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- PDB-3nwk: A second C2221 form of concanavalin A (Canavalia ensiformis) -

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Basic information

Entry
Database: PDB / ID: 3nwk
TitleA second C2221 form of concanavalin A (Canavalia ensiformis)
ComponentsConcanavalin-A
KeywordsSUGAR BINDING PROTEIN / lectin / Glycoprotein / Manganese / Metal-binding
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
Biological speciesCanavalia ensiformis (jack bean)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.09 Å
AuthorsForoughi, L.M. / Kang, Y.N. / Matzger, A.J.
CitationJournal: Cryst.Growth Des. / Year: 2011
Title: Polymer-Induced Heteronucleation for Protein Single Crystal Growth: Structural Elucidation of Bovine Liver Catalase and Concanavalin A Forms
Authors: Foroughi, L.M. / Kang, Y.N. / Matzger, A.J.
History
DepositionJul 9, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 13, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 5, 2017Group: Source and taxonomy / Category: entity_src_nat
Revision 1.2Sep 6, 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_ncs_dom_lim / 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_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.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 / _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 / _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: Concanavalin-A
C: Concanavalin-A
D: Concanavalin-A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)103,88323
Polymers102,4904
Non-polymers1,39319
Water8,017445
1
A: Concanavalin-A
C: Concanavalin-A
hetero molecules

A: Concanavalin-A
C: Concanavalin-A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)103,79122
Polymers102,4904
Non-polymers1,30118
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_555x,-y,-z1
2
B: Concanavalin-A
D: Concanavalin-A
hetero molecules

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


Theoretical massNumber of molelcules
Total (without water)103,97524
Polymers102,4904
Non-polymers1,48520
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_554-x,y,-z-1/21
3
A: Concanavalin-A
C: Concanavalin-A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)51,89511
Polymers51,2452
Non-polymers6519
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4020 Å2
ΔGint-53 kcal/mol
Surface area18450 Å2
MethodPISA
4
B: Concanavalin-A
D: Concanavalin-A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)51,98712
Polymers51,2452
Non-polymers74310
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4270 Å2
ΔGint-53 kcal/mol
Surface area18430 Å2
MethodPISA
Unit cell
Length a, b, c (Å)101.518, 118.118, 250.113
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
31C
41D

NCS domain segments:

Component-ID: 1 / Ens-ID: 1 / Beg auth comp-ID: ALA / Beg label comp-ID: ALA / End auth comp-ID: ASN / End label comp-ID: ASN / Refine code: 5 / Auth seq-ID: 1 - 237 / Label seq-ID: 1 - 237

Dom-IDAuth asym-IDLabel asym-ID
1AA
2BB
3CC
4DD

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Components

#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
#2: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Ca
#3: Chemical
ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Mn
#4: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 11 / Source method: obtained synthetically / Formula: C3H8O3
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 445 / 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: 3.66 Å3/Da / Density % sol: 66.37 %
Crystal growTemperature: 273 K
Method: hanging drop vapor diffusion using polymer-induced heteronucleation
pH: 8.5
Details: 10 mM Tris, pH 8.5, 1 M ammonium sulfate, hanging drop vapor diffusion using polymer-induced heteronucleation, temperature 273K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-G / Wavelength: 0.97856 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Jun 14, 2009 / Details: mirrors
RadiationMonochromator: C(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97856 Å / Relative weight: 1
ReflectionResolution: 2.09→50 Å / Num. all: 87288 / Num. obs: 87288 / % possible obs: 98.3 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 6.8 % / Biso Wilson estimate: 25.9 Å2 / Rmerge(I) obs: 0.116 / Net I/σ(I): 16.71
Reflection shellResolution: 2.09→2.13 Å / Redundancy: 3.9 % / Rmerge(I) obs: 0.463 / Mean I/σ(I) obs: 2.06 / Num. unique all: 3546 / % possible all: 81.3

