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- PDB-3sgh: Crystal structure of a SusD-like protein (BT_3752) from Bacteroid... -

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Basic information

Entry
Database: PDB / ID: 3sgh
TitleCrystal structure of a SusD-like protein (BT_3752) from Bacteroides thetaiotaomicron VPI-5482 at 1.70 A resolution
ComponentsSusD homolog
KeywordsSUGAR BINDING PROTEIN / alpha-alpha superhelix / Structural Genomics / Joint Center for Structural Genomics / JCSG / Protein Structure Initiative / PSI-BIOLOGY
Function / homologySusD-like / Susd and RagB outer membrane lipoprotein / Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat - #390 / Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat / Prokaryotic membrane lipoprotein lipid attachment site profile. / Alpha Horseshoe / Tetratricopeptide-like helical domain superfamily / Mainly Alpha / SusD homolog
Function and homology information
Biological speciesBacteroides thetaiotaomicron (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.7 Å
AuthorsJoint Center for Structural Genomics (JCSG)
CitationJournal: To be published
Title: Crystal structure of a Hypothetical SusD-like protein (BT_3752) from Bacteroides thetaiotaomicron VPI-5482 at 1.70 A resolution
Authors: Joint Center for Structural Genomics (JCSG)
History
DepositionJun 14, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 6, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 23, 2011Group: Structure summary
Revision 1.3Dec 24, 2014Group: Structure summary
Revision 1.4Nov 8, 2017Group: Refinement description / Category: software / Item: _software.classification / _software.name
Revision 1.5Feb 1, 2023Group: Database references / Derived calculations
Category: database_2 / pdbx_struct_special_symmetry ...database_2 / pdbx_struct_special_symmetry / 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
Revision 1.6Oct 30, 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 homolog
B: SusD homolog
hetero molecules


Theoretical massNumber of molelcules
Total (without water)112,59422
Polymers111,8852
Non-polymers70920
Water24,4101355
1
A: SusD homolog
hetero molecules


Theoretical massNumber of molelcules
Total (without water)56,26210
Polymers55,9431
Non-polymers3199
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: SusD homolog
hetero molecules


Theoretical massNumber of molelcules
Total (without water)56,33312
Polymers55,9431
Non-polymers39011
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)94.586, 173.545, 59.215
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP21212
Components on special symmetry positions
IDModelComponents
11A-928-

HOH

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Components

#1: Protein SusD homolog


Mass: 55942.598 Da / Num. of mol.: 2 / Fragment: sequence database residues 24-521
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacteroides thetaiotaomicron (bacteria)
Gene: BT_3752 / Plasmid: SpeedET / Production host: Escherichia Coli (E. coli) / Strain (production host): HK100 / References: UniProt: Q8A1B4
#2: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 20 / Source method: obtained synthetically / Formula: Cl
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1355 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY
Sequence detailsTHIS CONSTRUCT (RESIDUES 24-521) WAS EXPRESSED WITH A PURIFICATION TAG MGSDKIHHHHHHENLYFQG. THE TAG ...THIS CONSTRUCT (RESIDUES 24-521) 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: 2.17 Å3/Da / Density % sol: 43.37 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 20.00% polyethylene glycol 6000, 0.20M magnesium chloride, 0.1M sodium cacodylate pH 6.5, NANODROP, VAPOR DIFFUSION, SITTING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL11-1 / Wavelength: 0.91837,0.97944,0.97899
DetectorType: MARMOSAIC 325 mm CCD / Detector: CCD / Date: May 26, 2011
Details: Flat mirror (vertical focusing); single crystal Si(111) bent monochromator (ho rizontal focusing)
RadiationMonochromator: single crystal Si(111) bent / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.918371
20.979441
30.978991
ReflectionResolution: 1.7→29.633 Å / Num. obs: 107089 / % possible obs: 97.1 % / Observed criterion σ(I): -3 / Biso Wilson estimate: 16.942 Å2 / Rmerge(I) obs: 0.089 / Net I/σ(I): 8.12
Reflection shell
Resolution (Å)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. unique obsDiffraction-ID% possible all
1.7-1.760.6441.54147019409194.7
1.76-1.830.5071.94323720107197.3
1.83-1.910.3852.54204419535197.2
1.91-2.020.2763.54731721924197.1
2.02-2.140.2014.74135619148197.4
2.14-2.310.1486.24488720735197.2
2.31-2.540.1177.74346820026197.7
2.54-2.90.0810.84324119897197.6
2.9-3.660.04417.44480620493197.3
3.66-29.6330.02924.64449620270197.2

