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- PDB-3hdx: Crystal structure of SusD superfamily protein (NP_809182.1) from ... -

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Basic information

Entry
Database: PDB / ID: 3hdx
TitleCrystal structure of SusD superfamily protein (NP_809182.1) from BACTEROIDES THETAIOTAOMICRON VPI-5482 at 1.50 A resolution
ComponentsSusD superfamily protein
KeywordsPOLYSACCHARIDE BINDING PROTEIN / NP_809182.1 / SusD superfamily protein / Structural Genomics / Joint Center for Structural Genomics / JCSG / Protein Structure Initiative / PSI-2 / carbohydrate metabolism
Function / homology
Function and homology information


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 / Prokaryotic membrane lipoprotein lipid attachment site profile. / Mainly Alpha
Similarity search - Domain/homology
Biological speciesBacteroides thetaiotaomicron VPI-5482 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.5 Å
AuthorsJoint Center for Structural Genomics (JCSG)
CitationJournal: To be Published
Title: Crystal structure of SusD superfamily protein (NP_809182.1) from BACTEROIDES THETAIOTAOMICRON VPI-5482 at 1.50 A resolution
Authors: Joint Center for Structural Genomics (JCSG)
History
DepositionMay 7, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 19, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Oct 25, 2017Group: Author supporting evidence / Refinement description / Category: pdbx_struct_assembly_auth_evidence / software / Item: _software.classification / _software.name
Revision 1.3Jul 24, 2019Group: Data collection / Derived calculations / Refinement description
Category: pdbx_struct_special_symmetry / 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: SusD superfamily protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)55,85812
Polymers55,1761
Non-polymers68311
Water10,719595
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)56.221, 56.221, 301.899
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212
Components on special symmetry positions
IDModelComponents
11A-753-

HOH

21A-873-

HOH

31A-897-

HOH

DetailsSIZE EXCLUSION CHROMATOGRAPHY SUPPORTS THE ASSIGNMENT OF A MONOMER AS THE SIGNIFICANT OLIGOMERIZATION STATE.

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Components

#1: Protein SusD superfamily protein / SusD homolog


Mass: 55175.609 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacteroides thetaiotaomicron VPI-5482 (bacteria)
Gene: BT_0269, NP_809182.1 / Plasmid: SpeedET / Production host: Escherichia Coli (E. coli) / Strain (production host): HK100 / References: UniProt: Q8AB42
#2: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 11 / Source method: obtained synthetically / Formula: C2H6O2
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 595 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsSEQUENCE THIS CONSTRUCT (RESIDUES 36-512) WAS EXPRESSED WITH A PURIFICATION TAG MGSDKIHHHHHHENLYFQG. ...SEQUENCE THIS CONSTRUCT (RESIDUES 36-512) 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: 2.16 Å3/Da / Density % sol: 43.1 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 7.7
Details: 0.2000M MgAcetate, 20.0000% PEG-3350, No Buffer pH 7.7, NANODROP, VAPOR DIFFUSION, SITTING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL9-2 / Wavelength: 0.91162,0.97932,0.97918
DetectorType: MARMOSAIC 325 mm CCD / Detector: CCD / Date: Mar 19, 2009 / Details: Flat collimating mirror, toroid focusing mirror
RadiationMonochromator: Double crystal monochromator / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.911621
20.979321
30.979181
ReflectionResolution: 1.5→29.235 Å / Num. obs: 79386 / % possible obs: 100 % / Redundancy: 7.1 % / Biso Wilson estimate: 15.094 Å2 / Rmerge(I) obs: 0.106 / Rsym value: 0.106 / Net I/σ(I): 5.33
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allRsym value% possible all
1.5-1.5460.8140.93420057080.81499.9
1.54-1.587.20.76214056455990.762100
1.58-1.637.20.6151.23964954730.615100
1.63-1.687.20.5211.53865553350.521100
1.68-1.737.30.4351.83732451460.435100
1.73-1.797.30.3522.23626849850.352100
1.79-1.867.30.2862.73502948240.286100
1.86-1.947.30.2213.33418747100.221100
1.94-2.027.30.1714.33234444530.171100
2.02-2.127.30.1394.63098242700.139100
2.12-2.247.30.1116.52976641040.111100
2.24-2.377.20.0967.22809838920.096100
2.37-2.547.20.0927.32653736760.092100
2.54-2.747.20.0887.52467734340.088100
2.74-37.10.0768.52270131750.076100
3-3.357.10.0649.82072529150.064100
3.35-3.8770.06101811625750.06100
3.87-4.746.90.0511.61553222460.05100
4.74-6.716.70.04812.21195417820.048100
6.71-29.2460.04611.9647610840.04698.8

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Phasing

PhasingMethod: MAD

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Processing

Software
NameVersionClassificationNB
REFMAC5.5.0053refinement
PHENIXrefinement
SHELXphasing
MolProbity3beta29model building
SCALA3.2.5data scaling
PDB_EXTRACT3.006data extraction
MOSFLMdata reduction
autoSHARPphasing
RefinementMethod to determine structure: MAD / Resolution: 1.5→29.235 Å / Cor.coef. Fo:Fc: 0.976 / Cor.coef. Fo:Fc free: 0.971 / Occupancy max: 1 / Occupancy min: 0.15 / SU B: 2.299 / SU ML: 0.038 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.075 / ESU R Free: 0.06
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 REDUCED TO 0.75 FOR THE REDUCED SCATTERING POWER DUE TO PARTIAL S-MET INCORPORATION. 3. ETHYLNE GLYCOL (EDO) MOLECULES FROM THE CRYOPROTECTION SOLUTION ARE MODELED. 4. THERE IS SOME UNMODELED DENSITY NEAR RESIDUE THR 188.
RfactorNum. reflection% reflectionSelection details
Rfree0.16 3978 5 %RANDOM
Rwork0.134 ---
obs0.136 79233 99.97 %-
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: 55.73 Å2 / Biso mean: 18.753 Å2 / Biso min: 8.24 Å2
Baniso -1Baniso -2Baniso -3
1-0.31 Å20 Å20 Å2
2--0.31 Å20 Å2
3----0.62 Å2
Refinement stepCycle: LAST / Resolution: 1.5→29.235 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3941 0 48 603 4592
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.0224110
X-RAY DIFFRACTIONr_bond_other_d0.0030.022849
X-RAY DIFFRACTIONr_angle_refined_deg1.5371.955614
X-RAY DIFFRACTIONr_angle_other_deg1.32836941
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.0665539
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.27924.009212
X-RAY DIFFRACTIONr_dihedral_angle_3_deg10.43615721
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.0361529
X-RAY DIFFRACTIONr_chiral_restr0.1030.2608
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.024662
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02909
X-RAY DIFFRACTIONr_mcbond_it1.81122408
X-RAY DIFFRACTIONr_mcbond_other0.8722973
X-RAY DIFFRACTIONr_mcangle_it2.5333931
X-RAY DIFFRACTIONr_scbond_it2.18321702
X-RAY DIFFRACTIONr_scangle_it3.06531637
X-RAY DIFFRACTIONr_rigid_bond_restr1.33936959
X-RAY DIFFRACTIONr_sphericity_free7.3823603
X-RAY DIFFRACTIONr_sphericity_bonded2.98936838
LS refinement shellResolution: 1.5→1.539 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.237 287 -
Rwork0.203 5418 -
all-5705 -
obs--99.88 %

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