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- PDB-3otn: Crystal structure of a SusD superfamily protein (BDI_3964) from P... -

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Basic information

Entry
Database: PDB / ID: 3otn
TitleCrystal structure of a SusD superfamily protein (BDI_3964) from Parabacteroides distasonis ATCC 8503 at 1.95 A resolution
ComponentsSusD superfamily protein
KeywordsSUGAR BINDING PROTEIN / PUTATIVE OUTER MEMBRANE PROTEIN / SUSD / CARBOHYDRATE BINDING / STRUCTURAL GENOMICS / JOINT CENTER FOR STRUCTURAL GENOMICS / JCSG / PROTEIN STRUCTURE INITIATIVE / PSI-BIOLOGY
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 / Mainly Alpha
Similarity search - Domain/homology
ACETATE ION / DI(HYDROXYETHYL)ETHER / Putative outer membrane protein, probably involved in nutrient binding
Similarity search - Component
Biological speciesParabacteroides distasonis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.95 Å
AuthorsJoint Center for Structural Genomics (JCSG)
CitationJournal: To be published
Title: Crystal structure of a SusD superfamily protein (BDI_3964) from Parabacteroides distasonis ATCC 8503 at 1.95 A resolution
Authors: Joint Center for Structural Genomics (JCSG)
History
DepositionSep 13, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 3, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Jul 20, 2011Group: Structure summary
Revision 1.3Oct 25, 2017Group: Author supporting evidence / Category: pdbx_struct_assembly_auth_evidence
Revision 1.4Feb 1, 2023Group: Database references / Derived calculations
Category: database_2 / struct_conn ...database_2 / 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: SusD superfamily protein
B: SusD superfamily protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)113,75839
Polymers111,4772
Non-polymers2,28137
Water15,259847
1
A: SusD superfamily protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)56,91420
Polymers55,7391
Non-polymers1,17619
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: SusD superfamily protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)56,84419
Polymers55,7391
Non-polymers1,10518
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9900 Å2
ΔGint42 kcal/mol
Surface area33640 Å2
MethodPISA
Unit cell
Length a, b, c (Å)74.740, 92.479, 152.104
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
DetailsSIZE-EXCLUSION CHROMATOGRAPHY COUPLED WITH STATIC LIGHT SCATTERING SUPPORTS A MONOMER AS THE SIGNIFICANT OLIGOMERIC STATE IN SOLUTION, WHICH IS CONSISTENT WITH OTHER HOMOLOGS IN THE SAME PROTEIN FAMILY. HOWEVER, CRYSTAL PACKING ANALYSIS SUGGESTS THAT A DIMER MAY ALSO BE A STABLE OLIGOMERIC FORM.

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Components

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Protein , 1 types, 2 molecules AB

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


Mass: 55738.688 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Parabacteroides distasonis (bacteria) / Strain: ATCC 8503 / Gene: BDI_3964 / Plasmid: SpeedET / Production host: Escherichia Coli (E. coli) / Strain (production host): HK100 / References: UniProt: A6LIX4

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Non-polymers , 5 types, 884 molecules

#2: Chemical ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#3: Chemical
ChemComp-ACT / ACETATE ION / Acetate


Mass: 59.044 Da / Num. of mol.: 11 / Source method: obtained synthetically / Formula: C2H3O2
#4: Chemical...
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 24 / Source method: obtained synthetically / Formula: C2H6O2
#5: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER / Diethylene glycol


Mass: 106.120 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O3
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 847 / Source method: isolated from a natural source / Formula: H2O

