[English] 日本語
Yorodumi
- PDB-2yip: Crystal Structure of Parasite Sarcocystis muris Microneme Protein... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 2yip
TitleCrystal Structure of Parasite Sarcocystis muris Microneme Protein SML- 2 in complex with 1-Thio-beta-D-Galactose (SPACEGROUP P212121)
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 / carbohydrate binding / cytoplasmic vesicle / 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 / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.14 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 1.2Jan 30, 2019Group: Advisory / Data collection ...Advisory / Data collection / Experimental preparation / Other
Category: exptl_crystal_grow / pdbx_database_proc ...exptl_crystal_grow / pdbx_database_proc / pdbx_database_status / pdbx_unobs_or_zero_occ_atoms
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
Revision 1.6Jul 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 1.7Dec 20, 2023Group: Advisory / Data collection ...Advisory / 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 / pdbx_unobs_or_zero_occ_atoms / 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
Revision 1.8Oct 16, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
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)92,84732
Polymers90,5646
Non-polymers2,28326
Water9,314517
1
A: MICRONEME ANTIGEN L2
B: MICRONEME ANTIGEN L2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,85010
Polymers30,1882
Non-polymers6628
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4700 Å2
ΔGint-61.5 kcal/mol
Surface area12540 Å2
MethodPISA
2
C: MICRONEME ANTIGEN L2
D: MICRONEME ANTIGEN L2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,90610
Polymers30,1882
Non-polymers7188
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4840 Å2
ΔGint-63.4 kcal/mol
Surface area12470 Å2
MethodPISA
3
E: MICRONEME ANTIGEN L2
F: MICRONEME ANTIGEN L2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,09112
Polymers30,1882
Non-polymers90310
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5220 Å2
ΔGint-50.2 kcal/mol
Surface area12500 Å2
MethodPISA
Unit cell
Length a, b, c (Å)53.310, 130.000, 158.850
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
12C
22D
13E
23F

NCS domain segments:

Component-ID: 1 / Beg auth comp-ID: VAL / Beg label comp-ID: VAL / End auth comp-ID: TYR / End label comp-ID: TYR / Refine code: 4 / Auth seq-ID: 7 - 130 / Label seq-ID: 7 - 130

Dom-IDEns-IDAuth asym-IDLabel asym-ID
11AA
21BB
12CC
22DD
13EE
23FF

NCS ensembles :
ID
1
2
3

NCS oper:
IDCodeMatrixVector
1given(0.16025, 0.1529, -0.97516), (0.07097, -0.98716, -0.14311), (-0.98452, -0.04627, -0.16904)19.19785, 161.59627, 41.59678
2given(0.16025, 0.1529, -0.97516), (0.07097, -0.98716, -0.14311), (-0.98452, -0.04627, -0.16904)19.19785, 161.59627, 41.59678
3given(-0.01122, 0.00048, -0.99994), (0.02098, -0.99978, -0.00072), (-0.99972, -0.02099, 0.0112)148.19023, 160.14577, 148.27238

-
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: 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.: 6 / Source method: obtained synthetically / Formula: C6H12O5S
IdentifierTypeProgram
b-D-Galp1SHIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
#3: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 13 / Source method: obtained synthetically / Formula: Cl
#4: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: C3H8O3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 517 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
Sample preparation

CrystalDensity Matthews: 3.06 Å3/Da / Density % sol: 59.8 % / Description: NONE
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 7.9
Details: VAPOR DIFFUSION, HANGING DROP. PH 7.9, TEMPERATURE 291K. VAPOR DIFFUSION, HANGING DROP. PROTEIN SOLUTION: 50 MM TRIS-HCL, 150 MM NACL, PH 8.3, 12MG/ML SML-2. RESERVOIR: 0.1 M HEPES, PH 7.5, ...Details: VAPOR DIFFUSION, HANGING DROP. PH 7.9, TEMPERATURE 291K. VAPOR DIFFUSION, HANGING DROP. PROTEIN SOLUTION: 50 MM TRIS-HCL, 150 MM NACL, PH 8.3, 12MG/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.

-
Data collection

DiffractionMean temperature: 110 K
Diffraction sourceSource: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: BW7B / Wavelength: 0.8428
DetectorType: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: May 19, 2000 / Details: MIRRORS
RadiationMonochromator: SI(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.8428 Å / Relative weight: 1
ReflectionResolution: 2.14→35 Å / Num. obs: 61346 / % possible obs: 99.5 % / Observed criterion σ(I): -3 / Redundancy: 5 % / Biso Wilson estimate: 28.6 Å2 / Rmerge(I) obs: 0.03 / Net I/σ(I): 38.6
Reflection shellResolution: 2.14→2.2 Å / Redundancy: 4.6 % / Rmerge(I) obs: 0.1 / Mean I/σ(I) obs: 14.1 / % possible all: 95.8

-
Processing

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

2yil


Resolution: 2.14→33.89 Å / Cor.coef. Fo:Fc: 0.958 / Cor.coef. Fo:Fc free: 0.936 / SU B: 3.402 / SU ML: 0.091 / Cross valid method: THROUGHOUT / ESU R: 0.158 / ESU R Free: 0.149 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. U VALUES REFINED INDIVIDUALLY.
RfactorNum. reflection% reflectionSelection details
Rfree0.20242 3068 5 %RANDOM
Rwork0.15869 ---
obs0.16086 58275 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: 29.115 Å2
Baniso -1Baniso -2Baniso -3
1--0.01 Å20 Å20 Å2
2--0 Å20 Å2
3---0.01 Å2
Refinement stepCycle: LAST / Resolution: 2.14→33.89 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5985 0 127 517 6629
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0240.0216290
X-RAY DIFFRACTIONr_bond_other_d0.0010.024110
X-RAY DIFFRACTIONr_angle_refined_deg1.9051.9498555
X-RAY DIFFRACTIONr_angle_other_deg0.9593.0019995
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.5325779
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.59525.093269
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.23415952
X-RAY DIFFRACTIONr_dihedral_angle_4_deg12.2521512
X-RAY DIFFRACTIONr_chiral_restr0.120.2905
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.0216967
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021199
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_it1.59723907
X-RAY DIFFRACTIONr_mcbond_other0.53921576
X-RAY DIFFRACTIONr_mcangle_it2.66936256
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it4.0034.52383
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it5.93662299
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

Number: 1586 / Refine-ID: X-RAY DIFFRACTION

Ens-IDDom-IDAuth asym-IDTypeRms dev position (Å)Weight position
11Amedium positional0.70.5
12Bmedium positional0.70.5
21Cmedium positional0.60.5
22Dmedium positional0.60.5
31Emedium positional0.340.5
32Fmedium positional0.340.5
11Amedium thermal1.312
12Bmedium thermal1.312
21Cmedium thermal1.712
22Dmedium thermal1.712
31Emedium thermal0.992
32Fmedium thermal0.992
LS refinement shellResolution: 2.143→2.199 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.244 216 -
Rwork0.177 4088 -
obs--100 %

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more