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- PDB-5hca: Globular Domain of the Entamoeba histolytica calreticulin in comp... -

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Basic information

Entry
Database: PDB / ID: 5hca
TitleGlobular Domain of the Entamoeba histolytica calreticulin in complex with glucose
ComponentsCalreticulin,Calreticulin
KeywordsSUGAR BINDING PROTEIN / chaperone / legume lectin domain
Function / homology
Function and homology information


symbiont-mediated suppression of host complement activation / complement component C1q complex binding / host cell surface binding / uropod / phagocytic cup / positive regulation of phagocytosis / protein export from nucleus / carbohydrate binding / endoplasmic reticulum lumen / cell surface ...symbiont-mediated suppression of host complement activation / complement component C1q complex binding / host cell surface binding / uropod / phagocytic cup / positive regulation of phagocytosis / protein export from nucleus / carbohydrate binding / endoplasmic reticulum lumen / cell surface / endoplasmic reticulum / metal ion binding / cytosol
Similarity search - Function
Calreticulin / Calreticulin/calnexin / Calreticulin/calnexin, P domain superfamily / Calreticulin/calnexin, conserved site / Calreticulin family / Calreticulin family signature 1. / Calreticulin family signature 2. / Endoplasmic reticulum targeting sequence. / Jelly Rolls - #200 / Concanavalin A-like lectin/glucanase domain superfamily ...Calreticulin / Calreticulin/calnexin / Calreticulin/calnexin, P domain superfamily / Calreticulin/calnexin, conserved site / Calreticulin family / Calreticulin family signature 1. / Calreticulin family signature 2. / Endoplasmic reticulum targeting sequence. / Jelly Rolls - #200 / Concanavalin A-like lectin/glucanase domain superfamily / Jelly Rolls / Sandwich / Mainly Beta
Similarity search - Domain/homology
ACETATE ION / beta-D-glucopyranose / AMMONIUM ION / Calreticulin
Similarity search - Component
Biological speciesEntamoeba histolytica HM-1:IMSS (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.15 Å
AuthorsMoreau, C.P. / Gaboriaud, C.
Funding support France, 1items
OrganizationGrant numberCountry
French National Research Agency09-PIRI-0021 France
CitationJournal: IUCrJ / Year: 2016
Title: Structures of parasite calreticulins provide insights into their flexibility and dual carbohydrate/peptide-binding properties.
Authors: Moreau, C. / Cioci, G. / Iannello, M. / Laffly, E. / Chouquet, A. / Ferreira, A. / Thielens, N.M. / Gaboriaud, C.
History
DepositionJan 4, 2016Deposition site: RCSB / Processing site: PDBE
Revision 1.0Aug 31, 2016Provider: repository / Type: Initial release
Revision 1.1Nov 9, 2016Group: Database references
Revision 1.2Dec 21, 2016Group: Database references
Revision 1.3Sep 6, 2017Group: Advisory / Author supporting evidence / Category: pdbx_audit_support / pdbx_unobs_or_zero_occ_atoms / Item: _pdbx_audit_support.funding_organization
Revision 1.4Jun 12, 2019Group: Data collection / Structure summary
Category: audit_author / database_PDB_rev / database_PDB_rev_record
Item: _audit_author.name
Revision 1.5Jul 29, 2020Group: Data collection / Derived calculations / Structure summary
Category: chem_comp / entity ...chem_comp / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / struct_conn / struct_site / struct_site_gen
Item: _chem_comp.name / _chem_comp.type ..._chem_comp.name / _chem_comp.type / _entity.pdbx_description / _pdbx_entity_nonpoly.name / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id
Description: Carbohydrate remediation / Provider: repository / Type: Remediation

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
C: Calreticulin,Calreticulin
A: Calreticulin,Calreticulin
B: Calreticulin,Calreticulin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)95,34216
Polymers94,4143
Non-polymers92913
Water4,594255
1
C: Calreticulin,Calreticulin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,6073
Polymers31,4711
Non-polymers1362
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: Calreticulin,Calreticulin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,9968
Polymers31,4711
Non-polymers5257
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
B: Calreticulin,Calreticulin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,7395
Polymers31,4711
Non-polymers2684
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)74.360, 143.440, 171.590
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

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Protein / Sugars , 2 types, 4 molecules CAB

#1: Protein Calreticulin,Calreticulin


Mass: 31471.197 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Entamoeba histolytica HM-1:IMSS (eukaryote)
Plasmid: pJexpress411 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: F2VN92
#7: Sugar ChemComp-BGC / beta-D-glucopyranose / Glucose


