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- PDB-2yio: Crystal Structure of Parasite Sarcocystis muris Microneme Protein... -

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Basic information

Entry
Database: PDB / ID: 2yio
TitleCrystal Structure of Parasite Sarcocystis muris Microneme Protein SML- 2 in complex with 1-Thio-beta-D-Galactose (SPACEGROUP C2221)
ComponentsMICRONEME ANTIGEN L2
KeywordsSUGAR BINDING PROTEIN / APPLE-DOMAIN TANDEM REPEAT / PAN_AP / PAN_1 / GALACTOSE-BINDING LECTIN / CELLULAR ADHESION / MICRONEMAL PROTEIN
Function / homology
Function and homology information


microneme / cytoplasmic vesicle / carbohydrate binding / cell adhesion / proteolysis / extracellular region
Similarity search - Function
Defensin A-like - #180 / PAN domain / Hepatocyte Growth Factor / Hepatocyte Growth Factor / divergent subfamily of APPLE domains / Apple domain / APPLE domain / PAN/Apple domain profile. / PAN domain / PAN/Apple domain ...Defensin A-like - #180 / PAN domain / Hepatocyte Growth Factor / Hepatocyte Growth Factor / divergent subfamily of APPLE domains / Apple domain / APPLE domain / PAN/Apple domain profile. / PAN domain / PAN/Apple domain / Defensin A-like / 3-Layer(bba) Sandwich / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
1-thio-beta-D-galactopyranose / Microneme antigen L2
Similarity search - Component
Biological speciesSARCOCYSTIS MURIS (eukaryote)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.43 Å
AuthorsMueller, J.J. / Heinemann, U.
CitationJournal: Acta Crystallogr.,Sect.D / Year: 2011
Title: Pan-Modular Structure of Microneme Protein Sml-2 from Parasite Sarcocystis Muris at 1.95 A Resolution and its Complex with 1-Thio-Beta-D-Galactose.
Authors: Mueller, J.J. / Weiss, M.S. / Heinemann, U.
History
DepositionMay 16, 2011Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 2, 2011Provider: repository / Type: Initial release
Revision 1.1Nov 30, 2011Group: Database references
Revision 1.2Jun 13, 2018Group: Data collection / Database references / Structure summary
Category: citation / struct / Item: _citation.page_last / _struct.title
Revision 1.3Jan 30, 2019Group: Data collection / Experimental preparation / Category: exptl_crystal_grow / Item: _exptl_crystal_grow.method
Revision 1.4Feb 6, 2019Group: Data collection / Experimental preparation / Category: exptl_crystal_grow / Item: _exptl_crystal_grow.temp
Revision 1.5Jul 29, 2020Group: Data collection / Derived calculations ...Data collection / Derived calculations / Other / Structure summary
Category: chem_comp / entity ...chem_comp / entity / pdbx_chem_comp_identifier / pdbx_database_status / pdbx_entity_nonpoly / struct_site / struct_site_gen
Item: _chem_comp.name / _chem_comp.type ..._chem_comp.name / _chem_comp.type / _entity.pdbx_description / _pdbx_database_status.status_code_sf / _pdbx_entity_nonpoly.name
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.6Dec 20, 2023Group: Data collection / Database references ...Data collection / Database references / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ncs_dom_lim
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI ..._chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: MICRONEME ANTIGEN L2
B: MICRONEME ANTIGEN L2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,27617
Polymers30,1882
Non-polymers1,08815
Water1,63991
1
A: MICRONEME ANTIGEN L2
hetero molecules

A: MICRONEME ANTIGEN L2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,50320
Polymers30,1882
Non-polymers1,31518
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_566x,-y+1,-z+11
Buried area5970 Å2
ΔGint-135.5 kcal/mol
Surface area12590 Å2
MethodPISA
2
B: MICRONEME ANTIGEN L2
hetero molecules

B: MICRONEME ANTIGEN L2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,04814
Polymers30,1882
Non-polymers86012
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_655-x+1,y,-z+1/21
Buried area5320 Å2
ΔGint-74 kcal/mol
Surface area12650 Å2
MethodPISA
Unit cell
Length a, b, c (Å)74.730, 81.990, 130.960
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B

NCS domain segments:

Component-ID: 1 / Ens-ID: 1 / Beg auth comp-ID: VAL / Beg label comp-ID: VAL / End auth comp-ID: TYR / End label comp-ID: TYR / Refine code: 5 / Auth seq-ID: 7 - 130 / Label seq-ID: 7 - 130

Dom-IDAuth asym-IDLabel asym-ID
1AA
2BB

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Components

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Protein / Sugars , 2 types, 4 molecules AB

