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- PDB-4p9x: Structure of ConA/Rh3Glu complex -

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Basic information

Entry
Database: PDB / ID: 4p9x
TitleStructure of ConA/Rh3Glu complex
ComponentsConcanavalin-A
KeywordsSUGAR BINDING PROTEIN / lectin / carbohydrate / porous protein framework
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 ...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-R3G / Concanavalin-A
Similarity search - Component
Biological speciesCanavalia ensiformis (jack bean)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.06 Å
AuthorsSakai, F. / Weiss, M.S. / Chen, G.
CitationJournal: To Be Published
Title: Structure of ConA/Rh3Glu complex
Authors: Sakai, F. / Weiss, F.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: Database references / Derived calculations ...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 / 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.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
C: Concanavalin-A
D: Concanavalin-A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)106,14916
Polymers102,4904
Non-polymers3,66012
Water2,054114
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9690 Å2
ΔGint-112 kcal/mol
Surface area34110 Å2
MethodPISA
Unit cell
Length a, b, c (Å)84.173, 116.028, 84.255
Angle α, β, γ (deg.)90.000, 95.980, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
Concanavalin-A / Con A


Mass: 25622.385 Da / Num. of mol.: 4 / 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-R3G / 2-[2-(2-{4-[(alpha-D-glucopyranosyloxy)methyl]-1H-1,2,3-triazol-1-yl}ethoxy)ethoxy]ethyl 2-[3,6-bis(diethylamino)-9H-xanthen-9-yl]benzoate


Mass: 819.940 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C43H57N5O11
#3: Chemical
ChemComp-MN / MANGANESE (II) ION


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


Mass: 40.078 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Ca
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 114 / 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: 3.99 Å3/Da / Density % sol: 69.19 %
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: 2.06→39.4 Å / Num. obs: 98988 / % possible obs: 99.7 % / Redundancy: 3.42 % / Net I/σ(I): 17.63

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
MOLREP11.0.02phasing
PDB_EXTRACT3.14data extraction
REFMAC5.6.0117refinement
XDSdata scaling
Cootmodel building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.06→30 Å / Cor.coef. Fo:Fc: 0.891 / Cor.coef. Fo:Fc free: 0.855 / WRfactor Rfree: 0.2845 / WRfactor Rwork: 0.2369 / FOM work R set: 0.8099 / SU B: 10.555 / SU ML: 0.138 / SU R Cruickshank DPI: 0.1736 / SU Rfree: 0.173 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.174 / ESU R Free: 0.173 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.2953 2981 3 %RANDOM
Rwork0.245 96007 --
obs0.2465 96007 99.64 %-
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: 66.18 Å2 / Biso mean: 21.557 Å2 / Biso min: 8.88 Å2
Baniso -1Baniso -2Baniso -3
1--0.48 Å20 Å20.42 Å2
2--1.37 Å20 Å2
3----0.8 Å2
Refinement stepCycle: final / Resolution: 2.06→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7236 0 244 114 7594
Biso mean--16.25 28.61 -
Num. residues----948
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0190.027660
X-RAY DIFFRACTIONr_angle_refined_deg2.1111.97710448
X-RAY DIFFRACTIONr_dihedral_angle_1_deg8.5055944
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.08724.872312
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.418151156
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.0311524
X-RAY DIFFRACTIONr_chiral_restr0.1440.21184
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.0215784
LS refinement shellResolution: 2.06→2.113 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.337 221 -
Rwork0.288 6929 -
all-7150 -
obs--99.6 %
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)
12.56940.12750.08581.81760.0061.3626-0.00410.0026-0.05650.03120.002-0.07360.01610.03470.00210.02550.0076-0.02050.0031-0.00860.060914.643-0.23125.247
22.5847-0.08220.25871.57670.2941.14010.03120.0543-0.041-0.0294-0.02740.1128-0.0411-0.1023-0.00380.06290.0247-0.02060.06470.02310.0932-21.357-2.40818.706
31.47310.3319-0.13841.7807-0.38612.00990.0170.029-0.0212-0.0092-0.0106-0.0458-0.05110.0136-0.00640.09050.0101-0.0140.00380.00310.04030.195-31.46238.414
41.0781-0.28890.01371.56860.22712.4854-0.01520.0607-0.069-0.0371-0.02660.0274-0.0594-0.00730.04180.1103-0.0257-0.00910.0506-0.03580.0677-2.504-29.5172.025
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 237
2X-RAY DIFFRACTION1A301 - 303
3X-RAY DIFFRACTION1A403 - 406
4X-RAY DIFFRACTION2B1 - 237
5X-RAY DIFFRACTION2B301 - 303
6X-RAY DIFFRACTION2B404 - 407
7X-RAY DIFFRACTION3C1 - 237
8X-RAY DIFFRACTION3C301 - 303
9X-RAY DIFFRACTION3C405 - 408
10X-RAY DIFFRACTION4D1 - 237
11X-RAY DIFFRACTION4D301 - 303
12X-RAY DIFFRACTION4D401 - 403

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