Type: D-saccharide, beta linking / Mass: 180.156 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Formula: C6H12O6
IdentifierTypeProgram
DGlcpbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
b-D-glucopyranoseCOMMON NAMEGMML 1.0
b-D-GlcpIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcSNFG CARBOHYDRATE SYMBOLGMML 1.0

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Non-polymers , 6 types, 267 molecules

#2: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Ca
#3: Chemical
ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: SO4
#4: Chemical ChemComp-NH4 / AMMONIUM ION / Ammonium


Mass: 18.038 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: H4N
#5: Chemical ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Formula: Cl
#6: Chemical ChemComp-ACT / ACETATE ION / Acetate


Mass: 59.044 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Formula: C2H3O2
#8: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 255 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 4.85 Å3/Da / Density % sol: 74.62 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5 / Details: 2.6 M ammonium sulfate, 0.1 M Tri-sodium citrate

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 0.97625 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Dec 7, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97625 Å / Relative weight: 1
ReflectionResolution: 2.14→43 Å / Num. obs: 96632 / % possible obs: 99.2 % / Redundancy: 16.07 % / Net I/σ(I): 13.4
Reflection shellResolution: 2.15→2.2 Å / Redundancy: 3.48 % / Mean I/σ(I) obs: 1.57 / % possible all: 99.1

