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- PDB-8xvf: Globular domain of Trichinella spiralis calreticulin -

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Basic information

Entry
Database: PDB / ID: 8xvf
TitleGlobular domain of Trichinella spiralis calreticulin
ComponentsCalreticulin
KeywordsCHAPERONE / Calcium binding domain / complement inhibiting protein
Function / homology
Function and homology information


response to stimulus / unfolded protein binding / protein folding / calcium ion binding / endoplasmic reticulum / membrane
Similarity search - Function
Calreticulin/calnexin / Calreticulin/calnexin, P domain superfamily / Calreticulin/calnexin, conserved site / Calreticulin family / Calreticulin family signature 1. / Calreticulin family signature 2. / Concanavalin A-like lectin/glucanase domain superfamily
Similarity search - Domain/homology
Biological speciesTrichinella spiralis (invertebrata)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.76 Å
AuthorsZhu, X.P. / Jia, Z.H. / Yu, W.
Funding support China, 3items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)81672042 China
National Natural Science Foundation of China (NSFC)82202549 China
Other government7214213 China
CitationJournal: To Be Published
Title: structure of globular domain of Trichinella spiralis calreticulin at 2.76 Angstroms resolution.
Authors: Zhu, X.P. / Jia, Z.H. / Yu, W.
History
DepositionJan 15, 2024Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Apr 3, 2024Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Calreticulin
B: Calreticulin
C: Calreticulin
D: Calreticulin
E: Calreticulin
F: Calreticulin
G: Calreticulin
H: Calreticulin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)253,90816
Polymers253,5878
Non-polymers3218
Water7,152397
1
A: Calreticulin
hetero molecules


  • defined by author
  • Evidence: gel filtration
  • 31.7 kDa, 1 polymers
Theoretical massNumber of molelcules
Total (without water)31,7382
Polymers31,6981
Non-polymers401
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Calreticulin
hetero molecules


  • defined by author
  • 31.7 kDa, 1 polymers
Theoretical massNumber of molelcules
Total (without water)31,7382
Polymers31,6981
Non-polymers401
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Calreticulin
hetero molecules


  • defined by author
  • 31.7 kDa, 1 polymers
Theoretical massNumber of molelcules
Total (without water)31,7382
Polymers31,6981
Non-polymers401
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: Calreticulin
hetero molecules


  • defined by author
  • 31.7 kDa, 1 polymers
Theoretical massNumber of molelcules
Total (without water)31,7382
Polymers31,6981
Non-polymers401
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
5
E: Calreticulin
hetero molecules


  • defined by author
  • 31.7 kDa, 1 polymers
Theoretical massNumber of molelcules
Total (without water)31,7382
Polymers31,6981
Non-polymers401
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
6
F: Calreticulin
hetero molecules


  • defined by author
  • 31.7 kDa, 1 polymers
Theoretical massNumber of molelcules
Total (without water)31,7382
Polymers31,6981
Non-polymers401
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
7
G: Calreticulin
hetero molecules


  • defined by author
  • 31.7 kDa, 1 polymers
Theoretical massNumber of molelcules
Total (without water)31,7382
Polymers31,6981
Non-polymers401
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
8
H: Calreticulin
hetero molecules


  • defined by author
  • 31.7 kDa, 1 polymers
Theoretical massNumber of molelcules
Total (without water)31,7382
Polymers31,6981
Non-polymers401
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)83.516, 154.074, 100.781
Angle α, β, γ (deg.)90.000, 108.320, 90.000
Int Tables number4
Space group name H-MP1211
Space group name HallP2yb
Symmetry operation#1: x,y,z
#2: -x,y+1/2,-z
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
d_1ens_1chain "A"
d_2ens_1chain "B"
d_3ens_1chain "C"
d_4ens_1chain "D"
d_5ens_1chain "E"
d_6ens_1chain "F"
d_7ens_1chain "G"
d_8ens_1chain "H"

NCS domain segments:

Component-ID: 1 / Ens-ID: ens_1 / Beg auth comp-ID: SER / Beg label comp-ID: SER / End auth comp-ID: ASP / End label comp-ID: ASP / Auth seq-ID: 21 - 363 / Label seq-ID: 22 - 272

