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- PDB-1jw6: Crystal Structure of the Complex of Concanavalin A and Hexapeptide -

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Basic information

Entry
Database: PDB / ID: 1jw6
TitleCrystal Structure of the Complex of Concanavalin A and Hexapeptide
Components
  • Concanavalin A
  • PROTEIN (6-MER)
KeywordsSUGAR BINDING PROTEIN / Complex with Hexapeptide
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
ISOPROPYL ALCOHOL / : / PENTANEDIAL / Concanavalin-A
Similarity search - Component
Biological speciesCanavalia ensiformis (jack bean)
synthetic construct (others)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.93 Å
AuthorsZhang, Z. / Qian, M. / Huang, Q. / Jia, Y. / Tang, Y.
Citation
Journal: J.Protein Chem. / Year: 2001
Title: Crystal structure of the complex of concanavalin A and hexapeptide.
Authors: Zhang, Z. / Qian, M. / Huang, Q. / Jia, Y. / Tang, Y. / Wang, K. / Cui, D. / Li, M.
#1: Journal: J.PROTEIN CHEM. / Year: 2001
Title: Crystal Structure of the Complex of Concanavalin A and Tripeptide
Authors: Zhang, Z. / Qian, M. / Huang, Q. / Jia, Y. / Tang, Y. / Wang, K. / Cui, D. / Li, M.
History
DepositionSep 2, 2001Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Sep 26, 2001Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Jun 21, 2017Group: Database references / Source and taxonomy / Structure summary
Category: entity / entity_src_nat ...entity / entity_src_nat / pdbx_entity_src_syn / struct_ref / struct_ref_seq / struct_ref_seq_dif
Item: _entity.pdbx_description / _pdbx_entity_src_syn.ncbi_taxonomy_id ..._entity.pdbx_description / _pdbx_entity_src_syn.ncbi_taxonomy_id / _pdbx_entity_src_syn.organism_scientific / _pdbx_entity_src_syn.pdbx_beg_seq_num / _pdbx_entity_src_syn.pdbx_end_seq_num / _struct_ref_seq.ref_id
Revision 1.4Oct 4, 2017Group: Refinement description / Category: software
Revision 1.5Oct 25, 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_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / struct_site
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_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_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.ptnr2_auth_comp_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr2_label_atom_id / _pdbx_struct_conn_angle.ptnr2_label_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_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.value / _struct_conn.pdbx_dist_value / _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_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_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Concanavalin A
B: PROTEIN (6-MER)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,8006
Polymers26,5442
Non-polymers2554
Water1,71195
1
A: Concanavalin A
B: PROTEIN (6-MER)
hetero molecules

A: Concanavalin A
B: PROTEIN (6-MER)
hetero molecules

A: Concanavalin A
B: PROTEIN (6-MER)
hetero molecules

A: Concanavalin A
B: PROTEIN (6-MER)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)107,19924
Polymers106,1788
Non-polymers1,02116
Water1448
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,-y,z1
crystal symmetry operation3_555-x,y,-z1
crystal symmetry operation4_555x,-y,-z1
2
A: Concanavalin A
hetero molecules

A: Concanavalin A
hetero molecules

A: Concanavalin A
hetero molecules

A: Concanavalin A
hetero molecules

B: PROTEIN (6-MER)

B: PROTEIN (6-MER)

B: PROTEIN (6-MER)

B: PROTEIN (6-MER)


Theoretical massNumber of molelcules
Total (without water)107,19924
Polymers106,1788
Non-polymers1,02116
Water1448
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,-y,z1
crystal symmetry operation3_555-x,y,-z1
crystal symmetry operation4_555x,-y,-z1
crystal symmetry operation5_444x-1/2,y-1/2,z-1/21
crystal symmetry operation6_554-x+1/2,-y+1/2,z-1/21
crystal symmetry operation7_545-x+1/2,y-1/2,-z+1/21
crystal symmetry operation8_455x-1/2,-y+1/2,-z+1/21
Buried area14610 Å2
ΔGint-117 kcal/mol
Surface area34660 Å2
MethodPISA
Unit cell
Length a, b, c (Å)63.36, 86.38, 89.25
Angle α, β, γ (deg.)90, 90, 90
Int Tables number23
Space group name H-MI222
Components on special symmetry positions
IDModelComponents
11A-594-

