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- PDB-3vxb: Crystal Structure of BxlE from Streptomyces thermoviolaceus OPC-520 -

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Basic information

Entry
Database: PDB / ID: 3vxb
TitleCrystal Structure of BxlE from Streptomyces thermoviolaceus OPC-520
ComponentsPutative sugar-binding lipoprotein
KeywordsSUGAR BINDING PROTEIN / ABC Transporter
Function / homology: / Bacterial extracellular solute-binding protein / Bacterial extracellular solute-binding protein / Periplasmic binding protein-like II / D-Maltodextrin-Binding Protein; domain 2 / Prokaryotic membrane lipoprotein lipid attachment site profile. / 3-Layer(aba) Sandwich / Alpha Beta / Putative sugar-binding lipoprotein
Function and homology information
Biological speciesStreptomyces thermoviolaceus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.85 Å
AuthorsTomoo, K. / Ishida, T. / Miyamoto, K. / Tsujibo, H.
CitationJournal: To be published
Title: Crystal Structure of Xylooligosaccharide-Binding Protein from Streptomyces thermoviolaceus OPC-520: Dramatic Conformational Change with Ligand binding
Authors: Tomoo, K. / Ishida, T. / Miyamoto, K. / Tsujibo, H.
History
DepositionSep 11, 2012Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Sep 18, 2013Provider: repository / Type: Initial release
Revision 1.1Mar 20, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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: Putative sugar-binding lipoprotein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,0765
Polymers46,7081
Non-polymers3684
Water1,40578
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)44.634, 63.272, 66.402
Angle α, β, γ (deg.)90.00, 103.05, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Putative sugar-binding lipoprotein


Mass: 46707.672 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptomyces thermoviolaceus (bacteria)
Gene: bxlD / Production host: Escherichia coli (E. coli) / References: UniProt: Q76BU9
#2: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C3H8O3
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 78 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 2

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Sample preparation

CrystalDensity Matthews: 1.96 Å3/Da / Density % sol: 37.1 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 3.2
Details: 25% PEG 3350, 0.1M citrate, pH 3.2, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

Diffraction
IDCrystal-ID
11
21
Diffraction source
SourceSiteBeamlineTypeID
SYNCHROTRONSPring-8 BL41XU1
ROTATING ANODERIGAKU FR-E+ SUPERBRIGHT2
DetectorType: RIGAKU RAXIS VII / Detector: IMAGE PLATE
Radiation
IDProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1MADMx-ray1
2SINGLE WAVELENGTHMx-ray1
Radiation wavelengthRelative weight: 1
ReflectionResolution: 1.65→34.2 Å / Num. all: 43438 / Num. obs: 39659 / % possible obs: 91.3 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 1 / Rmerge(I) obs: 0.026

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Processing

Software
NameVersionClassification
CrystalCleardata collection
SOLVEphasing
REFMAC5.5.0109refinement
CrystalCleardata reduction
CrystalCleardata scaling
RefinementMethod to determine structure: MAD / Resolution: 1.85→29.31 Å / Cor.coef. Fo:Fc: 0.958 / Cor.coef. Fo:Fc free: 0.93 / SU B: 3.366 / SU ML: 0.102 / Cross valid method: THROUGHOUT / ESU R: 0.17 / ESU R Free: 0.158 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.23997 1419 5 %RANDOM
Rwork0.18955 ---
obs0.19202 27160 92.55 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 24.313 Å2
Baniso -1Baniso -2Baniso -3
1--0.01 Å2-0 Å2-0 Å2
2--0.01 Å20 Å2
3----0 Å2
Refinement stepCycle: LAST / Resolution: 1.85→29.31 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3046 0 24 78 3148
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0230.0223143
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.8351.964258
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.0425398
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.54425.303132
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.04815506
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.344159
X-RAY DIFFRACTIONr_chiral_restr0.1360.2453
X-RAY DIFFRACTIONr_gen_planes_refined0.010.0212395
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.2281.51980
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it2.07223164
X-RAY DIFFRACTIONr_scbond_it3.42131163
X-RAY DIFFRACTIONr_scangle_it5.2924.51094
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.85→1.898 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.4 96 -
Rwork0.307 1903 -
obs--88.22 %

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