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Details

Sequence detailsTHIS CONSTRUCT (RESIDUES 26-506) WAS EXPRESSED WITH A PURIFICATION TAG MGSDKIHHHHHHENLYFQG. THE TAG ...THIS CONSTRUCT (RESIDUES 26-506) 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: 2.36 Å3/Da / Density % sol: 47.83 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8
Details: 0.17M sodium acetate, 25.3% polyethylene glycol 4000, 15.0% Glycerol, 0.1M TRIS pH 8.0, NANODROP, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL9-2 / Wavelength: 0.91162,0.97918,0.97896
DetectorType: MARMOSAIC 325 mm CCD / Detector: CCD / Date: Jul 23, 2010
RadiationProtocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.911621
20.979181
30.978961
ReflectionResolution: 1.95→29.37 Å / Num. all: 76628 / Num. obs: 76628 / % possible obs: 99.2 % / Redundancy: 3.8 % / Biso Wilson estimate: 20.344 Å2 / Rsym value: 0.123 / Net I/σ(I): 7.7
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allRsym value% possible all
1.95-23.70.69922122456600.699100
2-2.063.70.5672.42070355310.567100
2.06-2.123.80.4872.82024053700.487100
2.12-2.183.80.3913.51954251900.39199.9
2.18-2.253.80.3224.11918150860.32299.9
2.25-2.333.80.2814.61845248900.28199.9
2.33-2.423.80.2375.31783947290.23799.7
2.42-2.523.80.225.61706845180.2299.7
2.52-2.633.80.1956.31650843660.19599.6
2.63-2.763.80.1717.51587341750.17199.4
2.76-2.913.80.1468.41493839450.14699.3
2.91-3.083.80.119101428837550.11999
3.08-3.33.80.09412.11335535170.09499
3.3-3.563.80.07614.71257632830.07698.5
3.56-3.93.80.063171141729810.06398.2
3.9-4.363.80.05118.81045427420.05198
4.36-5.033.80.0518.4920424010.0597.4
5.03-6.173.80.05615.8775920290.05696.5
6.17-8.723.80.05216.2599515780.05295.9
8.72-29.373.60.04818.232108820.04891.9

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Phasing

PhasingMethod: MAD

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Processing

Software
NameVersionClassificationNB
SOLVEphasing
REFMAC5.5.0110refinement
SCALA3.3.15data scaling
PDB_EXTRACT3.1data extraction
MOSFLMdata reduction
RefinementMethod to determine structure: MAD / Resolution: 1.95→29.37 Å / Cor.coef. Fo:Fc: 0.97 / Cor.coef. Fo:Fc free: 0.947 / Occupancy max: 1 / Occupancy min: 0.37 / SU B: 5.999 / SU ML: 0.088 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.132
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.ATOM RECORDS CONTAIN SUM OF TLS AND RESIDUAL B FACTORS. ANISOU RECORD CONTAINS SUM OF TLS AND RESIDUAL U FACTORS. 4.WATERS WERE EXCLUDED FROM AUTOMATIC TLS ASSIGNMENT. 5.CHLORIDE (CL) FROM THE PROTEIN BUFFER; ACETATE (ACT) AND PEG4000 FRAGMENT (PEG) FROM THE CRYSTALLIZATION REAGENT; AND 1,2-ETHANEDIOL (EDO) FROM THE CRYOPROTECTANT SOLUTION HAVE BEEN MODELED IN THE SOLVENT
RfactorNum. reflection% reflectionSelection details
Rfree0.1906 3860 5 %RANDOM
Rwork0.1436 ---
obs0.146 76591 98.82 %-
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: 78.7 Å2 / Biso mean: 27.8721 Å2 / Biso min: 10.9 Å2
Baniso -1Baniso -2Baniso -3
1-0.71 Å20 Å20 Å2
2---0.68 Å20 Å2
3----0.04 Å2
Refinement stepCycle: LAST / Resolution: 1.95→29.37 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7591 0 148 847 8586
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.0228027
X-RAY DIFFRACTIONr_bond_other_d0.0020.025436
X-RAY DIFFRACTIONr_angle_refined_deg1.4511.9610853
X-RAY DIFFRACTIONr_angle_other_deg1.088313205
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.325982
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.7324.722413
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.968151329
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.0061539
X-RAY DIFFRACTIONr_chiral_restr0.0930.21146
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.029022
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021695
X-RAY DIFFRACTIONr_mcbond_it1.834782
X-RAY DIFFRACTIONr_mcbond_other0.52231927
X-RAY DIFFRACTIONr_mcangle_it2.80857682
X-RAY DIFFRACTIONr_scbond_it4.55383245
X-RAY DIFFRACTIONr_scangle_it6.1113150
LS refinement shellResolution: 1.95→2 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.259 276 -
Rwork0.204 5348 -
all-5624 -
obs--99.96 %
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)
10.58520.05380.10730.6327-0.03880.51870.007-0.00860.00130.0285-0.01610.0450.0723-0.07310.00910.0349-0.01810.00720.0151-0.00450.004256.699210.520648.2528
20.70830.17140.1610.70650.16240.6382-0.02230.11330.051-0.05380.02320.0002-0.04280.0393-0.00090.0071-0.0072-0.0050.03410.00350.045683.22897.156419.1182
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A36 - 506
2X-RAY DIFFRACTION2B36 - 506

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