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- PDB-1nxd: Crystal structure of MnMn Concanavalin A -

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Basic information

Entry
Database: PDB / ID: 1nxd
TitleCrystal structure of MnMn Concanavalin A
Componentsconcanavalin A
KeywordsMETAL BINDING PROTEIN / Lectin
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
AZIDE ION / : / Concanavalin-A
Similarity search - Component
Biological speciesCanavalia ensiformis (jack bean)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsLopez-Jaramillo, F.J. / Gonzalez-Ramirez, L.A. / Albert, A. / Santoyo-Gonzalez, F. / Vargas-Berenguel, A. / Otalora, F.
Citation
Journal: Acta Crystallogr.,Sect.D / Year: 2004
Title: Structure of concanavalin A at pH 8: bound solvent and crystal contacts.
Authors: Lopez-Jaramillo, F.J. / Gonzalez-Ramirez, L.A. / Albert, A. / Santoyo-Gonzalez, F. / Vargas-Berenguel, A. / Otalora, F.
#1: Journal: J.Appl.Crystallogr. / Year: 2001
Title: Crystallization and cryocrystallography inside X-ray capillaries
Authors: Lopez-Jaramillo, F.J. / Garcia-Ruiz, J.M. / Gavira, J.A. / Otalora, F.
History
DepositionFeb 10, 2003Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 30, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Non-polymer description / Version format compliance
Revision 1.3Nov 16, 2011Group: Atomic model
Revision 1.4Jul 5, 2017Group: Source and taxonomy / Category: entity_src_nat
Revision 1.5Oct 11, 2017Group: Refinement description / Category: software / Item: _software.classification / _software.name
Revision 1.6Aug 16, 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 / diffrn_source / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / struct_conn_type / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _diffrn_source.pdbx_synchrotron_site / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _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_asym_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_asym_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.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _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 / _struct_conn.ptnr2_label_seq_id / _struct_conn_type.id / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.7Dec 25, 2024Group: Advisory / Derived calculations / Structure summary
Category: pdbx_distant_solvent_atoms / pdbx_entry_details ...pdbx_distant_solvent_atoms / pdbx_entry_details / pdbx_validate_close_contact / struct_conn / struct_conn_type

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
1: concanavalin A
2: concanavalin A
3: concanavalin A
4: concanavalin A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)105,99657
Polymers102,4904
Non-polymers3,50653
Water13,763764
1
1: concanavalin A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,61815
Polymers25,6221
Non-polymers99614
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
2: concanavalin A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,51815
Polymers25,6221
Non-polymers89614
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
3: concanavalin A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,38413
Polymers25,6221
Non-polymers76112
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
4
4: concanavalin A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,47614
Polymers25,6221
Non-polymers85413
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
5
1: concanavalin A
2: concanavalin A
hetero molecules

1: concanavalin A
2: concanavalin A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)106,27260
Polymers102,4904
Non-polymers3,78256
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_655-x+1,y,-z+1/21
Buried area19750 Å2
ΔGint-109 kcal/mol
Surface area33060 Å2
MethodPISA
6
3: concanavalin A
hetero molecules

3: concanavalin A
hetero molecules

4: concanavalin A
hetero molecules

4: concanavalin A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)105,71954
Polymers102,4904
Non-polymers3,23050
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_565x,-y+1,-z1
crystal symmetry operation5_555x+1/2,y+1/2,z1
crystal symmetry operation8_555x+1/2,-y+1/2,-z1
Buried area17400 Å2
ΔGint-113 kcal/mol
Surface area32370 Å2
MethodPISA
7
1: concanavalin A
2: concanavalin A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)53,13630
Polymers51,2452
Non-polymers1,89128
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7890 Å2
ΔGint-52 kcal/mol
Surface area18360 Å2
MethodPISA
8
3: concanavalin A
hetero molecules

4: concanavalin A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)52,86027
Polymers51,2452
Non-polymers1,61525
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation5_555x+1/2,y+1/2,z1
Buried area6740 Å2
ΔGint-55 kcal/mol
Surface area18140 Å2
MethodPISA
Unit cell
Length a, b, c (Å)101.300, 118.000, 249.500
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221
Components on special symmetry positions
IDModelComponents
113-1156-

HOH

214-1166-

HOH

314-1182-

HOH

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Components

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Protein , 1 types, 4 molecules 1234

#1: Protein
concanavalin A / Con A


Mass: 25622.385 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Source: (natural) Canavalia ensiformis (jack bean) / References: UniProt: P02866

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Non-polymers , 5 types, 817 molecules

#2: Chemical
ChemComp-AZI / AZIDE ION


Mass: 42.020 Da / Num. of mol.: 16 / Source method: obtained synthetically / Formula: N3
#3: Chemical
ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: Mn
#4: Chemical
ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Na
#5: Chemical...
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 25 / Source method: obtained synthetically / Formula: C3H8O3
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 764 / Source method: isolated from a natural source / Formula: H2O

