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- PDB-2ccv: Structure of Helix Pomatia agglutinin with zinc and N-acetyl-alph... -

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Basic information

Entry
Database: PDB / ID: 2ccv
TitleStructure of Helix Pomatia agglutinin with zinc and N-acetyl-alpha-D- galactoseamine (GalNAc)
ComponentsHELIX POMATIA AGGLUTININ
KeywordsLECTIN / SNAIL / HELIX POMATIA
Function / homology
Function and homology information


carbohydrate binding / cell adhesion / metal ion binding
Similarity search - Function
Immunoglobulin-like - #2080 / H-type lectin domain / H-type lectin domain superfamily / H-type lectin domain / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
2-acetamido-2-deoxy-alpha-D-galactopyranose / ACETATE ION / Agglutinin
Similarity search - Component
Biological speciesHELIX POMATIA (Roman snail)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.3 Å
AuthorsSanchez, J.-F. / Lescar, J. / Chazalet, V. / Audfray, A. / Gautier, C. / Gagnon, J. / Breton, C. / Imberty, A. / Mitchell, E.P.
CitationJournal: J.Biol.Chem. / Year: 2006
Title: Biochemical and Structural Analysis of Helix Pomatia Agglutinin. A Hexameric Lectin with a Novel Fold.
Authors: Sanchez, J.-F. / Lescar, J. / Chazalet, V. / Audfray, A. / Gagnon, J. / Alvarez, R. / Breton, C. / Imberty, A. / Mitchell, E.P.
History
DepositionJan 18, 2006Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 15, 2006Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3May 8, 2019Group: Data collection / Derived calculations ...Data collection / Derived calculations / Experimental preparation / Other
Category: database_PDB_rev / database_PDB_rev_record ...database_PDB_rev / database_PDB_rev_record / exptl_crystal_grow / pdbx_database_proc / pdbx_database_status / struct_conn
Item: _exptl_crystal_grow.method / _pdbx_database_status.recvd_author_approval / _struct_conn.pdbx_leaving_atom_flag
Revision 1.4May 22, 2019Group: Data collection / Refinement description / Category: refine / Item: _refine.pdbx_ls_cross_valid_method
Revision 2.0Jul 29, 2020Group: Atomic model / Data collection ...Atomic model / Data collection / Derived calculations / Other / Structure summary
Category: atom_site / atom_site_anisotrop ...atom_site / atom_site_anisotrop / chem_comp / entity / pdbx_chem_comp_identifier / pdbx_database_status / pdbx_entity_nonpoly / pdbx_struct_conn_angle / struct_conn / struct_site / struct_site_gen
Item: _atom_site.auth_atom_id / _atom_site.label_atom_id ..._atom_site.auth_atom_id / _atom_site.label_atom_id / _atom_site_anisotrop.pdbx_auth_atom_id / _atom_site_anisotrop.pdbx_label_atom_id / _chem_comp.name / _chem_comp.type / _entity.pdbx_description / _pdbx_database_status.status_code_sf / _pdbx_entity_nonpoly.name / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_alt_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr1_symmetry / _pdbx_struct_conn_angle.ptnr2_symmetry / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_alt_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.ptnr3_symmetry / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_ptnr2_label_alt_id / _struct_conn.pdbx_role / _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.ptnr1_symmetry / _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 / _struct_conn.ptnr2_label_seq_id / _struct_conn.ptnr2_symmetry
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Remark 650 HELIX DETERMINATION METHOD: AUTHOR PROVIDED.
Remark 700 SHEET DETERMINATION METHOD: AUTHOR PROVIDED.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: HELIX POMATIA AGGLUTININ
hetero molecules


Theoretical massNumber of molelcules
Total (without water)11,9866
Polymers11,3271
Non-polymers6595
Water1,78399
1
A: HELIX POMATIA AGGLUTININ
hetero molecules
x 6


Theoretical massNumber of molelcules
Total (without water)71,91436
Polymers67,9606
Non-polymers3,95430
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-y,x-y,z1
crystal symmetry operation3_555-x+y,-x,z1
crystal symmetry operation5_556x-y,-y,-z+11
crystal symmetry operation4_556y,x,-z+11
crystal symmetry operation6_556-x,-x+y,-z+11
MethodPQS
Unit cell
Length a, b, c (Å)48.450, 48.450, 286.120
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number155
Space group name H-MH32
Components on special symmetry positions
IDModelComponents
11A-1100-

ZN

21A-2030-

HOH

31A-2032-

HOH

41A-2072-

HOH

51A-2074-

HOH

61A-2075-

HOH

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Components

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Protein , 1 types, 1 molecules A

