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- PDB-3snx: Crystal structure of a PUTATIVE SUSD-LIKE CARBOHYDRATE BINDING PR... -

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Basic information

Entry
Database: PDB / ID: 3snx
TitleCrystal structure of a PUTATIVE SUSD-LIKE CARBOHYDRATE BINDING PROTEIN (BT_1439) from BACTEROIDES THETAIOTAOMICRON VPI-5482 at 1.88 A resolution
ComponentsPUTATIVE SUSD-LIKE CARBOHYDRATE BINDING PROTEIN
KeywordsSUGAR BINDING PROTEIN / alpha-alpha superhelix / Structural Genomics / Joint Center for Structural Genomics / JCSG / Protein Structure Initiative / PSI-BIOLOGY
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
DI(HYDROXYETHYL)ETHER / SusD homolog
Similarity search - Component
Biological speciesBacteroides thetaiotaomicron (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.88 Å
AuthorsJoint Center for Structural Genomics (JCSG)
CitationJournal: To be published
Title: Crystal structure of a PUTATIVE SUSD-LIKE CARBOHYDRATE BINDING PROTEIN (BT_1439) from BACTEROIDES THETAIOTAOMICRON VPI-5482 at 1.88 A resolution
Authors: Joint Center for Structural Genomics (JCSG)
History
DepositionJun 29, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 20, 2011Provider: repository / Type: Initial release
Revision 1.1Oct 25, 2017Group: Author supporting evidence / Refinement description / Category: pdbx_struct_assembly_auth_evidence / software / Item: _software.classification / _software.name
Revision 1.2Jan 24, 2018Group: Database references / Category: citation_author / Item: _citation_author.name
Revision 1.3Feb 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: PUTATIVE SUSD-LIKE CARBOHYDRATE BINDING PROTEIN
B: PUTATIVE SUSD-LIKE CARBOHYDRATE BINDING PROTEIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)105,7528
Polymers105,2032
Non-polymers5496
Water6,936385
1
A: PUTATIVE SUSD-LIKE CARBOHYDRATE BINDING PROTEIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)52,8764
Polymers52,6021
Non-polymers2743
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: PUTATIVE SUSD-LIKE CARBOHYDRATE BINDING PROTEIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)52,8764
Polymers52,6021
Non-polymers2743
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)64.112, 114.452, 67.663
Angle α, β, γ (deg.)90.000, 90.020, 90.000
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B

NCS domain segments:
Dom-IDComponent-IDEns-IDRefine codeAuth asym-IDAuth seq-ID
1112A39 - 493
2112B39 - 493
DetailsANALYTICAL SIZE EXCLUSION CHROMATOGRAPHY SUPPORTS THE ASSIGNMENT OF A MONOMER AS A SIGNIFICANT OLIGOMERIZATION STATE IN SOLUTION.

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Components

#1: Protein PUTATIVE SUSD-LIKE CARBOHYDRATE BINDING PROTEIN / SusD homolog


Mass: 52601.695 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacteroides thetaiotaomicron (bacteria)
Strain: VPI-5482 / Gene: BT_1439 / Plasmid: SpeedET / Production host: Escherichia Coli (E. coli) / Strain (production host): HK100 / References: UniProt: Q8A7T5
#2: Chemical
ChemComp-PEG / DI(HYDROXYETHYL)ETHER / Diethylene glycol


Mass: 106.120 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C4H10O3
#3: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6O2
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 385 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsTHE CONSTRUCT WAS EXPRESSED WITH AN N-TERMINAL PURIFICATION TAG MGSDKIHHHHHHENLYFQG. THE TAG WAS ...THE CONSTRUCT WAS EXPRESSED WITH AN N-TERMINAL PURIFICATION TAG MGSDKIHHHHHHENLYFQG. THE TAG WAS REMOVED WITH TEV PROTEASE LEAVING ONLY A GLYCINE (0) FOLLOWED BY RESIDUES 35-493 OF 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: 47.87 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 9.5
Details: 40.0% polyethylene glycol 600, 0.1M CHES pH 9.5, Additive: 0.005 M maltotriose, 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: 0.91837,0.97932,0.97913
DetectorType: MARMOSAIC 325 mm CCD / Detector: CCD / Date: May 14, 2010 / Details: double crystal monochromator
RadiationMonochromator: double crystal / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.918371
20.979321
30.979131
Reflection twin
Crystal-IDIDOperatorDomain-IDFraction
11H, K, L10.599
11-h,-k,l20.401
ReflectionResolution: 1.88→46.545 Å / Num. obs: 77723 / % possible obs: 98.2 % / Observed criterion σ(I): -3 / Biso Wilson estimate: 21.034 Å2 / Rmerge(I) obs: 0.103 / Net I/σ(I): 9.61
Reflection shell

