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

ID or keywords:

Entry

Database: PDB / ID: 5hca

Title

Globular Domain of the Entamoeba histolytica calreticulin in complex with glucose

Components

Calreticulin,Calreticulin

Keywords

SUGAR BINDING PROTEIN / chaperone / legume lectin domain

Function / homology

Function and homology information

symbiont-mediated suppression of host complement activation / complement component C1q complex binding / uropod / host cell surface binding / phagocytic cup / positive regulation of phagocytosis / protein export from nucleus / unfolded protein binding / protein folding / carbohydrate binding ...
Similarity search - Function

Biological species

Entamoeba histolytica HM-1:IMSS (eukaryote)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 2.15 Å

Authors

Moreau, C.P. / Gaboriaud, C.

Funding support

France, 1items

Citation

Journal: 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

Deposition	Jan 4, 2016	Deposition site: RCSB / Processing site: PDBE
Revision 1.0	Aug 31, 2016	Provider: repository / Type: Initial release
Revision 1.1	Nov 9, 2016	Group: Database references
Revision 1.2	Dec 21, 2016	Group: Database references
Revision 1.3	Sep 6, 2017	Group: Advisory / Author supporting evidence / Category: pdbx_audit_support / pdbx_unobs_or_zero_occ_atoms / Item: _pdbx_audit_support.funding_organization
Revision 1.4	Jun 12, 2019	Group: Data collection / Structure summary Category: audit_author / database_PDB_rev / database_PDB_rev_record Item: _audit_author.name
Revision 1.5	Jul 29, 2020	Group: 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
Revision 1.6	Nov 6, 2024	Group: Advisory / Data collection ...Advisory / Data collection / Database references / Derived calculations / Structure summary Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / pdbx_unobs_or_zero_occ_atoms / struct_sheet Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI ..._chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_sheet.number_strands

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	5hca.cif.gz	343.7 KB	Display	PDBx/mmCIF format
PDB format	pdb5hca.ent.gz	282 KB	Display	PDB format
PDBx/mmJSON format	5hca.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	5hca_validation.pdf.gz	489.8 KB	Display	wwPDB validaton report
Full document	5hca_full_validation.pdf.gz	497.9 KB	Display
Data in XML	5hca_validation.xml.gz	37 KB	Display
Data in CIF	5hca_validation.cif.gz	48.7 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/hc/5hca ftp://data.pdbj.org/pub/pdb/validation_reports/hc/5hca	HTTPS FTP

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Related structure data

Related structure data	5hcbC 5hcfC 5lk5C C: citing same article (ref.)
Similar structure data	2euo-d 4oq7-d 4nvn-d 4jmt-d 3m25-d 1cmu-d 6o9w-2 2p87-d 2ddr-2 3v2g-d Search similar-shape structures by Omokage search (details) Search similar-shape structures by Omokage search (details) Search similar-shape structures by Omokage search (details) Search similar-shape structures by Omokage search (details) Similarity search - Function & homologyF&H Search Similarity search - FunctionF&H Search Similarity search - HomologyF&H Search

Related structure data

5hcbC

5hcfC

5lk5C

C: citing same article (ref.)

Similar structure data

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Links

PDB pages	PDBj / wwPDB / NCBI
Related items in Molecule of the Month	#32 - Aug 2002 Chaperones similarity (1) #108 - Dec 2008 Hsp90 similarity (1) #110 - Feb 2009 Auxin and TIR1 Ubiquitin Ligase similarity (1) #135 - Mar 2011 Integrase similarity (1) #198 - Jun 2016 Beta-galactosidase similarity (1) #75 - Mar 2006 Tissue Factor similarity (1) #77 - May 2006 Glucose Oxidase similarity (1)

Deposited unit

C: Calreticulin,Calreticulin

A: Calreticulin,Calreticulin

B: Calreticulin,Calreticulin

hetero molecules

95.3 kDa, 3 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

C: Calreticulin,Calreticulin

hetero molecules

defined by author
31.6 kDa, 1 polymers
Search similar-shape structures of this assembly by Omokage search (details)