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Details

Has protein modificationN

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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: 3.24 Å3/Da / Density % sol: 61.78 %
Crystal growTemperature: 293 K / Method: gel acupuncture method (game) / pH: 8
Details: PEG 6000, Sodium Chloride, Calcium Chloride, Manganese Chloride, Sodium Azide, Tris-HCl , pH 8, Gel Acupuncture Method (GAME), temperature 293K
Crystal grow
*PLUS
pH: 8
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetailsChemical formula
110 mg/mlprotein1drop
2100 mMTris-HCl1droppH8.0
3200 mM1dropNaCl
41 mM1dropMnCl2
51 mM1dropCaCl2
63 mM1dropNaN3
74.2 mMheptakis(6-S-beta-D-galactopyranosyl-6-thio)-cyclomaltoheptaose1drop
812 %(w/v)PEG60001reservoir
9100 mMTris-HCl1reservoirpH8.0
10200 mM1reservoirNaCl
111 mM1reservoirMnCl2
121 mM1reservoirCaCl2
133 mM1reservoirNaN3

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: BW7B / Wavelength: 0.8423 Å
DetectorType: MARRESEARCH / Detector: AREA DETECTOR
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.8423 Å / Relative weight: 1
ReflectionResolution: 1.84→19.61 Å / Num. all: 120751 / Num. obs: 120751 / % possible obs: 87.5 % / Observed criterion σ(F): 0 / Redundancy: 2.88 % / Biso Wilson estimate: 21.67 Å2 / Limit h max: 54 / Limit h min: 0 / Limit k max: 63 / Limit k min: 0 / Limit l max: 134 / Limit l min: 0 / Observed criterion F max: 7393670.09 / Observed criterion F min: 64.53 / Rsym value: 0.021 / Net I/σ(I): 34.6
Reflection shellResolution: 1.8→2 Å / Redundancy: 2.57 % / Mean I/σ(I) obs: 16.71 / Num. unique all: 24782 / Rsym value: 0.052 / % possible all: 66.8
Reflection
*PLUS
Highest resolution: 1.9 Å / Lowest resolution: 19 Å / Num. obs: 111379 / % possible obs: 94.9 % / Num. measured all: 324343 / Rmerge(I) obs: 0.02
Reflection shell
*PLUS
Highest resolution: 1.9 Å / Lowest resolution: 2 Å / % possible obs: 93 % / Num. unique obs: 15414 / Num. measured obs: 40384 / Rmerge(I) obs: 0.048 / Mean I/σ(I) obs: 18.15

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Processing

Software
NameVersionClassificationNB
CNS1refinement
MAR345data collection
XDSdata scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1NLS

1nls


Resolution: 1.9→19 Å / Rfactor Rfree error: 0.002 / Occupancy max: 1 / Occupancy min: 1 / Isotropic thermal model: isotropic / Cross valid method: THROUGHOUT / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.201 11146 10 %RANDOM
Rwork0.184 ---
all-111372 --
obs-111372 95 %-
Solvent computationSolvent model: CNS bulk solvent model used / Bsol: 50.299 Å2 / ksol: 0.398921 e/Å3
Displacement parametersBiso max: 58.09 Å2 / Biso mean: 18.96 Å2 / Biso min: 5.56 Å2
Baniso -1Baniso -2Baniso -3
1-1.75 Å20 Å20 Å2
2---3.32 Å20 Å2
3---1.56 Å2
Refine Biso
ClassRefine-IDTreatment
polymerX-RAY DIFFRACTIONisotropic
waterX-RAY DIFFRACTIONisotropic
nonpolymerX-RAY DIFFRACTIONisotropic
Refine analyze
FreeObs
Luzzati coordinate error0.21 Å0.19 Å
Luzzati d res low-5 Å
Luzzati sigma a0.13 Å0.09 Å
Luzzati d res high-1.9
Refinement stepCycle: LAST / Resolution: 1.9→19 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7236 0 210 764 8210
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONx_bond_d0.007
X-RAY DIFFRACTIONx_angle_deg1.7
X-RAY DIFFRACTIONx_torsion_deg25.9
X-RAY DIFFRACTIONx_torsion_impr_deg1.32
X-RAY DIFFRACTIONx_mcbond_it1.171.5
X-RAY DIFFRACTIONx_mcangle_it1.832
X-RAY DIFFRACTIONx_scbond_it1.882
X-RAY DIFFRACTIONx_scangle_it2.772.5
LS refinement shellResolution: 1.9→1.97 Å / Rfactor Rfree error: 0.006
RfactorNum. reflection% reflection
Rfree0.19 1098 9.5 %
Rwork0.19 9628 -
all-11596 -
obs-10726 92.5 %
Software
*PLUS
Name: CNS / Classification: refinement
Refinement
*PLUS
Highest resolution: 1.9 Å / Lowest resolution: 19 Å / % reflection Rfree: 10 %
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d
X-RAY DIFFRACTIONc_angle_deg1.7
X-RAY DIFFRACTIONc_mcbond_it
X-RAY DIFFRACTIONc_scbond_it
X-RAY DIFFRACTIONc_mcangle_it
X-RAY DIFFRACTIONc_scangle_it
LS refinement shell
*PLUS
Rfactor Rfree: 0.19 / Rfactor Rwork: 0.19

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