#1: Protein HELIX POMATIA AGGLUTININ


Mass: 11326.722 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: GLYCOLYSIS SITE AT N34 WITH GLUCOSEAMINE BOUND / Source: (natural) HELIX POMATIA (Roman snail) / Organ: ALBUMIN GLAND / References: UniProt: Q2F1K8

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Sugars , 2 types, 2 molecules

#3: Sugar ChemComp-A2G / 2-acetamido-2-deoxy-alpha-D-galactopyranose / N-Acetylgalactosamine


Type: D-saccharide, alpha linking / Mass: 221.208 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Formula: C8H15NO6
IdentifierTypeProgram
DGalpNAcaCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
N-acetyl-a-D-galactopyranosamineCOMMON NAMEGMML 1.0
a-D-GalpNAcIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GalNAcSNFG CARBOHYDRATE SYMBOLGMML 1.0
#6: Sugar ChemComp-NAG / 2-acetamido-2-deoxy-beta-D-glucopyranose / N-Acetylglucosamine


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Formula: C8H15NO6
IdentifierTypeProgram
DGlcpNAcbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
N-acetyl-b-D-glucopyranosamineCOMMON NAMEGMML 1.0
b-D-GlcpNAcIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcNAcSNFG CARBOHYDRATE SYMBOLGMML 1.0

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Non-polymers , 4 types, 102 molecules

#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#5: Chemical ChemComp-ACT / ACETATE ION / Acetate


Mass: 59.044 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H3O2
#7: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 99 / Source method: isolated from a natural source / Formula: H2O

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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: 2.9 Å3/Da / Density % sol: 57 %
Description: HYSS WAS USED TO DETERMINE THE POSITION OF THE ZINC ION AND THEN PHASES WERE GROWN USING ACORN AND ALL DATA TO 1.15A. THE DATA SET WAS SUBSEQUENTLY CUT TO 1.3A FOR REFINEMENT OF THE STRUCTURE.
Crystal growMethod: vapor diffusion, hanging drop
Details: HANGING DROP METHOD WITH PRECIPITATION SOLUTION CONTAINING LITHIUM SULPHATE (2 M) AND AMMONIUM SULPHATE (3.5 M) IN SODIUM CITRATE BUFFER (1.5 M, PH 6.5)

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-2 / Wavelength: 0.933
DetectorType: ADSC CCD / Detector: CCD / Date: Oct 20, 2004 / Details: TOROIDAL MIRROR
RadiationMonochromator: DIAMOND / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.933 Å / Relative weight: 1
ReflectionResolution: 1.3→11.2 Å / Num. obs: 32736 / % possible obs: 99.8 % / Redundancy: 7.44 % / Rmerge(I) obs: 0.05 / Net I/σ(I): 22.4
Reflection shellResolution: 1.3→1.33 Å / Redundancy: 5.25 % / Rmerge(I) obs: 0.31 / Mean I/σ(I) obs: 4.27 / % possible all: 100

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Processing

Software
NameClassification
SHELXL-97refinement
MOSFLMdata reduction
SCALAdata scaling
HYSSphasing
RefinementMethod to determine structure: SAD / Resolution: 1.3→40 Å / Num. parameters: 8627 / Num. restraintsaints: 11315 / Cross valid method: FREE R-VALUE / σ(F): 0 / Stereochemistry target values: ENGH AND HUBER
Details: THE ASN34 GLYCOLYSATION SITE HAS SOME WEAK DENSITY FOR THE FIRST GLCNAC RESIDUE OF THE SUGAR BUT NO FURTHER. THE FIRST SUGAR WAS THEREFORE MODELLED TO GIVE AN INDICATION OF THE LOCATION.
RfactorNum. reflection% reflectionSelection details
Rfree0.179 1643 5 %RANDOM
obs0.1443 -94.7 %-
all-30995 --
Refine analyzeNum. disordered residues: 7 / Occupancy sum hydrogen: 754 / Occupancy sum non hydrogen: 898.48
Refinement stepCycle: LAST / Resolution: 1.3→40 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms771 0 40 99 910
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONs_bond_d0.013
X-RAY DIFFRACTIONs_angle_d0.032
X-RAY DIFFRACTIONs_similar_dist0
X-RAY DIFFRACTIONs_from_restr_planes0.0325
X-RAY DIFFRACTIONs_zero_chiral_vol0.081
X-RAY DIFFRACTIONs_non_zero_chiral_vol0.086
X-RAY DIFFRACTIONs_anti_bump_dis_restr0.054
X-RAY DIFFRACTIONs_rigid_bond_adp_cmpnt0.005
X-RAY DIFFRACTIONs_similar_adp_cmpnt0.057
X-RAY DIFFRACTIONs_approx_iso_adps0.115

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