Diffraction-ID: 1

Resolution (Å)Highest resolution (Å)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. unique obs% possible all
1.88-1.950.7461.928354766593.5
1.95-2.030.522.830169784698.1
2.03-2.120.3643.828965754898.3
2.12-2.230.2834.829132758398.2
2.23-2.370.2295.829866778498.6
2.37-2.550.1797.329375766598.6
2.55-2.810.1319.530416795999
2.81-3.210.08413.829569776499.1
3.21-4.040.05420.629606785299.2
4.040.04424.730062802699.1

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Phasing

PhasingMethod: MAD

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Processing

Software
NameVersionClassificationNB
MolProbity3beta29model building
PDB_EXTRACT3.1data extraction
SHELXphasing
SHARPphasing
XSCALEDecember 6, 2010data scaling
REFMAC5.6.0116refinement
XDSdata reduction
SHELXDphasing
autoSHARPphasing
RefinementMethod to determine structure: MAD / Resolution: 1.88→46.545 Å / Cor.coef. Fo:Fc: 0.956 / Cor.coef. Fo:Fc free: 0.934 / Occupancy max: 1 / Occupancy min: 0.37 / SU B: 6.804 / SU ML: 0.096 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.027 / Stereochemistry target values: MAXIMUM LIKELIHOOD
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 TO ACCOUNT FOR THE REDUCED SCATTERING POWER DUE TO PARTIAL S-MET INCORPORATION. 3. ATOM RECORD CONTAINS 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. POLYETHYENE GLYCOL 600 FRAGMENTS (PEG) FROM THE CRYSTALLIZATION CONDITION AND 1,2-ETHANEDIOL (EDO) FROM THE CRYOPROTECTANT SOLUTION HAVE BEEN MODELED INTO THE STRUCTURE. 6. THE DIFFRACTION DATA SHOW PSEUDO-MEROHEDERAL TWINNING WITH TWIN LAW "H,-K, -L". THE REFINED TWIN FRACTION WAS 0.40. 7. THE R-FREE TEST SET REFLECTIONS WERE CHOSEN IN THIN SHELLS.
RfactorNum. reflection% reflectionSelection details
Rfree0.2073 4017 5.2 %THIN SHELL
Rwork0.1732 ---
obs0.175 77691 97.9 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 60.98 Å2 / Biso mean: 25.6074 Å2 / Biso min: 10.54 Å2
Baniso -1Baniso -2Baniso -3
1--25.88 Å20 Å2-0.74 Å2
2--40.18 Å20 Å2
3----14.3 Å2
Refinement stepCycle: LAST / Resolution: 1.88→46.545 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7156 0 36 385 7577
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0227436
X-RAY DIFFRACTIONr_bond_other_d0.0010.024935
X-RAY DIFFRACTIONr_angle_refined_deg1.141.94310107
X-RAY DIFFRACTIONr_angle_other_deg0.849311964
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.7315936
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.93324.208366
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.655151164
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.3881542
X-RAY DIFFRACTIONr_chiral_restr0.0680.21070
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.028494
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021610
Refine LS restraints NCS

Dom-ID: 1 / Ens-ID: 1 / Refine-ID: X-RAY DIFFRACTION

Auth asym-IDNumberTypeRms dev position (Å)Weight position
A2667TIGHT POSITIONAL0.140.05
B3252MEDIUM POSITIONAL0.240.5
A2667TIGHT THERMAL1.440.5
B3252MEDIUM THERMAL1.362
LS refinement shellResolution: 1.879→1.928 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.596 1 -
Rwork0.293 5152 -
all-5153 -
obs--87.94 %
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)
10.5956-0.11350.02390.29470.10990.60650.0003-0.06460.01030.03590.0039-0.01560.0070.0012-0.00420.1048-0.0093-0.02290.05890.00270.114534.801410.52918.7571
20.513-0.15510.04820.2786-0.10460.50060.0058-0.0304-0.00780.0107-0.0042-0.0007-0.00210.0078-0.00160.102-0.0067-0.03160.0679-0.00220.119565.13477.626552.8026
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A39 - 493
2X-RAY DIFFRACTION2B39 - 493

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