2

A: Calreticulin,Calreticulin

hetero molecules

defined by author
32 kDa, 1 polymers
Search similar-shape structures of this assembly by Omokage search (details)

3

B: Calreticulin,Calreticulin

hetero molecules

defined by author
31.7 kDa, 1 polymers
Search similar-shape structures of this assembly by Omokage search (details)

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 number	19
Space group name H-M	P2₁2₁2₁

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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 / beta-D-glucose / D-glucose / glucose

Type: D-saccharide, beta linking / Mass: 180.156 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Formula: C₆H₁₂O₆

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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 Mass: 96.063 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: SO₄
#4: Chemical	ChemComp-NH4 / AMMONIUM ION Mass: 18.038 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: H₄N
#5: Chemical	ChemComp-CL / CHLORIDE ION Mass: 35.453 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Formula: Cl
#6: Chemical	ChemComp-ACT / ACETATE ION Mass: 59.044 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Formula: C₂H₃O₂
#8: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 255 / Source method: isolated from a natural source / Formula: H₂O

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Details

Has protein modification	Y

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Experiment

Experiment	Method: X-RAY DIFFRACTION

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Sample preparation

Crystal	Density Matthews: 4.85 Å³/Da / Density % sol: 74.62 %
Crystal grow	Temperature: 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

Diffraction	Mean temperature: 100 K
Diffraction source	Source: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 0.97625 Å
Detector	Type: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Dec 7, 2014
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.97625 Å / Relative weight: 1
Reflection	Resolution: 2.14→43 Å / Num. obs: 96632 / % possible obs: 99.2 % / Redundancy: 16.07 % / Net I/σ(I): 13.4
Reflection shell	Resolution: 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

Name	Version	Classification
PHENIX	(1.10.1_2155: ???)	refinement
PHASER		phasing
Coot		model building
XDS		data reduction
XSCALE		data scaling

Refinement

Method 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

	R_factor	Num. reflection	% reflection
R_free	0.2213	4982	5 %
R_work	0.1933	-	-
obs	0.1947	99629	99.2 %

Solvent computation

Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL

Refinement step

Cycle: LAST / Resolution: 2.15→43.229 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	6409	0	47	255	6711

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.009	6697
X-RAY DIFFRACTION	f_angle_d	0.913	9041
X-RAY DIFFRACTION	f_dihedral_angle_d	16.024	4059
X-RAY DIFFRACTION	f_chiral_restr	0.064	939
X-RAY DIFFRACTION	f_plane_restr	0.005	1181

