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- PDB-3wob: Crystal structure of a prostate-specific WGA16 glycoprotein lecti... -

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Basic information

Entry
Database: PDB / ID: 3wob
TitleCrystal structure of a prostate-specific WGA16 glycoprotein lectin, form I
Componentshypothetical protein
KeywordsUNKNOWN FUNCTION / beta-prism-fold
Function / homology
Function and homology information


: / Jacalin-like lectin domain / Aligned Prism / Vitelline Membrane Outer Layer Protein I, subunit A / Jacalin-like lectin domain / Jacalin-type lectin domain profile. / Jacalin-like lectin domain / Jacalin-like lectin domain / Jacalin-like lectin domain superfamily / Mainly Beta
Similarity search - Domain/homology
Heparin-binding protein WGA16
Similarity search - Component
Biological speciesSus scrofa (pig)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.6 Å
AuthorsGarenaux, E. / Kanagawa, M. / Tsuchiyama, T. / Hori, K. / Kanazawa, T. / Goshima, A. / Chiba, M. / Yasue, H. / Ikeda, A. / Yamaguchi, Y. ...Garenaux, E. / Kanagawa, M. / Tsuchiyama, T. / Hori, K. / Kanazawa, T. / Goshima, A. / Chiba, M. / Yasue, H. / Ikeda, A. / Yamaguchi, Y. / Sato, C. / Kitajima, K.
CitationJournal: J.Biol.Chem. / Year: 2015
Title: Discovery, Primary, and Crystal Structures and Capacitation-related Properties of a Prostate-derived Heparin-binding Protein WGA16 from Boar Sperm
Authors: Garenaux, E. / Kanagawa, M. / Tsuchiyama, T. / Hori, K. / Kanazawa, T. / Goshima, A. / Chiba, M. / Yasue, H. / Ikeda, A. / Yamaguchi, Y. / Sato, C. / Kitajima, K.
History
DepositionDec 26, 2013Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Dec 31, 2014Provider: repository / Type: Initial release
Revision 1.1Mar 25, 2015Group: Database references
Revision 1.2Nov 8, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: hypothetical protein


Theoretical massNumber of molelcules
Total (without water)14,7721
Polymers14,7721
Non-polymers00
Water1,09961
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)26.880, 52.333, 45.300
Angle α, β, γ (deg.)90.00, 103.18, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein hypothetical protein


Mass: 14771.708 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Sus scrofa (pig) / Production host: Escherichia coli (E. coli) / References: UniProt: A0A0A8IK66*PLUS
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 61 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsTHE SEQUENCE OF THIS PROTEIN WAS NOT AVAILABLE AT THE UNIPROT KNOWLEDGEBASE DATABASE (UNIPROTKB) AT ...THE SEQUENCE OF THIS PROTEIN WAS NOT AVAILABLE AT THE UNIPROT KNOWLEDGEBASE DATABASE (UNIPROTKB) AT THE TIME OF DEPOSITION. DNA SEQUENCE FOR EACH CHAIN HAS DDBJ ACCESSION NUMBER AB851481.

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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: 2.1 Å3/Da / Density % sol: 41.43 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 5.6
Details: 0.5M Sodium chloride, 0.1M Sodium citrate tribasic dihydrate pH 5.6, 2%(v/v) Ethylene imine polymer, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: AR-NE3A / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 270 / Detector: CCD / Date: May 13, 2013
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.6→50 Å / Num. obs: 3847 / % possible obs: 99.8 % / Redundancy: 3.7 % / Rmerge(I) obs: 0.162 / Net I/σ(I): 7.3
Reflection shellResolution: 2.6→2.64 Å / Redundancy: 3.6 % / Rmerge(I) obs: 0.51 / Mean I/σ(I) obs: 2.1 / % possible all: 100

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Processing

Software
NameVersionClassification
HKL-2000data collection
MOLREPphasing
REFMAC5.2.0019refinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3AQG

3aqg


Resolution: 2.6→44.11 Å / Cor.coef. Fo:Fc: 0.923 / Cor.coef. Fo:Fc free: 0.884 / SU B: 13.978 / SU ML: 0.296 / Cross valid method: THROUGHOUT / ESU R Free: 0.41 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.28317 172 4.5 %RANDOM
Rwork0.21404 ---
obs0.21712 3654 99.04 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 24.673 Å2
Baniso -1Baniso -2Baniso -3
1--1.85 Å20 Å20.61 Å2
2--0.94 Å20 Å2
3---1.2 Å2
Refinement stepCycle: LAST / Resolution: 2.6→44.11 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1039 0 0 61 1100
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0060.0221069
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg0.9351.9281444
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.7185133
X-RAY DIFFRACTIONr_dihedral_angle_2_deg28.05222.60946
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.12815165
X-RAY DIFFRACTIONr_dihedral_angle_4_deg24.235155
X-RAY DIFFRACTIONr_chiral_restr0.0590.2148
X-RAY DIFFRACTIONr_gen_planes_refined0.0020.02825
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.1650.2423
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.310.2714
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1110.245
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1950.220
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.0080.23
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.2891.5662
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it0.52621034
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it0.3763472
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it0.6114.5410
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.59→2.66 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.363 10 -
Rwork0.302 242 -
obs--90 %

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