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- PDB-3jq0: Crystal structure of SusD superfamily protein (YP_001299712.1) fr... -

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Basic information

Entry
Database: PDB / ID: 3jq0
TitleCrystal structure of SusD superfamily protein (YP_001299712.1) from Bacteroides vulgatus ATCC 8482 at 1.13 A resolution
ComponentsSusD superfamily protein
KeywordsSUGAR BINDING PROTEIN / YP_001299712.1 / SusD superfamily protein / Structural Genomics / Joint Center for Structural Genomics / JCSG / Protein Structure Initiative / PSI-2 / RagB / SusD and hypothetical proteins / unknown function
Function / homology
Function and homology information


cell outer membrane
Similarity search - Function
Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat - #390 / SusD-like, N-terminal / Starch-binding associating with outer membrane / RagB/SusD domain / SusD family / Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat / Alpha Horseshoe / Tetratricopeptide-like helical domain superfamily / Mainly Alpha
Similarity search - Domain/homology
Putative outer membrane protein, probably involved in nutrient binding
Similarity search - Component
Biological speciesBacteroides vulgatus ATCC 8482 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.13 Å
AuthorsJoint Center for Structural Genomics (JCSG)
CitationJournal: To be published
Title: Crystal structure of SusD superfamily protein (YP_001299712.1) from Bacteroides vulgatus ATCC 8482 at 1.13 A resolution
Authors: Joint Center for Structural Genomics (JCSG)
History
DepositionSep 4, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 22, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Non-polymer description / Version format compliance
Revision 1.2Nov 1, 2017Group: Refinement description / Category: software / Item: _software.classification / _software.name
Revision 1.3Jul 24, 2019Group: Data collection / Derived calculations / Refinement description
Category: software / struct_conn
Item: _software.classification / _software.contact_author ..._software.classification / _software.contact_author / _software.contact_author_email / _software.language / _software.location / _software.name / _software.type / _software.version / _struct_conn.pdbx_leaving_atom_flag
Revision 1.4Feb 1, 2023Group: Database references / Derived calculations / Category: database_2 / 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_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.5Nov 6, 2024Group: Data collection / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_entry_details / pdbx_modification_feature
Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: SusD superfamily protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)58,10810
Polymers57,2941
Non-polymers8149
Water15,006833
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)75.804, 75.804, 323.966
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number179
Space group name H-MP6522
Components on special symmetry positions
IDModelComponents
11A-784-

HOH

DetailsCRYSTAL PACKING ANALYSIS SUGGESTS THE ASSIGNMENT OF A MONOMER AS THE SIGNIFICANT OLIGOMERIZATION STATE.

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Components

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Protein , 1 types, 1 molecules A

#1: Protein SusD superfamily protein / Putative outer membrane protein / probably involved in nutrient binding


Mass: 57293.695 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacteroides vulgatus ATCC 8482 (bacteria)
Strain: ATCC 8482 / DSM 1447 / NCTC 11154 / Gene: BVU_2431, YP_001299712.1 / Plasmid: SpeedET / Production host: Escherichia Coli (E. coli) / Strain (production host): HK100 / References: UniProt: A6L326

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Non-polymers , 5 types, 842 molecules

#2: Chemical ChemComp-TRS / 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL / TRIS BUFFER


Mass: 122.143 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H12NO3 / Comment: pH buffer*YM
#3: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C3H8O3
#4: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: SO4
#5: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 833 / Source method: isolated from a natural source / Formula: H2O

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Details

Has protein modificationY
Sequence detailsSEQUENCE THIS CONSTRUCT (RESIDUES 33-524) WAS EXPRESSED WITH A PURIFICATION TAG MGSDKIHHHHHHENLYFQG. ...SEQUENCE THIS CONSTRUCT (RESIDUES 33-524) WAS EXPRESSED WITH A PURIFICATION TAG MGSDKIHHHHHHENLYFQG. THE TAG WAS REMOVED WITH TEV PROTEASE LEAVING ONLY A GLYCINE (0) FOLLOWED BY THE TARGET SEQUENCE.