LS refinement shell

Resolution (Å)	R_factor R_free	Num. reflection R_free	R_factor R_work	Num. reflection R_work	Refine-ID	% reflection obs (%)
2.15-2.1744	0.3551	164	0.328	3129	X-RAY DIFFRACTION	100
2.1744-2.2	0.3397	166	0.3256	3137	X-RAY DIFFRACTION	99
2.2-2.2268	0.3234	162	0.2928	3088	X-RAY DIFFRACTION	99
2.2268-2.255	0.299	165	0.2837	3127	X-RAY DIFFRACTION	100
2.255-2.2847	0.3165	165	0.2651	3148	X-RAY DIFFRACTION	100
2.2847-2.316	0.2849	166	0.2534	3147	X-RAY DIFFRACTION	100
2.316-2.3491	0.2663	163	0.2387	3104	X-RAY DIFFRACTION	100
2.3491-2.3841	0.239	167	0.2362	3173	X-RAY DIFFRACTION	100
2.3841-2.4214	0.2605	165	0.2326	3129	X-RAY DIFFRACTION	100
2.4214-2.4611	0.2601	166	0.2343	3155	X-RAY DIFFRACTION	100
2.4611-2.5035	0.2533	165	0.2259	3131	X-RAY DIFFRACTION	100
2.5035-2.549	0.3027	167	0.2302	3168	X-RAY DIFFRACTION	100
2.549-2.5981	0.2638	165	0.223	3129	X-RAY DIFFRACTION	100
2.5981-2.6511	0.2692	166	0.2216	3162	X-RAY DIFFRACTION	99
2.6511-2.7087	0.2756	164	0.2134	3111	X-RAY DIFFRACTION	99
2.7087-2.7717	0.2008	165	0.2161	3142	X-RAY DIFFRACTION	99
2.7717-2.841	0.2447	167	0.2136	3169	X-RAY DIFFRACTION	100
2.841-2.9178	0.2515	165	0.2122	3142	X-RAY DIFFRACTION	100
2.9178-3.0037	0.2315	167	0.2174	3171	X-RAY DIFFRACTION	100
3.0037-3.1006	0.2256	168	0.2179	3182	X-RAY DIFFRACTION	100
3.1006-3.2114	0.2304	166	0.2168	3155	X-RAY DIFFRACTION	100
3.2114-3.3399	0.1972	166	0.2092	3164	X-RAY DIFFRACTION	100
3.3399-3.4918	0.1996	164	0.184	3121	X-RAY DIFFRACTION	98
3.4918-3.6758	0.2	167	0.1814	3167	X-RAY DIFFRACTION	99
3.6758-3.906	0.2148	168	0.1636	3184	X-RAY DIFFRACTION	99
3.906-4.2074	0.1762	166	0.1626	3164	X-RAY DIFFRACTION	99
4.2074-4.6303	0.1919	168	0.1468	3183	X-RAY DIFFRACTION	98
4.6303-5.2993	0.1878	163	0.143	3110	X-RAY DIFFRACTION	96
5.2993-6.6726	0.2082	171	0.1885	3240	X-RAY DIFFRACTION	99
6.6726-43.2373	0.2251	175	0.19	3315	X-RAY DIFFRACTION	97

Refinement TLS params.

