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- PDB-8a9m: Hippeastrum hybrid agglutinin, HHA, complex with beta-mannose -

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Basic information

Entry
Database: PDB / ID: 8a9m
TitleHippeastrum hybrid agglutinin, HHA, complex with beta-mannose
ComponentsAgglutinin
KeywordsSUGAR BINDING PROTEIN / Agglutinin / mannose / lectin / hippeastrum hybrid
Function / homologyBulb-type lectin domain / Bulb-type lectin domain superfamily / Bulb-type lectin domain profile. / Bulb-type mannose-specific lectin / beta-D-mannopyranose / PHOSPHATE ION / Agglutinin
Function and homology information
Biological speciesHippeastrum hybrid cultivar (plant)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.2 Å
AuthorsRizkallah, P.J.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: Acta Crystallogr D Biol Crystallogr / Year: 1996
Title: X-ray structure solution of amaryllis lectin by molecular replacement with only 4% of the total diffracting matter.
Authors: Chantalat, L. / Wood, S.D. / Rizkallah, P. / Reynolds, C.D.
History
DepositionJun 28, 2022Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 5, 2022Provider: repository / Type: Initial release
Revision 1.1Jan 31, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model / struct_ncs_dom_lim
Item: _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id ..._struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Agglutinin
B: Agglutinin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,4719
Polymers23,6362
Non-polymers8357
Water82946
1
A: Agglutinin
hetero molecules

A: Agglutinin
hetero molecules

B: Agglutinin
hetero molecules

B: Agglutinin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,94218
Polymers47,2724
Non-polymers1,67014
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_655-x+1,y,-z1
crystal symmetry operation3_555x+1/2,y+1/2,z1
crystal symmetry operation4_555-x+1/2,y+1/2,-z1
Buried area12070 Å2
ΔGint-112 kcal/mol
Surface area16280 Å2
MethodPISA
Unit cell
Length a, b, c (Å)73.370, 100.318, 62.177
Angle α, β, γ (deg.)90.000, 137.270, 90.000
Int Tables number5
Space group name H-MC121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B

NCS domain segments:

Component-ID: 0 / Ens-ID: 1 / Beg auth comp-ID: ASP / Beg label comp-ID: ASP / End auth comp-ID: ILE / End label comp-ID: ILE / Refine code: 0 / Auth seq-ID: 1 - 107 / Label seq-ID: 1 - 108

Dom-IDAuth asym-IDLabel asym-ID
1AA
2BB

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Components

#1: Protein Agglutinin /


Mass: 11818.026 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Hippeastrum hybrid cultivar (plant) / References: UniProt: Q7Y041
#2: Sugar ChemComp-BMA / beta-D-mannopyranose / beta-D-mannose / D-mannose / mannose / Mannose


Type: D-saccharide, beta linking / Mass: 180.156 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H12O6
IdentifierTypeProgram
DManpbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
b-D-mannopyranoseCOMMON NAMEGMML 1.0
b-D-ManpIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
ManSNFG CARBOHYDRATE SYMBOLGMML 1.0
#3: Chemical
ChemComp-PO4 / PHOSPHATE ION / Phosphate


Mass: 94.971 Da / Num. of mol.: 5 / Source method: isolated from a natural source / Formula: PO4
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 46 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 3.29 Å3/Da / Density % sol: 62.6 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / Details: 50mM PBS, 2M Ammonium sulphate / PH range: 5.0 - 8.0

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Data collection

DiffractionMean temperature: 293 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SRS / Beamline: PX9.6 / Wavelength: 0.8975 Å
DetectorType: MAR scanner 300 mm plate / Detector: IMAGE PLATE / Date: Apr 30, 1993
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.8975 Å / Relative weight: 1
ReflectionResolution: 2.2→23.82 Å / Num. obs: 15296 / % possible obs: 98.5 % / Redundancy: 4.9 % / CC1/2: 0.986 / Rmerge(I) obs: 0.133 / Rpim(I) all: 0.063 / Rrim(I) all: 0.148 / Net I/σ(I): 8.2
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. measured allNum. unique obsCC1/2Rpim(I) allRrim(I) allNet I/σ(I) obs% possible all
2.2-2.274.70.389632913350.8960.1910.4363.899.5
9.07-23.814.20.0988482040.9260.0590.11613.889.1

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Phasing

PhasingMethod: molecular replacement
Phasing MRModel details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation2.98 Å23.81 Å
Translation2.98 Å23.81 Å

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Processing

Software
NameVersionClassificationNB
REFMAC5.8.0267refinement
MOSFLMdata reduction
Aimless0.7.7data scaling
PHASER2.8.3phasing
PDB_EXTRACT3.27data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1MSA

1msa


Resolution: 2.2→23.82 Å / Cor.coef. Fo:Fc: 0.964 / Cor.coef. Fo:Fc free: 0.922 / SU B: 10.791 / SU ML: 0.128 / SU R Cruickshank DPI: 0.1866 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.187 / ESU R Free: 0.174 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.2191 765 5 %RANDOM
Rwork0.1665 ---
obs0.1691 14531 98.3 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 96.2 Å2 / Biso mean: 39.862 Å2 / Biso min: 27.9 Å2
Baniso -1Baniso -2Baniso -3
1--0.45 Å20 Å21.3 Å2
2---5.34 Å20 Å2
3---0.89 Å2
Refinement stepCycle: final / Resolution: 2.2→23.82 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1658 0 49 46 1753
Biso mean--48.8 47.12 -
Num. residues----216
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0131802
X-RAY DIFFRACTIONr_bond_other_d0.0010.0151592
X-RAY DIFFRACTIONr_angle_refined_deg1.4741.6522470
X-RAY DIFFRACTIONr_angle_other_deg1.2181.5973658
X-RAY DIFFRACTIONr_dihedral_angle_1_deg8.6015226
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.67424.04394
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.38615270
X-RAY DIFFRACTIONr_dihedral_angle_4_deg11.191158
X-RAY DIFFRACTIONr_chiral_restr0.0550.2236
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.022116
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02436
Refine LS restraints NCS

Ens-ID: 1 / Number: 3288 / Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Rms dev position: 0.08 Å / Weight position: 0.05

Dom-IDAuth asym-ID
1A
2B
LS refinement shellResolution: 2.2→2.256 Å / Rfactor Rfree error: 0
RfactorNum. reflection% reflection
Rfree0.321 53 -
Rwork0.222 1070 -
obs--99.38 %
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)
13.5305-0.6243-0.3121.64650.06941.1570.0695-0.3123-0.07620.1455-0.11350.13420.0609-0.00310.04390.0243-0.02870.02130.0513-0.01780.036526.316437.83535.7948
23.5036-0.64530.60231.7585-0.15071.09990.0049-0.27510.12240.1857-0.1033-0.1218-0.0583-0.00320.09840.0247-0.0189-0.00990.0410.0170.077910.309715.82365.8998
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 109
2X-RAY DIFFRACTION2B1 - 109

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