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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: 47.55 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 8
Details: 1.60M (NH4)2SO4, 0.1M TRIS pH 8.0, NANODROP, VAPOR DIFFUSION, SITTING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL12-2 / Wavelength: 0.97936
DetectorType: MARMOSAIC 325 mm CCD / Detector: CCD / Date: May 8, 2009
Details: Flat mirror, vertical and horizontal focussing mirrors
RadiationMonochromator: Double crystal monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97936 Å / Relative weight: 1
ReflectionResolution: 1.13→29.45 Å / Num. obs: 187091 / % possible obs: 91.5 % / Redundancy: 5 % / Biso Wilson estimate: 7.466 Å2 / Rmerge(I) obs: 0.111 / Rsym value: 0.111 / Net I/σ(I): 9.3
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allRsym value% possible all
1.13-1.163.60.581.33048885840.5858.1
1.16-1.1940.511.540314101970.5170.7
1.19-1.234.40.4461.753826122470.44686.7
1.23-1.265.30.3971.969281129940.39794.4
1.26-1.35.30.3492.267216126050.34995
1.3-1.355.30.3042.565431122710.30495.4
1.35-1.45.30.2652.963631119460.26595.8
1.4-1.465.30.2343.261592115770.23496.2
1.46-1.525.30.23.659002111120.296.6
1.52-1.65.30.176456744107160.17697.1
1.6-1.685.30.1524.554582103150.15297.4
1.68-1.795.30.1414.65131497340.14197.8
1.79-1.915.20.12654855592670.12698.1
1.91-2.065.20.1125.54506786640.11298.5
2.06-2.265.20.0976.34173480790.09798.9
2.26-2.535.10.096.83789474120.0999.3
2.53-2.925.10.0866.83338865750.08699.4
2.92-3.5750.0787.32820756360.07899.7
3.57-5.054.90.0757.52196445160.07599.7
5.05-29.454.40.0787.41175026440.07898.8

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Phasing

PhasingMethod: SAD

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Processing

Software
NameVersionClassificationNB
REFMAC5.5.0053refinement
PHENIXrefinement
SOLVEphasing
MolProbity3beta29model building
SCALA3.2.5data scaling
PDB_EXTRACT3.006data extraction
MOSFLMdata reduction
RefinementMethod to determine structure: SAD / Resolution: 1.13→29.45 Å / Cor.coef. Fo:Fc: 0.982 / Cor.coef. Fo:Fc free: 0.979 / Occupancy max: 1 / Occupancy min: 0.28 / SU B: 0.753 / SU ML: 0.016 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.027 / ESU R Free: 0.027
Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES
Details: 1. HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. 2. A MET-INHIBITION PROTOCOL WAS USED FOR SELENOMETHIONINE INCORPORATION DURING PROTEIN EXPRESSION. THE OCCUPANCY OF THE SE ATOMS IN THE ...Details: 1. HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. 2. A MET-INHIBITION PROTOCOL WAS USED FOR SELENOMETHIONINE INCORPORATION DURING PROTEIN EXPRESSION. THE OCCUPANCY OF THE SE ATOMS IN THE MSE RESIDUES WAS ADJUSTED TO QUENCH THE DIFFERENCE FOURIER DENSITY. 3. GLYCEROL (GOL), SULFATE (SO4), CHLORIDE (CL), AND 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL (TRIS BASE, TRS) MOLECULES FROM THE CRYSTALLIZATION/CRYOPROTECTION SOLUTION ARE MODELED. 4. RAMACHANDRAN OUTLIER RESIDUES 66, 69 AND 440 ARE SUPPORTED BY ELECTRON DENSITY.
RfactorNum. reflection% reflectionSelection details
Rfree0.137 9433 5 %RANDOM
Rwork0.117 ---
obs0.118 187080 90.93 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso max: 54.74 Å2 / Biso mean: 13.075 Å2 / Biso min: 5.43 Å2
Baniso -1Baniso -2Baniso -3
1-0.16 Å20.08 Å20 Å2
2--0.16 Å20 Å2
3----0.24 Å2
Refinement stepCycle: LAST / Resolution: 1.13→29.45 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3866 0 48 833 4747
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.0224249
X-RAY DIFFRACTIONr_bond_other_d0.0010.022936
X-RAY DIFFRACTIONr_angle_refined_deg1.6731.9545782
X-RAY DIFFRACTIONr_angle_other_deg1.01337142
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.1135543
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.01524.42224
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.57815736
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.4351524
X-RAY DIFFRACTIONr_chiral_restr0.1120.2582
X-RAY DIFFRACTIONr_gen_planes_refined0.010.024812
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02922
X-RAY DIFFRACTIONr_mcbond_it1.5531.52483
X-RAY DIFFRACTIONr_mcbond_other0.7321.51016
X-RAY DIFFRACTIONr_mcangle_it2.20624010
X-RAY DIFFRACTIONr_scbond_it3.21331766
X-RAY DIFFRACTIONr_scangle_it4.4214.51740
X-RAY DIFFRACTIONr_rigid_bond_restr1.52937185
X-RAY DIFFRACTIONr_sphericity_free9.2393861
X-RAY DIFFRACTIONr_sphericity_bonded3.89737061
LS refinement shellResolution: 1.13→1.159 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.229 454 -
Rwork0.228 8128 -
all-8582 -
obs--57.32 %

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