Dom-IDAuth asym-IDLabel asym-ID
d_1AA
d_2BB
d_3CC
d_4DD
d_5EE
d_6FF
d_7GG
d_8HH

NCS oper:
IDCodeMatrixVector
1given(0.999986661292, 0.00288373475075, -0.00428501011204), (0.00501401505188, -0.342865688682, 0.93937105511), (0.00123971401239, -0.939380010219, -0.342875574386)11.3069928407, -69.7816174316, 4.90750700347
2given(0.679499269465, -0.484906788141, 0.550587095391), (0.427320585136, -0.348449557727, -0.834254171844), (0.596387340841, 0.802152300087, -0.0295605674757)-4.30071004416, -64.038616929, 18.1268672111
3given(0.67823245003, -0.481994389521, 0.55469104211), (-0.410803880319, 0.37717945469, 0.830045679993), (-0.609295425587, -0.790833147655, 0.0578101801481)-45.9594398749, -66.099339258, 8.77071929956
4given(-0.999994022538, -0.00216759320706, 0.00269377571843), (-0.0033251880113, 0.389371693308, -0.921074713351), (0.000947635278976, -0.921078164973, -0.389376573508)30.5932841812, 16.4583956029, -21.4642424172
5given(-0.680253111733, 0.48749656583, -0.547359847158), (0.714915745508, 0.606036308615, -0.348734095645), (0.161713267241, -0.628543626922, -0.760777055551)56.9260887083, -81.7405878316, -1.68463795081
6given(-0.999942975016, -0.0101624358009, 0.00328201396371), (0.00999890927307, -0.998868472535, -0.0464951221977), (0.00375080396916, -0.0464596542542, 0.99891312535)41.2591499396, -52.4498150559, 27.3762790927
7given(-0.671594178944, 0.487704252118, -0.55776860908), (-0.715853406525, -0.621271198889, 0.318709895984), (-0.191089401002, 0.613324269777, 0.766366870974)15.0578741814, -47.6742102563, 29.6454663425

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Components

#1: Protein
Calreticulin /


Mass: 31698.381 Da / Num. of mol.: 8
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Trichinella spiralis (invertebrata) / Strain: DH5a / Gene: CALR, T01_9409 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A0V1BA72
#2: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: Ca / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 397 / 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: 2.43 Å3/Da / Density % sol: 49.33 %
Crystal growTemperature: 291.15 K / Method: vapor diffusion, hanging drop
Details: 0.2 M ammonium acetate, 30% w/v polyethylene glycol 4000, 0.1 M sodium citrate tribasic dihydrate, pH 5.6

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL18U1 / Wavelength: 0.987 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Sep 25, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.987 Å / Relative weight: 1
ReflectionResolution: 2.76→81.28 Å / Num. obs: 60804 / % possible obs: 98.3 % / Redundancy: 6 % / Biso Wilson estimate: 34.88 Å2 / CC1/2: 0.983 / Rmerge(I) obs: 0.133 / Net I/σ(I): 9.4
Reflection shellResolution: 2.76→2.864 Å / Num. unique obs: 6140 / CC1/2: 0.983

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
XDSdata reduction
XDSdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.76→73.43 Å / SU ML: 0.3822 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 24.8254
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2427 2000 3.29 %
Rwork0.194 58766 -
obs0.1956 60766 98.25 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 33.09 Å2
Refinement stepCycle: LAST / Resolution: 2.76→73.43 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms16488 0 8 397 16893
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.011216920
X-RAY DIFFRACTIONf_angle_d1.585922880
X-RAY DIFFRACTIONf_chiral_restr0.10362336
X-RAY DIFFRACTIONf_plane_restr0.01932976
X-RAY DIFFRACTIONf_dihedral_angle_d9.39712176
Refine LS restraints NCS
Ens-IDDom-IDAsym-IDAuth asym-IDRefine-IDTypeRms dev position (Å)
ens_1d_2AAX-RAY DIFFRACTIONTorsion NCS0.729328491868
ens_1d_3AAX-RAY DIFFRACTIONTorsion NCS0.776082244263
ens_1d_4AAX-RAY DIFFRACTIONTorsion NCS0.83026986649
ens_1d_5AAX-RAY DIFFRACTIONTorsion NCS0.723481437501
ens_1d_6AAX-RAY DIFFRACTIONTorsion NCS0.799249387002
ens_1d_7AAX-RAY DIFFRACTIONTorsion NCS0.65636160792
ens_1d_8AAX-RAY DIFFRACTIONTorsion NCS0.83197911678
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.76-2.830.33031440.27384225X-RAY DIFFRACTION98.78
2.83-2.910.3351420.28154193X-RAY DIFFRACTION98.86
2.91-30.34251440.26744215X-RAY DIFFRACTION98.98
3-3.090.32871450.25054279X-RAY DIFFRACTION99.86
3.09-3.20.31211450.23864250X-RAY DIFFRACTION99.95
3.2-3.330.26411440.22224233X-RAY DIFFRACTION99.91
3.33-3.480.26891460.21074277X-RAY DIFFRACTION99.77
3.48-3.640.2771270.19733734X-RAY DIFFRACTION99.66
3.68-3.90.2191350.18313993X-RAY DIFFRACTION98.4
3.9-4.20.19631460.15974282X-RAY DIFFRACTION99.86
4.2-4.620.18181450.13984236X-RAY DIFFRACTION99.57
4.62-5.290.19061450.1494262X-RAY DIFFRACTION99.66
5.29-6.660.22141460.18114288X-RAY DIFFRACTION99.84
6.66-73.430.20411460.17584299X-RAY DIFFRACTION98.84

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