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Processing

Software
NameVersionClassification
PHENIX(1.10.1_2155: ???)refinement
PHASERphasing
Cootmodel building
XDSdata reduction
XSCALEdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.15→43.229 Å / SU ML: 0.28 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 21.89 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2213 4982 5 %
Rwork0.1933 --
obs0.1947 99629 99.2 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.15→43.229 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6409 0 47 255 6711
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0096697
X-RAY DIFFRACTIONf_angle_d0.9139041
X-RAY DIFFRACTIONf_dihedral_angle_d16.0244059
X-RAY DIFFRACTIONf_chiral_restr0.064939
X-RAY DIFFRACTIONf_plane_restr0.0051181
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.15-2.17440.35511640.3283129X-RAY DIFFRACTION100
2.1744-2.20.33971660.32563137X-RAY DIFFRACTION99
2.2-2.22680.32341620.29283088X-RAY DIFFRACTION99
2.2268-2.2550.2991650.28373127X-RAY DIFFRACTION100
2.255-2.28470.31651650.26513148X-RAY DIFFRACTION100
2.2847-2.3160.28491660.25343147X-RAY DIFFRACTION100
2.316-2.34910.26631630.23873104X-RAY DIFFRACTION100
2.3491-2.38410.2391670.23623173X-RAY DIFFRACTION100
2.3841-2.42140.26051650.23263129X-RAY DIFFRACTION100
2.4214-2.46110.26011660.23433155X-RAY DIFFRACTION100
2.4611-2.50350.25331650.22593131X-RAY DIFFRACTION100
2.5035-2.5490.30271670.23023168X-RAY DIFFRACTION100
2.549-2.59810.26381650.2233129X-RAY DIFFRACTION100
2.5981-2.65110.26921660.22163162X-RAY DIFFRACTION99
2.6511-2.70870.27561640.21343111X-RAY DIFFRACTION99
2.7087-2.77170.20081650.21613142X-RAY DIFFRACTION99
2.7717-2.8410.24471670.21363169X-RAY DIFFRACTION100
2.841-2.91780.25151650.21223142X-RAY DIFFRACTION100
2.9178-3.00370.23151670.21743171X-RAY DIFFRACTION100
3.0037-3.10060.22561680.21793182X-RAY DIFFRACTION100
3.1006-3.21140.23041660.21683155X-RAY DIFFRACTION100
3.2114-3.33990.19721660.20923164X-RAY DIFFRACTION100
3.3399-3.49180.19961640.1843121X-RAY DIFFRACTION98
3.4918-3.67580.21670.18143167X-RAY DIFFRACTION99
3.6758-3.9060.21481680.16363184X-RAY DIFFRACTION99
3.906-4.20740.17621660.16263164X-RAY DIFFRACTION99
4.2074-4.63030.19191680.14683183X-RAY DIFFRACTION98
4.6303-5.29930.18781630.1433110X-RAY DIFFRACTION96
5.2993-6.67260.20821710.18853240X-RAY DIFFRACTION99
6.6726-43.23730.22511750.193315X-RAY DIFFRACTION97
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
14.04960.1746-0.66511.7688-0.28882.6383-0.09270.2469-0.60340.30420.06980.29750.3671-0.32910.00980.3982-0.03650.07490.2801-0.05470.3912-27.498913.2636-3.9821
26.6816-2.41771.55233.8123-1.86854.6075-0.1534-0.3843-0.30720.71990.21530.4015-0.0702-0.099-0.04360.4575-0.01970.07210.2045-0.00420.3394-21.955219.44582.5163
37.499-1.60640.24392.2343-0.42971.5123-0.06730.16940.13550.20510.00930.0297-0.1425-0.06460.04240.2942-0.02190.02770.2027-0.02420.2194-15.295323.2073-10.0247
44.01561.09425.41526.55851.85745.9093-0.1698-0.08480.17670.5741-0.0038-0.0416-0.28750.04990.14040.3739-0.02150.04350.360.03910.2922-7.643628.4269-6.4705
55.3774-0.7655-0.08681.27-0.40582.5074-0.1067-0.0196-0.39690.28410.07790.10460.20030.03290.01930.35680.0140.03010.2052-0.03590.2213-16.605416.7323-3.6539
68.1309-5.22663.257310.8204-4.29274.5385-0.31391.2864-0.3742-0.16250.15821.01730.2993-0.7704-0.10180.4232-0.1663-0.01190.8222-0.10080.432-31.156615.3331-22.473
72.13110.1468-0.33363.2383-0.0981.8328-0.01720.197-0.19060.00640.0051-0.56430.21180.4250.02020.28280.0542-0.01450.4668-0.10470.387610.983210.8892-23.251
82.24751.1939-0.0815.64441.87431.8345-0.00680.35470.223-0.1169-0.02640.4378-0.0898-0.29430.05660.26270.04980.01130.4715-0.00460.35261.541123.9446-29.1686
96.4679-5.7897-0.7415.95552.95494.1123-0.596-0.5559-1.8010.7946-0.15740.8882-0.0323-0.87540.70110.5009-0.05140.04370.57520.03920.6903-1.641942.4932-15.5556
101.35180.1854-0.63314.23340.07762.67-0.160.4199-0.2464-0.41390.0673-0.08880.21810.10840.11220.24790.0692-0.00020.4962-0.09810.34527.470912.9234-32.2214
112.2609-0.2209-0.37071.5878-1.293.12160.00060.34740.7340.04410.06270.0789-0.5443-0.138-0.08440.573-0.0046-0.08020.29950.12520.5048-6.716767.5556-22.0112
122.71850.3348-0.41121.8961-0.96952.0392-0.06710.15390.180.0340.1970.16430.0989-0.2647-0.13620.5082-0.0016-0.06470.34360.0880.3456-15.301454.9636-18.2761
138.30115.2191-8.88758.657-5.30598.2717-0.265-0.4534-0.04440.6682-0.2724-0.3078-0.32580.36870.66490.46330.0216-0.08580.3043-0.03710.4587-23.720340.2423-9.8551
142.61210.1145-1.49131.9873-0.84962.08540.15570.24370.5060.02720.11910.3389-0.2317-0.2603-0.25470.4911-0.0103-0.07420.3350.08270.3755-17.082858.1891-16.4541
156.93640.2509-4.6612.7262-1.04777.00270.32980.88840.2709-0.6343-0.01880.1915-0.1761-0.5594-0.29030.6536-0.0798-0.11450.70410.20380.4511-14.373861.5128-38.9194
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'C' and (resid 14 through 91 )
2X-RAY DIFFRACTION2chain 'C' and (resid 92 through 123 )
3X-RAY DIFFRACTION3chain 'C' and (resid 124 through 181 )
4X-RAY DIFFRACTION4chain 'C' and (resid 182 through 293 )
5X-RAY DIFFRACTION5chain 'C' and (resid 294 through 330 )
6X-RAY DIFFRACTION6chain 'C' and (resid 331 through 360 )
7X-RAY DIFFRACTION7chain 'A' and (resid 13 through 133 )
8X-RAY DIFFRACTION8chain 'A' and (resid 134 through 192 )
9X-RAY DIFFRACTION9chain 'A' and (resid 193 through 294 )
10X-RAY DIFFRACTION10chain 'A' and (resid 295 through 360 )
11X-RAY DIFFRACTION11chain 'B' and (resid 14 through 71 )
12X-RAY DIFFRACTION12chain 'B' and (resid 72 through 181 )
13X-RAY DIFFRACTION13chain 'B' and (resid 182 through 294 )
14X-RAY DIFFRACTION14chain 'B' and (resid 295 through 330 )
15X-RAY DIFFRACTION15chain 'B' and (resid 331 through 359 )

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