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- PDB-4p9y: Structure of ConA/Rh4man -

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Basic information

Entry
Database: PDB / ID: 4p9y
TitleStructure of ConA/Rh4man
ComponentsConcanavalin-A
KeywordsSUGAR BINDING PROTEIN / lectin / Mannose
Function / homology
Function and homology information


regulation of defense response to virus / D-mannose binding / defense response / metal ion binding
Similarity search - Function
Legume lectin / Legume lectin, alpha chain, conserved site / Legume lectins alpha-chain signature. / Legume lectins beta-chain signature. / Legume lectin domain / Legume lectin, beta chain, Mn/Ca-binding site / Legume lectin domain / Jelly Rolls - #200 / Concanavalin A-like lectin/glucanase domain superfamily / Jelly Rolls ...Legume lectin / Legume lectin, alpha chain, conserved site / Legume lectins alpha-chain signature. / Legume lectins beta-chain signature. / Legume lectin domain / Legume lectin, beta chain, Mn/Ca-binding site / Legume lectin domain / Jelly Rolls - #200 / Concanavalin A-like lectin/glucanase domain superfamily / Jelly Rolls / Sandwich / Mainly Beta
Similarity search - Domain/homology
Chem-2KO / : / Concanavalin-A
Similarity search - Component
Biological speciesCanavalia ensiformis (jack bean)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.89 Å
AuthorsSakai, F. / Weiss, M.S. / Chen, G.
CitationJournal: To Be Published
Title: Structure of ConA/Rh4Man
Authors: Sakai, F. / Weiss, M.S. / Chen, G.
History
DepositionApr 6, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 27, 2014Provider: repository / Type: Initial release
Revision 1.1Nov 22, 2017Group: Advisory / Database references ...Advisory / Database references / Derived calculations / Other / Refinement description / Source and taxonomy
Category: citation / entity_src_nat ...citation / entity_src_nat / pdbx_database_status / pdbx_struct_assembly / pdbx_struct_conn_angle / pdbx_struct_oper_list / pdbx_validate_close_contact / software
Item: _citation.journal_id_CSD / _entity_src_nat.pdbx_alt_source_flag ..._citation.journal_id_CSD / _entity_src_nat.pdbx_alt_source_flag / _pdbx_database_status.pdb_format_compatible / _pdbx_struct_assembly.oligomeric_details / _pdbx_struct_oper_list.symmetry_operation
Revision 1.2Dec 27, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_conn_angle / refine_hist / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.value / _refine_hist.number_atoms_total / _refine_hist.pdbx_number_atoms_nucleic_acid / _refine_hist.pdbx_number_atoms_protein / _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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Concanavalin-A
B: Concanavalin-A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)53,1638
Polymers51,2452
Non-polymers1,9186
Water1,58588
1
A: Concanavalin-A
B: Concanavalin-A
hetero molecules

A: Concanavalin-A
B: Concanavalin-A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)106,32616
Polymers102,4904
Non-polymers3,83612
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,-y,z1
Buried area10230 Å2
ΔGint-120 kcal/mol
Surface area34000 Å2
MethodPISA
Unit cell
Length a, b, c (Å)61.600, 116.110, 58.690
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP21212
Components on special symmetry positions
IDModelComponents
11A-402-

HOH

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Components

#1: Protein Concanavalin-A / Con A


Mass: 25622.385 Da / Num. of mol.: 2 / Fragment: UNP residues 164-281, 30-148
Source method: isolated from a genetically manipulated source
Source: (natural) Canavalia ensiformis (jack bean) / References: UniProt: P02866
#2: Chemical ChemComp-2KO / 2-{2-[2-(2-{4-[(alpha-D-mannopyranosyloxy)methyl]-1H-1,2,3-triazol-1-yl}ethoxy)ethoxy]ethoxy}ethyl 2-[3,6-bis(diethylamino)-9H-xanthen-9-yl]benzoate


Mass: 863.992 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C45H61N5O12
#3: Chemical ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mn
#4: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ca
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 88 / 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: 2.05 Å3/Da / Density % sol: 39.94 %
Crystal growTemperature: 298 K / Method: liquid diffusion / pH: 7.2
Details: buffer: 20 mM HEPES, 5 mM of CaCl2, and 5 mM of MnCl2; pH = 7.2. The crystal was obtained by diffusion method in glass tube sequentially put with ConA solution, pure buffer, and the ligand solution.

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.1 / Wavelength: 0.918 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jul 9, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.918 Å / Relative weight: 1
ReflectionResolution: 1.89→39.9 Å / Num. obs: 34408 / % possible obs: 99.9 % / Redundancy: 6.68 % / Net I/σ(I): 46.74

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
MOLREP11.0.05phasing
PDB_EXTRACT3.14data extraction
REFMAC5.7.0029refinement
Cootmodel building
XDSdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.89→30 Å / Cor.coef. Fo:Fc: 0.957 / Cor.coef. Fo:Fc free: 0.918 / WRfactor Rfree: 0.2366 / WRfactor Rwork: 0.1795 / FOM work R set: 0.8144 / SU B: 9.259 / SU ML: 0.129 / SU R Cruickshank DPI: 0.1776 / SU Rfree: 0.1675 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.178 / ESU R Free: 0.168 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: U VALUES : RESIDUAL ONLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2581 1086 3.2 %RANDOM
Rwork0.2007 33322 --
obs0.2025 33322 99.86 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso max: 102.62 Å2 / Biso mean: 16.861 Å2 / Biso min: 3.16 Å2
Baniso -1Baniso -2Baniso -3
1--1.81 Å20 Å20 Å2
2--3.83 Å20 Å2
3----2.02 Å2
Refinement stepCycle: final / Resolution: 1.89→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3618 0 128 88 3834
Biso mean--9.82 29.29 -
Num. residues----474
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0180.0193848
X-RAY DIFFRACTIONr_angle_refined_deg1.9551.9785250
X-RAY DIFFRACTIONr_dihedral_angle_1_deg8.0155476
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.61624.937158
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.02215580
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.9121512
X-RAY DIFFRACTIONr_chiral_restr0.1390.2592
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.0212910
LS refinement shellResolution: 1.89→1.939 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.321 69 -
Rwork0.29 2387 -
all-2456 -
obs--98.67 %
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)
12.13790.25950.90541.83560.03322.38190.0341-0.0679-0.16040.07350.048-0.00670.1304-0.0244-0.08210.09590.0096-0.00320.0095-0.02370.18719.4815.55329.321
21.6799-0.02690.91291.86930.15082.95280.07440.1039-0.0371-0.21210.04220.05990.0525-0.1191-0.11660.1843-0.0334-0.03060.03150.04170.2119-12.35713.452-0.202
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 237
2X-RAY DIFFRACTION1A301 - 303
3X-RAY DIFFRACTION1A422 - 425
4X-RAY DIFFRACTION2B1 - 237
5X-RAY DIFFRACTION2B301 - 303
6X-RAY DIFFRACTION2B409 - 412

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