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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
REFMAC5.5.0110refinement
XDSdata reduction
SHELXDphasing
RefinementMethod to determine structure: MAD / Resolution: 1.7→29.633 Å / Cor.coef. Fo:Fc: 0.974 / Cor.coef. Fo:Fc free: 0.959 / Occupancy max: 1 / Occupancy min: 0.23 / SU B: 3.457 / SU ML: 0.059 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.09 / ESU R Free: 0.09
Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES
Details: 1. HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. 2. SOLVENT MOLECULES WERE NOT INCLUDED IN THE TLS GROUP DEFINITIONS. 3. ATOM RECORD CONTAINS SUM OF TLS AND RESIDUAL B FACTORS. 4. ...Details: 1. HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. 2. SOLVENT MOLECULES WERE NOT INCLUDED IN THE TLS GROUP DEFINITIONS. 3. ATOM RECORD CONTAINS SUM OF TLS AND RESIDUAL B FACTORS. 4. ANISOU RECORD CONTAINS SUM OF TLS AND RESIDUAL U FACTORS. 5. 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. 6. CHLORIDE (CL) IONS MODELED ARE FROM CRYSTALLIZATION CONDITION.
RfactorNum. reflection% reflectionSelection details
Rfree0.1742 5339 5 %RANDOM
Rwork0.1387 ---
obs0.1404 107051 99.18 %-
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: 57.98 Å2 / Biso mean: 20.9933 Å2 / Biso min: 10.49 Å2
Baniso -1Baniso -2Baniso -3
1-0.82 Å20 Å20 Å2
2---0.64 Å20 Å2
3----0.19 Å2
Refinement stepCycle: LAST / Resolution: 1.7→29.633 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7530 0 20 1355 8905
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.0227940
X-RAY DIFFRACTIONr_bond_other_d0.0010.025268
X-RAY DIFFRACTIONr_angle_refined_deg1.4531.93310845
X-RAY DIFFRACTIONr_angle_other_deg0.958312841
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.44651039
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.90824.716388
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.094151257
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.3361539
X-RAY DIFFRACTIONr_chiral_restr0.0930.21139
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.029178
X-RAY DIFFRACTIONr_gen_planes_other0.0020.021681
X-RAY DIFFRACTIONr_mcbond_it0.7751.54913
X-RAY DIFFRACTIONr_mcbond_other0.2681.52023
X-RAY DIFFRACTIONr_mcangle_it1.30227894
X-RAY DIFFRACTIONr_scbond_it2.18233027
X-RAY DIFFRACTIONr_scangle_it3.3184.52916
LS refinement shellResolution: 1.7→1.744 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.256 376 -
Rwork0.222 7388 -
all-7764 -
obs--98.08 %
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)
10.2640.1168-0.17970.4613-0.13750.28680.00510.00410.00480.0086-0.0145-0.0107-0.01920.0210.00940.0242-0.0096-0.00520.02350.00140.024571.1578.60342.755
20.18080.07540.05930.6186-0.13460.26250.00270.00950.0043-0.0501-0.01360.02130.02670.02560.01090.01840.00870.00020.03370.00660.016774.10133.56940.55
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A38 - 521
2X-RAY DIFFRACTION2B38 - 521

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