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- PDB-2yil: Crystal Structure of Parasite Sarcocystis muris Lectin SML-2 -

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Basic information

Entry
Database: PDB / ID: 2yil
TitleCrystal Structure of Parasite Sarcocystis muris Lectin SML-2
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
Microneme antigen L2
Similarity search - Component
Biological speciesSARCOCYSTIS MURIS (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.95 Å
AuthorsMueller, J.J. / Weiss, M.S. / 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 1.2Jan 30, 2019Group: Data collection / Experimental preparation / Other
Category: exptl_crystal_grow / pdbx_database_proc / pdbx_database_status
Item: _exptl_crystal_grow.method / _pdbx_database_status.recvd_author_approval
Revision 1.3Feb 6, 2019Group: Data collection / Experimental preparation / Category: diffrn_source / exptl_crystal_grow
Item: _diffrn_source.pdbx_synchrotron_site / _exptl_crystal_grow.temp
Revision 1.4Jul 10, 2019Group: Data collection / Category: diffrn_source / Item: _diffrn_source.pdbx_synchrotron_site
Revision 1.5Jul 17, 2019Group: Data collection / Category: diffrn_source / Item: _diffrn_source.pdbx_synchrotron_site

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: MICRONEME ANTIGEN L2
B: MICRONEME ANTIGEN L2
C: MICRONEME ANTIGEN L2
D: MICRONEME ANTIGEN L2
E: MICRONEME ANTIGEN L2
F: MICRONEME ANTIGEN L2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)92,02126
Polymers90,5646
Non-polymers1,45720
Water11,890660
1
A: MICRONEME ANTIGEN L2
B: MICRONEME ANTIGEN L2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,5357
Polymers30,1882
Non-polymers3475
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4910 Å2
ΔGint-50.6 kcal/mol
Surface area12280 Å2
MethodPISA
2
C: MICRONEME ANTIGEN L2
D: MICRONEME ANTIGEN L2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,85111
Polymers30,1882
Non-polymers6639
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5600 Å2
ΔGint-55.8 kcal/mol
Surface area12200 Å2
MethodPISA
3
E: MICRONEME ANTIGEN L2
F: MICRONEME ANTIGEN L2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,6358
Polymers30,1882
Non-polymers4476
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4930 Å2
ΔGint-64.1 kcal/mol
Surface area12260 Å2
MethodPISA
Unit cell
Length a, b, c (Å)53.170, 129.040, 158.100
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS oper:
IDCodeMatrixVector
1given(-0.18765, 0.15718, 0.96958), (0.08955, -0.98026, 0.17624), (0.97815, 0.1199, 0.16987)-125.78256, 79.8706, 94.9
2given(-0.01209, 0.00183, 0.99993), (-0.01661, -0.99986, 0.00162), (0.99979, -0.01659, 0.01211)-64.28546, 98.12782, 64.23483
3given(0.1608, -0.1564, 0.97452), (-0.07416, -0.98649, -0.14609), (0.9842, -0.04878, -0.17023)-5.57628, 92.08926, 16.95106

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Components

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


Mass: 15094.004 Da / Num. of mol.: 6 / 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
#2: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: Cl
#3: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: C3H8O3
#4: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: SO4
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 660 / 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: 3.06 Å3/Da / Density % sol: 59.8 % / Description: SULFUR SAD
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 7.9
Details: VAPOR DIFFUSION, HANGING DROP. 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% ...Details: VAPOR DIFFUSION, HANGING DROP. 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.

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: X12 / Wavelength: 1
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Nov 11, 2006 / Details: MIRROR
RadiationMonochromator: DOUBLE CRYSTAL SI(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.95→35 Å / Num. obs: 79584 / % possible obs: 99.5 % / Observed criterion σ(I): -3 / Redundancy: 7.2 % / Biso Wilson estimate: 30.8 Å2 / Rmerge(I) obs: 0.06 / Net I/σ(I): 23.8
Reflection shellResolution: 1.95→2 Å / Redundancy: 6.4 % / Rmerge(I) obs: 0.42 / Mean I/σ(I) obs: 4.2 / % possible all: 96.5

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Processing

Software
NameVersionClassification
REFMAC5.5.0109refinement
XDSdata reduction
XSCALEdata scaling
SHELXCDphasing
SHELXEphasing
RefinementMethod to determine structure: SAD
Starting model: NONE

Resolution: 1.95→33.44 Å / Cor.coef. Fo:Fc: 0.959 / Cor.coef. Fo:Fc free: 0.947 / SU B: 2.495 / SU ML: 0.073 / Cross valid method: THROUGHOUT / ESU R: 0.124 / ESU R Free: 0.116 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. U VALUES REFINED INDIVIDUALLY.
RfactorNum. reflection% reflectionSelection details
Rfree0.19716 3980 5 %RANDOM
Rwork0.16837 ---
obs0.16981 75603 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: 21.297 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2---0.01 Å20 Å2
3---0.01 Å2
Refinement stepCycle: LAST / Resolution: 1.95→33.44 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5943 0 82 660 6685
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.0216208
X-RAY DIFFRACTIONr_bond_other_d0.0010.024056
X-RAY DIFFRACTIONr_angle_refined_deg1.4911.9358437
X-RAY DIFFRACTIONr_angle_other_deg0.89739930
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.4745773
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.74125.075268
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.5415946
X-RAY DIFFRACTIONr_dihedral_angle_4_deg12.6341512
X-RAY DIFFRACTIONr_chiral_restr0.0980.2870
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0216921
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021193
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_it1.32823878
X-RAY DIFFRACTIONr_mcbond_other0.36421564
X-RAY DIFFRACTIONr_mcangle_it2.2636211
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it3.3294.52330
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it4.8962226
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: 1.95→2.001 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.256 282 -
Rwork0.21 5349 -
obs--100 %

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