#1: Protein MICRONEME ANTIGEN L2 / LECTIN SML2 / LECTIN SML-2


Mass: 15094.004 Da / Num. of mol.: 2 / Source method: isolated from a natural source
Details: CYST MEROZOITES OF SARCOCYSTIS MURIS FROM SKELETAL MOUSE MUSCLES.
Source: (natural) SARCOCYSTIS MURIS (eukaryote) / References: UniProt: P81860
#5: Sugar ChemComp-YIO / 1-thio-beta-D-galactopyranose / (2R,3R,4S,5R,6S)-2-(HYDROXYMETHYL)-6-SULFANYL-OXANE-3,4,5-TRIOL / 1-thio-beta-D-galactose / 1-thio-D-galactose / 1-thio-galactose


Type: D-saccharide, beta linking / Mass: 196.221 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H12O5S
IdentifierTypeProgram
b-D-Galp1SHIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0

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Non-polymers , 4 types, 104 molecules

#2: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: Cl
#3: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#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
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 91 / 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: 1

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Sample preparation

CrystalDensity Matthews: 3.34 Å3/Da / Density % sol: 63.2 % / Description: NONE
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 7.9
Details: VAPOR DIFFUSION, HANGING DROP. PH 7.9, TEMPERATURE 291K. PROTEIN SOLUTION:50 MM TRIS-HCL, 150 MM NACL, PH 8.3, 12 MG/ML SML-2. RESERVOIR: 0.1 M HEPES, PH 7.5, 0.1 M NACL, 1.7 M AMMONIUM ...Details: VAPOR DIFFUSION, HANGING DROP. PH 7.9, TEMPERATURE 291K. PROTEIN SOLUTION:50 MM TRIS-HCL, 150 MM NACL, PH 8.3, 12 MG/ML SML-2. RESERVOIR: 0.1 M HEPES, PH 7.5, 0.1 M NACL, 1.7 M AMMONIUM SULFATE, 15% GLYCEROL. DROPLET: 1 MICROLITER PROTEIN SOLUTION: 1 MICROLITER RESERVOIR SOLUTION. PROTEIN:1-THIO-BETA-D-GALACTOSE, MOLAR RATIO 1:100.

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Data collection

DiffractionMean temperature: 110 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU H2B / Wavelength: 1.542
DetectorType: MARRESEARCH MAR30 / Detector: IMAGE PLATE / Date: May 5, 2000 / Details: GOEBEL MIRROR
RadiationMonochromator: MAXFLUX MIRROR OSMIC / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.542 Å / Relative weight: 1
ReflectionResolution: 2.43→23.9 Å / Num. obs: 15317 / % possible obs: 99.1 % / Observed criterion σ(I): -3 / Redundancy: 5 % / Biso Wilson estimate: 30.2 Å2 / Rmerge(I) obs: 0.04 / Net I/σ(I): 29.1
Reflection shellResolution: 2.43→2.5 Å / Redundancy: 3.9 % / Rmerge(I) obs: 0.15 / Mean I/σ(I) obs: 8.44 / % possible all: 92.6

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Processing

Software
NameVersionClassification
REFMAC5.5.0109refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2YIL

2yil


Resolution: 2.43→23.83 Å / Cor.coef. Fo:Fc: 0.944 / Cor.coef. Fo:Fc free: 0.919 / SU B: 5.768 / SU ML: 0.138 / Cross valid method: THROUGHOUT / ESU R: 0.25 / ESU R Free: 0.202 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. U VALUES REFINED INDIVIDUALLY.
RfactorNum. reflection% reflectionSelection details
Rfree0.21379 765 5 %RANDOM
Rwork0.17045 ---
obs0.17267 14549 100 %-
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 mean: 36.229 Å2
Baniso -1Baniso -2Baniso -3
1--0.01 Å20 Å20 Å2
2--0.01 Å20 Å2
3---0 Å2
Refinement stepCycle: LAST / Resolution: 2.43→23.83 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1976 0 55 91 2122
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0190.0212084
X-RAY DIFFRACTIONr_bond_other_d0.0030.021357
X-RAY DIFFRACTIONr_angle_refined_deg1.7911.9532836
X-RAY DIFFRACTIONr_angle_other_deg0.9693.0013299
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.9275257
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.99225.05689
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.16315314
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.126154
X-RAY DIFFRACTIONr_chiral_restr0.1090.2298
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0212301
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02397
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_it1.30721289
X-RAY DIFFRACTIONr_mcbond_other0.392520
X-RAY DIFFRACTIONr_mcangle_it2.38232063
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it3.7514.5795
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it5.4916773
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
Refine LS restraints NCS

Ens-ID: 1 / Refine-ID: X-RAY DIFFRACTION

Dom-IDAuth asym-IDNumberTypeRms dev position (Å)Weight position
1A728medium positional0.950.5
2B728medium positional0.950.5
1A858loose positional1.165
2B858loose positional1.165
1A728medium thermal1.222
2B728medium thermal1.222
1A858loose thermal1.3710
2B858loose thermal1.3710
LS refinement shellResolution: 2.434→2.497 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.245 52 -
Rwork0.187 998 -
obs--100 %

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