HOH

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Components

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Protein / Protein/peptide , 2 types, 2 molecules AB

#1: Protein Concanavalin A


Mass: 25622.385 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Canavalia ensiformis (jack bean) / References: UniProt: P02866
#2: Protein/peptide PROTEIN (6-MER)


Mass: 922.057 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: This sequence coming from polypeptide libery. / Source: (synth.) synthetic construct (others)

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Non-polymers , 5 types, 99 molecules

#3: Chemical ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mn
#4: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca
#5: Chemical ChemComp-PTD / PENTANEDIAL


Mass: 100.116 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C5H8O2
#6: Chemical ChemComp-IPA / ISOPROPYL ALCOHOL / 2-PROPANOL


Mass: 60.095 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O / Comment: alkaloid*YM
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 95 / 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: 2.3 Å3/Da / Density % sol: 46.5 %
Crystal growTemperature: 300 K / Method: vapor diffusion, hanging drop / pH: 5.45
Details: Sodium phosphate , pH 5.45, VAPOR DIFFUSION, HANGING DROP, temperature 300.0K
Crystal grow
*PLUS
Temperature: 25 ℃
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
10.35 M1dropNaCl
20.01 MTris-HCl1drop
325 mg/mlprotein1drop
42.2 Msodium phosphate1drop
52.2 Msodium phosphate1reservoir

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Data collection

DiffractionMean temperature: 298 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU300 / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS IIC / Detector: IMAGE PLATE / Date: Oct 22, 1998
RadiationMonochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.93→25 Å / Num. all: 17973 / Num. obs: 15289 / % possible obs: 87.1 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Redundancy: 4.5 % / Biso Wilson estimate: 15 Å2 / Rmerge(I) obs: 0.0527 / Net I/σ(I): 14.5
Reflection shellResolution: 1.93→2.02 Å / Redundancy: 3.2 % / Rmerge(I) obs: 0.127 / Mean I/σ(I) obs: 4 / Num. unique all: 1961 / % possible all: 80.7
Reflection
*PLUS
Num. measured all: 71922
Reflection shell
*PLUS
Lowest resolution: 2.51 Å / % possible obs: 80.7 %

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Processing

Software
NameVersionClassification
X-PLORmodel building
X-PLOR3.1refinement
X-PLORphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1HQW

1hqw


Resolution: 1.93→62.01 Å / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / σ(F): 1 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.25 1520 9.9 %RANDOM
Rwork0.19 ---
obs0.21 15289 87.1 %-
all-17573 --
Refinement stepCycle: LAST / Resolution: 1.93→62.01 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1875 0 13 95 1983
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.01
X-RAY DIFFRACTIONx_angle_deg1.55
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkRefine-IDNum. reflection obs
1.93-2.050.2511890.256X-RAY DIFFRACTION1961
2.05-2.210.2482500.248X-RAY DIFFRACTION2186
2.21-2.430.2472600.229X-RAY DIFFRACTION2441
2.43-2.780.2413230.211X-RAY DIFFRACTION2541
2.78-3.510.2422940.177X-RAY DIFFRACTION2706
3.51-62.010.2352880.153X-RAY DIFFRACTION2557
Software
*PLUS
Name: X-PLOR / Version: 3.1 / Classification: refinement
Refinement
*PLUS
σ(F): 1 / % reflection Rfree: 9.9 % / Rfactor all: 0.21 / Rfactor obs: 0.19 / Rfactor Rfree: 0.25 / Rfactor Rwork: 0.19
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.01
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg1.26
LS refinement shell
*PLUS
Rfactor Rfree: 0.235 / Rfactor Rwork: 0.153

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