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- PDB-3lew: Crystal structure of SusD-like carbohydrate binding protein (YP_0... -

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Basic information

Entry
Database: PDB / ID: 3lew
TitleCrystal structure of SusD-like carbohydrate binding protein (YP_001298396.1) from Bacteroides vulgatus ATCC 8482 at 1.70 A resolution
ComponentsSusD-like carbohydrate binding protein
KeywordsSUGAR BINDING PROTEIN / SusD-like carbohydrate binding protein / Structural Genomics / Joint Center for Structural Genomics / JCSG / Protein Structure Initiative / PSI-2
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 / Prokaryotic membrane lipoprotein lipid attachment site profile. / 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 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.7 Å
AuthorsJoint Center for Structural Genomics (JCSG)
CitationJournal: To be published
Title: Crystal structure of SusD-like carbohydrate binding protein (YP_001298396.1) from Bacteroides vulgatus ATCC 8482 at 1.70 A resolution
Authors: Joint Center for Structural Genomics (JCSG)
History
DepositionJan 15, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 9, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2Nov 1, 2017Group: Refinement description / Category: software / Item: _software.classification / _software.name
Revision 1.3Jul 17, 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 27, 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-like carbohydrate binding protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)59,96614
Polymers56,6921
Non-polymers3,27413
Water9,494527
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)191.772, 46.707, 73.524
Angle α, β, γ (deg.)90.000, 106.550, 90.000
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-10-

1PE

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

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Components

#1: Protein SusD-like carbohydrate binding protein / Putative outer membrane protein / probably involved in nutrient binding


Mass: 56691.859 Da / Num. of mol.: 1 / Fragment: sequence database residues 23-516
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacteroides vulgatus (bacteria) / Strain: ATCC 8482 / DSM 1447 / NCTC 11154 / Gene: BVU_1083 / Plasmid: SpeedET / Production host: Escherichia coli (E. coli) / Strain (production host): HK100 / References: UniProt: A6KZB0
#2: Chemical
ChemComp-1PE / PENTAETHYLENE GLYCOL / PEG400


Mass: 238.278 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: C10H22O6 / Comment: precipitant*YM
#3: Chemical ChemComp-2PE / NONAETHYLENE GLYCOL


Mass: 414.488 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C18H38O10 / Comment: precipitant*YM
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 527 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY
Sequence detailsTHIS CONSTRUCT (RESIDUES 23-516) WAS EXPRESSED WITH A PURIFICATION TAG MGSDKIHHHHHHENLYFQG. THE TAG ...THIS CONSTRUCT (RESIDUES 23-516) 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: 2.78 Å3/Da / Density % sol: 55.82 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 5.0000% polyethylene glycol 3000, 32.0000% polyethylene glycol 400, 0.1M MES 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: BL9-2 / Wavelength: 0.91837,0.97954
DetectorType: MARMOSAIC 325 mm CCD / Detector: CCD / Date: Nov 6, 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
10.918371
20.979541
ReflectionResolution: 1.7→39.368 Å / Num. obs: 68815 / % possible obs: 99.5 % / Observed criterion σ(I): -3 / Biso Wilson estimate: 27.053 Å2 / Rmerge(I) obs: 0.07 / Net I/σ(I): 11.49
Reflection shell

Diffraction-ID: 1

Resolution (Å)Highest resolution (Å)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. unique obs% possible all
1.7-1.760.6272.122357666198.6
1.76-1.830.4952.824990682499.8
1.83-1.910.3553.824472662699.9
1.91-2.020.2355.627712748899.8
2.02-2.140.1627.924002649299.6
2.14-2.310.11810.426143705899.5
2.31-2.540.08613.425273681199.8
2.54-2.90.0641725219680699.6
2.9-3.660.04322.825614699899.4
3.660.03728.425020705198.5

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Phasing

PhasingMethod: MAD

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Processing

Software
NameVersionClassificationNB
REFMAC5.5.0102refinement
PHENIXrefinement
SHELXphasing
MolProbity3beta29model building
XSCALEdata scaling
PDB_EXTRACT3.006data extraction
XDSdata reduction
SHELXDphasing
autoSHARPphasing
RefinementMethod to determine structure: MAD / Resolution: 1.7→39.368 Å / Cor.coef. Fo:Fc: 0.973 / Cor.coef. Fo:Fc free: 0.966 / Occupancy max: 1 / Occupancy min: 0.22 / SU B: 3.611 / SU ML: 0.052 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.078 / ESU R Free: 0.078
Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES
Details: 1. HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. 2. ATOM RECORDS CONTAIN RESIDUAL B FACTORS ONLY. 3. A MET-INHIBITION PROTOCOL WAS USED FOR SELENOMETHIONINE INCORPORATION DURING PROTEIN ...Details: 1. HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. 2. ATOM RECORDS CONTAIN RESIDUAL B FACTORS ONLY. 3. 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. 4. PEG-400 FRAGMENTS (1PE AND 2PE) FROM THE CRYOPROTECTION SOLUTION ARE MODELED.
RfactorNum. reflection% reflectionSelection details
Rfree0.17 3490 5.1 %RANDOM
Rwork0.145 ---
obs0.146 68804 99.54 %-
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: 70.37 Å2 / Biso mean: 20.068 Å2 / Biso min: 5.67 Å2
Baniso -1Baniso -2Baniso -3
1-0.1 Å20 Å2-0.44 Å2
2---0.97 Å20 Å2
3---0.62 Å2
Refinement stepCycle: LAST / Resolution: 1.7→39.368 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3813 0 113 527 4453
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0170.0224126
X-RAY DIFFRACTIONr_bond_other_d0.0010.022816
X-RAY DIFFRACTIONr_angle_refined_deg1.4861.9575583
X-RAY DIFFRACTIONr_angle_other_deg0.96236859
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.0475515
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.61924.593209
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.65515671
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.8241521
X-RAY DIFFRACTIONr_chiral_restr0.1010.2590
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.024600
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02856
X-RAY DIFFRACTIONr_mcbond_it0.8271.52429
X-RAY DIFFRACTIONr_mcbond_other0.2471.5988
X-RAY DIFFRACTIONr_mcangle_it1.46323916
X-RAY DIFFRACTIONr_scbond_it2.28831697
X-RAY DIFFRACTIONr_scangle_it3.6244.51645
LS refinement shellResolution: 1.7→1.744 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.261 261 -
Rwork0.238 4711 -
all-4972 -
obs--98.24 %
Refinement TLS params.Method: refined / Origin x: 58.508 Å / Origin y: 2.349 Å / Origin z: 22.912 Å
111213212223313233
T0.0327 Å2-0.0011 Å20.0089 Å2-0.027 Å2-0.0024 Å2--0.0118 Å2
L0.593 °20.0379 °2-0.0576 °2-0.7673 °20.129 °2--0.7115 °2
S0.0194 Å °-0.0569 Å °0.0197 Å °-0.0082 Å °-0.0181 Å °-0.0647 Å °0.0315 Å °-0.016 Å °-0.0013 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A37 - 456
2X-RAY DIFFRACTION1A460 - 516

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