8492 Å
111213212223313233
T0.0406 Å20.0071 Å20.0281 Å2-0.0146 Å20.0007 Å2--0.0872 Å2
L1.9757 °2-0.2811 °20.9569 °2-1.229 °20.1659 °2--3.0658 °2
S0.0017 Å °-0.0549 Å °0.0692 Å °0.1412 Å °-0.0278 Å °0.0943 Å °0.0176 Å °-0.1217 Å °0.0261 Å °

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