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

ID	L11 (°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)
1	4.0496	0.1746	-0.6651	1.7688	-0.2888	2.6383	-0.0927	0.2469	-0.6034	0.3042	0.0698	0.2975	0.3671	-0.3291	0.0098	0.3982	-0.0365	0.0749	0.2801	-0.0547	0.3912	-27.4989	13.2636	-3.9821
2	6.6816	-2.4177	1.5523	3.8123	-1.8685	4.6075	-0.1534	-0.3843	-0.3072	0.7199	0.2153	0.4015	-0.0702	-0.099	-0.0436	0.4575	-0.0197	0.0721	0.2045	-0.0042	0.3394	-21.9552	19.4458	2.5163
3	7.499	-1.6064	0.2439	2.2343	-0.4297	1.5123	-0.0673	0.1694	0.1355	0.2051	0.0093	0.0297	-0.1425	-0.0646	0.0424	0.2942	-0.0219	0.0277	0.2027	-0.0242	0.2194	-15.2953	23.2073	-10.0247
4	4.0156	1.0942	5.4152	6.5585	1.8574	5.9093	-0.1698	-0.0848	0.1767	0.5741	-0.0038	-0.0416	-0.2875	0.0499	0.1404	0.3739	-0.0215	0.0435	0.36	0.0391	0.2922	-7.6436	28.4269	-6.4705
5	5.3774	-0.7655	-0.0868	1.27	-0.4058	2.5074	-0.1067	-0.0196	-0.3969	0.2841	0.0779	0.1046	0.2003	0.0329	0.0193	0.3568	0.014	0.0301	0.2052	-0.0359	0.2213	-16.6054	16.7323	-3.6539
6	8.1309	-5.2266	3.2573	10.8204	-4.2927	4.5385	-0.3139	1.2864	-0.3742	-0.1625	0.1582	1.0173	0.2993	-0.7704	-0.1018	0.4232	-0.1663	-0.0119	0.8222	-0.1008	0.432	-31.1566	15.3331	-22.473
7	2.1311	0.1468	-0.3336	3.2383	-0.098	1.8328	-0.0172	0.197	-0.1906	0.0064	0.0051	-0.5643	0.2118	0.425	0.0202	0.2828	0.0542	-0.0145	0.4668	-0.1047	0.3876	10.9832	10.8892	-23.251
8	2.2475	1.1939	-0.081	5.6444	1.8743	1.8345	-0.0068	0.3547	0.223	-0.1169	-0.0264	0.4378	-0.0898	-0.2943	0.0566	0.2627	0.0498	0.0113	0.4715	-0.0046	0.3526	1.5411	23.9446	-29.1686
9	6.4679	-5.7897	-0.741	5.9555	2.9549	4.1123	-0.596	-0.5559	-1.801	0.7946	-0.1574	0.8882	-0.0323	-0.8754	0.7011	0.5009	-0.0514	0.0437	0.5752	0.0392	0.6903	-1.6419	42.4932	-15.5556
10	1.3518	0.1854	-0.6331	4.2334	0.0776	2.67	-0.16	0.4199	-0.2464	-0.4139	0.0673	-0.0888	0.2181	0.1084	0.1122	0.2479	0.0692	-0.0002	0.4962	-0.0981	0.3452	7.4709	12.9234	-32.2214
11	2.2609	-0.2209	-0.3707	1.5878	-1.29	3.1216	0.0006	0.3474	0.734	0.0441	0.0627	0.0789	-0.5443	-0.138	-0.0844	0.573	-0.0046	-0.0802	0.2995	0.1252	0.5048	-6.7167	67.5556	-22.0112
12	2.7185	0.3348	-0.4112	1.8961	-0.9695	2.0392	-0.0671	0.1539	0.18	0.034	0.197	0.1643	0.0989	-0.2647	-0.1362	0.5082	-0.0016	-0.0647	0.3436	0.088	0.3456	-15.3014	54.9636	-18.2761
13	8.3011	5.2191	-8.8875	8.657	-5.3059	8.2717	-0.265	-0.4534	-0.0444	0.6682	-0.2724	-0.3078	-0.3258	0.3687	0.6649	0.4633	0.0216	-0.0858	0.3043	-0.0371	0.4587	-23.7203	40.2423	-9.8551
14	2.6121	0.1145	-1.4913	1.9873	-0.8496	2.0854	0.1557	0.2437	0.506	0.0272	0.1191	0.3389	-0.2317	-0.2603	-0.2547	0.4911	-0.0103	-0.0742	0.335	0.0827	0.3755	-17.0828	58.1891	-16.4541
15	6.9364	0.2509	-4.661	2.7262	-1.0477	7.0027	0.3298	0.8884	0.2709	-0.6343	-0.0188	0.1915	-0.1761	-0.5594	-0.2903	0.6536	-0.0798	-0.1145	0.7041	0.2038	0.4511	-14.3738	61.5128	-38.9194

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	chain 'C' and (resid 14 through 91 )
2	X-RAY DIFFRACTION	2	chain 'C' and (resid 92 through 123 )
3	X-RAY DIFFRACTION	3	chain 'C' and (resid 124 through 181 )
4	X-RAY DIFFRACTION	4	chain 'C' and (resid 182 through 293 )
5	X-RAY DIFFRACTION	5	chain 'C' and (resid 294 through 330 )
6	X-RAY DIFFRACTION	6	chain 'C' and (resid 331 through 360 )
7	X-RAY DIFFRACTION	7	chain 'A' and (resid 13 through 133 )
8	X-RAY DIFFRACTION	8	chain 'A' and (resid 134 through 192 )
9	X-RAY DIFFRACTION	9	chain 'A' and (resid 193 through 294 )
10	X-RAY DIFFRACTION	10	chain 'A' and (resid 295 through 360 )
11	X-RAY DIFFRACTION	11	chain 'B' and (resid 14 through 71 )
12	X-RAY DIFFRACTION	12	chain 'B' and (resid 72 through 181 )
13	X-RAY DIFFRACTION	13	chain 'B' and (resid 182 through 294 )
14	X-RAY DIFFRACTION	14	chain 'B' and (resid 295 through 330 )
15	X-RAY DIFFRACTION	15	chain 'B' and (resid 331 through 359 )

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Yorodumi