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

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Basic information

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


carbohydrate binding
Similarity search - Function
: / Jacalin-like lectin domain / Jacalin-like lectin domain / Jacalin-type lectin domain profile. / Aligned Prism / Vitelline Membrane Outer Layer Protein I, subunit A / Jacalin-like lectin domain / Jacalin-like lectin domain / Jacalin-like lectin domain superfamily / Mainly Beta
Similarity search - Domain/homology
1,4-DIETHYLENE DIOXIDE / Heparin-binding protein WGA16
Similarity search - Component
Biological speciesSus scrofa (pig)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.4 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 ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / 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: hypothetical protein
B: hypothetical protein
C: hypothetical protein
D: hypothetical protein
E: hypothetical protein
F: hypothetical protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)100,29730
Polymers98,1276
Non-polymers2,17024
Water4,594255
1
A: hypothetical protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)17,24711
Polymers16,3541
Non-polymers89310
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: hypothetical protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)16,7195
Polymers16,3541
Non-polymers3644
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: hypothetical protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)16,4512
Polymers16,3541
Non-polymers961
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: hypothetical protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)16,6274
Polymers16,3541
Non-polymers2723
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
5
E: hypothetical protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)16,6274
Polymers16,3541
Non-polymers2723
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
6
F: hypothetical protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)16,6274
Polymers16,3541
Non-polymers2723
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
7
A: hypothetical protein
E: hypothetical protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,87415
Polymers32,7092
Non-polymers1,16513
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1540 Å2
ΔGint-13 kcal/mol
Surface area13160 Å2
MethodPISA
8
B: hypothetical protein
hetero molecules

D: hypothetical protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,3469
Polymers32,7092
Non-polymers6377
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation1_554x,y,z-11
Buried area1640 Å2
ΔGint-14 kcal/mol
Surface area13390 Å2
MethodPISA
9
C: hypothetical protein
F: hypothetical protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,0776
Polymers32,7092
Non-polymers3684
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1650 Å2
ΔGint-13 kcal/mol
Surface area12870 Å2
MethodPISA
Unit cell
Length a, b, c (Å)134.483, 77.848, 87.187
Angle α, β, γ (deg.)90.00, 91.30, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein
hypothetical protein


Mass: 16354.448 Da / Num. of mol.: 6
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: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: SO4
#3: Chemical
ChemComp-DIO / 1,4-DIETHYLENE DIOXIDE


Mass: 88.105 Da / Num. of mol.: 16 / Source method: obtained synthetically / Formula: C4H8O2
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 255 / 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: 2.32 Å3/Da / Density % sol: 47.09 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 0.1M MES pH 6.5, 1.6M (NH4)2SO4, 10%(v/v) 1,4-dioxane, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: AR-NW12A / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Jan 30, 2013
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.4→87.04 Å / Num. obs: 35861 / % possible obs: 99.7 % / Redundancy: 5.7 % / Rmerge(I) obs: 0.069 / Net I/σ(I): 22.4
Reflection shellResolution: 2.4→2.44 Å / Redundancy: 5.7 % / Rmerge(I) obs: 0.612 / Mean I/σ(I) obs: 2.2 / % possible all: 99.3

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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: 2.4→50 Å / Cor.coef. Fo:Fc: 0.915 / Cor.coef. Fo:Fc free: 0.865 / SU B: 12.965 / SU ML: 0.306 / Cross valid method: THROUGHOUT / ESU R: 0.604 / ESU R Free: 0.347 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.31954 1784 5 %RANDOM
Rwork0.25223 ---
obs0.25569 33943 99.21 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 39.536 Å2
Baniso -1Baniso -2Baniso -3
1-0.5 Å20 Å20.46 Å2
2--1.9 Å20 Å2
3----2.37 Å2
Refinement stepCycle: LAST / Resolution: 2.4→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6352 0 138 255 6745
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0060.0226668
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.0151.9468972
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.635818
X-RAY DIFFRACTIONr_dihedral_angle_2_deg28.48222.518278
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.281151002
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.6881532
X-RAY DIFFRACTIONr_chiral_restr0.070.2902
X-RAY DIFFRACTIONr_gen_planes_refined0.0020.025040
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.1760.22798
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3110.24409
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1230.2274
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.150.2133
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1180.213
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.3411.54126
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it0.61426352
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it0.45632999
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it0.7324.52620
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: 2.4→2.448 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.425 104 -
Rwork0.323 2381 -
obs--93.53 %

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