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- PDB-7wbo: Crystal structure of Sarcoplasmic Calcium-Binding Protein from Sc... -

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Basic information

Entry
Database: PDB / ID: 7wbo
TitleCrystal structure of Sarcoplasmic Calcium-Binding Protein from Scylla paramamosain
ComponentsSarcoplasmic calcium-binding protein
KeywordsALLERGEN / allergy / Scylla paramamosain / EF-hand
Function / homology
Function and homology information


calcium ion binding / protein homodimerization activity
Similarity search - Function
EF-hand / Recoverin; domain 1 / EF-hand domain pair / EF-hand, calcium binding motif / EF-Hand 1, calcium-binding site / EF-hand calcium-binding domain. / EF-hand calcium-binding domain profile. / EF-hand domain / EF-hand domain pair / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
Sarcoplasmic calcium-binding protein
Similarity search - Component
Biological speciesScylla paramamosain (green mud crab)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.6 Å
AuthorsChen, Y. / Jin, T. / Liu, G.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: J.Agric.Food Chem. / Year: 2023
Title: Crystal Structure Analysis of Sarcoplasmic-Calcium-Binding Protein: An Allergen in Scylla paramamosain.
Authors: Chen, Y. / Jin, T. / Li, M. / Yun, X. / Huan, F. / Liu, Q. / Hu, M. / Wei, X. / Zheng, P. / Liu, G.
History
DepositionDec 17, 2021Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Dec 21, 2022Provider: repository / Type: Initial release
Revision 1.1Jul 5, 2023Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Nov 29, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Sarcoplasmic calcium-binding protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,97813
Polymers22,3601
Non-polymers61812
Water4,504250
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)81.121, 46.893, 64.474
Angle α, β, γ (deg.)90.000, 125.350, 90.000
Int Tables number5
Space group name H-MC121

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Components

#1: Protein Sarcoplasmic calcium-binding protein / SCP


Mass: 22360.053 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Scylla paramamosain (green mud crab) / Production host: Escherichia coli (E. coli) / References: UniProt: I2DDG2
#2: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: C2H6O2
#3: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Ca / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 250 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 2.27 Å3/Da / Density % sol: 45.93 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / Details: 20% (v/v) PEG 3350, 0.2M NH4Cl

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: NFPSS / Beamline: BL19U1 / Wavelength: 0.97852 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Dec 15, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97852 Å / Relative weight: 1
ReflectionResolution: 1.6→50 Å / Num. obs: 24946 / % possible obs: 95.5 % / Redundancy: 3.7 % / CC1/2: 0.98 / Rmerge(I) obs: 0.055 / Rrim(I) all: 0.033 / Net I/σ(I): 18.6
Reflection shellResolution: 1.6→1.63 Å / Redundancy: 3.8 % / Rmerge(I) obs: 0.082 / Mean I/σ(I) obs: 15 / Num. unique obs: 1235 / CC1/2: 0.986 / Rpim(I) all: 0.048 / % possible all: 95.4

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Phasing

PhasingMethod: molecular replacement
Phasing MRR rigid body: 0.605
Highest resolutionLowest resolution
Rotation40.48 Å1.72 Å

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Processing

Software
NameVersionClassificationNB
REFMAC5.8.0267refinement
HKL-2000data reduction
SCALEPACKdata scaling
MOLREPphasing
PDB_EXTRACT3.27data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3AKA

3aka


Resolution: 1.6→40.52 Å / Cor.coef. Fo:Fc: 0.964 / Cor.coef. Fo:Fc free: 0.938 / WRfactor Rfree: 0.2156 / WRfactor Rwork: 0.175 / FOM work R set: 0.8991 / SU B: 1.246 / SU ML: 0.046 / SU R Cruickshank DPI: 0.0818 / SU Rfree: 0.085 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.082 / ESU R Free: 0.085 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.1855 1162 4.7 %RANDOM
Rwork0.1486 ---
obs0.1504 23796 95.33 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 56.7 Å2 / Biso mean: 14.713 Å2 / Biso min: 5.03 Å2
Baniso -1Baniso -2Baniso -3
1-0.1 Å2-0 Å20.02 Å2
2---0.16 Å2-0 Å2
3---0.01 Å2
Refinement stepCycle: final / Resolution: 1.6→40.52 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1544 0 33 250 1827
Biso mean--25.36 29.77 -
Num. residues----193
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0131595
X-RAY DIFFRACTIONr_bond_other_d0.0010.0171482
X-RAY DIFFRACTIONr_angle_refined_deg1.8321.6462137
X-RAY DIFFRACTIONr_angle_other_deg1.6161.5953408
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.1065192
X-RAY DIFFRACTIONr_dihedral_angle_2_deg29.50323.87193
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.65615272
X-RAY DIFFRACTIONr_dihedral_angle_4_deg25.191158
X-RAY DIFFRACTIONr_chiral_restr0.1010.2196
X-RAY DIFFRACTIONr_gen_planes_refined0.010.021829
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02383
LS refinement shellResolution: 1.601→1.643 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.206 70 -
Rwork0.145 1723 -
all-1793 -
obs--93.73 %

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