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- PDB-3see: Crystal structure of a putative sugar binding protein (BT_4411) f... -

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Basic information

Entry
Database: PDB / ID: 3see
TitleCrystal structure of a putative sugar binding protein (BT_4411) from Bacteroides thetaiotaomicron VPI-5482 at 1.25 A resolution
ComponentsHypothetical sugar binding protein
KeywordsSUGAR BINDING PROTEIN / Galactose-binding domain-like / Structural Genomics / Joint Center for Structural Genomics / JCSG / Protein Structure Initiative / PSI-BIOLOGY
Function / homologyDomain of unknown function DUF4627 / Domain of unknown function (DUF4627) / Galactose-binding domain-like / Galactose-binding-like domain superfamily / Jelly Rolls / Sandwich / Mainly Beta / DUF4627 domain-containing protein
Function and homology information
Biological speciesBacteroides thetaiotaomicron (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.25 Å
AuthorsJoint Center for Structural Genomics (JCSG)
CitationJournal: To be published
Title: Crystal structure of a Hypothetical sugar binding protein (BT_4411) from Bacteroides thetaiotaomicron VPI-5482 at 1.25 A resolution
Authors: Joint Center for Structural Genomics (JCSG)
History
DepositionJun 10, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 3, 2011Provider: repository / Type: Initial release
Revision 1.1Dec 24, 2014Group: Structure summary
Revision 1.2Nov 8, 2017Group: Refinement description / Category: software / Item: _software.classification / _software.name
Revision 1.3Feb 1, 2023Group: Database references / Derived calculations
Category: database_2 / pdbx_struct_conn_angle ...database_2 / pdbx_struct_conn_angle / 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 / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _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: Hypothetical sugar binding protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,5922
Polymers24,5691
Non-polymers231
Water7,152397
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)50.473, 50.473, 228.461
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number95
Space group name H-MP4322
Components on special symmetry positions
IDModelComponents
11A-237-

HOH

Detailsmonomer

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Components

#1: Protein Hypothetical sugar binding protein


Mass: 24568.830 Da / Num. of mol.: 1 / Fragment: sequence database residues 13-233
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacteroides thetaiotaomicron (bacteria)
Gene: BT_4411 / Plasmid: SpeedET / Production host: Escherichia Coli (E. coli) / Strain (production host): HK100 / References: UniProt: Q89ZG6
#2: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 397 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsTHIS CONSTRUCT (RESIDUES 13-233) WAS EXPRESSED WITH A PURIFICATION TAG MGSDKIHHHHHHENLYFQG. THE TAG ...THIS CONSTRUCT (RESIDUES 13-233) 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: 2.96 Å3/Da / Density % sol: 58.46 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 5.5
Details: 40.00% polyethylene glycol 600, 0.10M sodium chloride, 0.1M sodium citrate pH 5.5, 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: 0.91837,0.97944,0.97901
DetectorType: MARMOSAIC 325 mm CCD / Detector: CCD / Date: May 25, 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
30.979011
ReflectionResolution: 1.25→28.558 Å / Num. obs: 83306 / % possible obs: 99.8 % / Observed criterion σ(I): -3 / Biso Wilson estimate: 9.938 Å2 / Rmerge(I) obs: 0.071 / Net I/σ(I): 13.41
Reflection shell
Resolution (Å)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. unique obsDiffraction-ID% possible all
1.25-1.290.7082.15905413793197.9
1.29-1.350.6042.579569181291100
1.35-1.410.4693.367763151911100
1.41-1.480.3574.366549147361100
1.48-1.570.256669776152591100
1.57-1.70.1778.477340167721100
1.7-1.870.11712.571729154521100
1.87-2.140.06421.172387154931100
2.14-2.690.04429.472781154861100
2.69-28.5580.02744.37388515731199.9

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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: 1.25→28.558 Å / Cor.coef. Fo:Fc: 0.977 / Cor.coef. Fo:Fc free: 0.972 / Occupancy max: 1 / Occupancy min: 0.25 / SU B: 0.953 / SU ML: 0.019 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.033 / ESU R Free: 0.032
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. SODIUM (NA) HAS BEEN MODELED INTO THE STRUCTURE. 4. THE REFINEMENT WAS RESTRAINED AGAINST THE MAD PHASES. 5. UNEXPLAINED DIFFERENCE ELECTRON DENSITIES OBSERVED AT THE PUTATIVE ACTIVE SITE NEAR THE SIDECHAIN OF GLN 217 WERE NOT MODELED. 6. GLY 216 IS A RAMACHANDRAN OUTLIER IN MOLPROBITY; HOWEVER, ITS MODELING IS SUPPORTED BY ELECTRON DENSITY.
RfactorNum. reflection% reflectionSelection details
Rfree0.1488 4159 5 %RANDOM
Rwork0.1298 ---
obs0.1307 83175 99.82 %-
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: 52.42 Å2 / Biso mean: 14.8998 Å2 / Biso min: 6.36 Å2
Baniso -1Baniso -2Baniso -3
1-0.23 Å20 Å20 Å2
2--0.23 Å20 Å2
3----0.46 Å2
Refinement stepCycle: LAST / Resolution: 1.25→28.558 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1645 0 1 397 2043
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0221974
X-RAY DIFFRACTIONr_bond_other_d0.0010.021351
X-RAY DIFFRACTIONr_angle_refined_deg1.5341.9622738
X-RAY DIFFRACTIONr_angle_other_deg0.84733387
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.9515300
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.25626.77890
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.10315385
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.258154
X-RAY DIFFRACTIONr_chiral_restr0.0960.2311
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.022301
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02367
X-RAY DIFFRACTIONr_mcbond_it1.3941.51218
X-RAY DIFFRACTIONr_mcbond_other0.5631.5493
X-RAY DIFFRACTIONr_mcangle_it2.2322016
X-RAY DIFFRACTIONr_scbond_it2.9583756
X-RAY DIFFRACTIONr_scangle_it4.4624.5681
X-RAY DIFFRACTIONr_rigid_bond_restr1.28133325
X-RAY DIFFRACTIONr_sphericity_free7.443420
X-RAY DIFFRACTIONr_sphericity_bonded3.23233249
LS refinement shellResolution: 1.25→1.282 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.209 288 -
Rwork0.189 5623 -
all-5911 -
obs--97.96 %

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