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Processing

Software
NameVersionClassification
HKL-2000data collection
PHASERphasing
REFMAC5.5.0109refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1nls

1nls


Resolution: 2.09→36.66 Å / Cor.coef. Fo:Fc: 0.954 / Cor.coef. Fo:Fc free: 0.938 / SU B: 7.07 / SU ML: 0.089 / Cross valid method: THROUGHOUT / ESU R Free: 0.139 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.21191 4383 5 %RANDOM
Rwork0.1765 ---
all0.1783 82853 --
obs0.1783 82853 98.03 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 25.093 Å2
Baniso -1Baniso -2Baniso -3
1--0.15 Å20 Å20 Å2
2--0.17 Å20 Å2
3----0.02 Å2
Refinement stepCycle: LAST / Resolution: 2.09→36.66 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7236 0 74 445 7755
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0180.0227577
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.5841.94510287
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.5835966
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.1224.811318
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.659151179
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.3721525
X-RAY DIFFRACTIONr_chiral_restr0.1420.21179
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0215703
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.5391.54773
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it2.35927734
X-RAY DIFFRACTIONr_scbond_it3.99532804
X-RAY DIFFRACTIONr_scangle_it5.8854.52542
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Dom-ID: 1 / Ens-ID: 1 / Refine-ID: X-RAY DIFFRACTION

Auth asym-IDNumberTypeRms dev position (Å)Weight position
A940medium positional0.20.5
B940medium positional0.20.5
C940medium positional0.180.5
D940medium positional0.20.5
A815loose positional0.535
B815loose positional0.465
C815loose positional0.445
D815loose positional0.435
A940medium thermal2.12
B940medium thermal2.412
C940medium thermal2.952
D940medium thermal1.662
A815loose thermal2.9710
B815loose thermal3.0410
C815loose thermal3.3110
D815loose thermal2.5110
LS refinement shellResolution: 2.144→2.3 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.29 265 -
Rwork0.266 4894 -
obs-4894 79.84 %
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)
11.1065-0.093-0.0550.9165-0.03891.2514-0.0621-0.13830.02250.1330.0752-0.06830.01250.1354-0.01310.1110.0411-0.0120.1035-0.02490.074417.46-13.582-9.573
22.8676-0.25640.94237.33870.68081.7759-0.1086-0.0880.24590.2640.04480.198-0.0713-0.01790.06390.16140.0607-0.00330.1885-0.01970.14220.885-1.756-10.225
31.5225-1.34650.14691.6230.45031.2451-0.0474-0.0123-0.24450.01050.00180.19390.1413-0.06880.04560.13140.00290.00980.1022-0.0060.12573.984-19.956-17.932
42.2582-0.5409-0.98233.4730.38191.6038-0.0431-0.19450.14130.3510.1160.3991-0.12830.1416-0.07290.1767-0.0002-0.03510.1897-0.03490.126911.235-9.439-8.746
50.89120.1412-0.39171.42260.2431.1095-0.0536-0.0189-0.02770.0150.0832-0.0583-0.11170.1563-0.02960.11760.0257-0.0090.115-0.01950.097516.399-16.12-20.291
61.08980.07180.03271.51290.31171.1686-0.05980.0803-0.0184-0.10060.1314-0.1392-0.02690.1186-0.07160.1096-0.02960.01160.0983-0.01970.088716.343-26.357-47.501
71.93831.560.59163.90231.09351.7445-0.09660.05340.0692-0.16910.05240.1378-0.0596-0.11360.04410.1149-0.014-0.00110.13520.01150.1208-0.065-29.354-47.38
81.0510.3108-0.07371.31730.47641.3915-0.05390.0418-0.0668-0.03450.065-0.01530.09890.0692-0.01110.1387-0.00460.00110.1221-0.00640.127410.267-27.562-42.106
91.3471-0.604-0.00312.3305-0.0811.19140.0117-0.0347-0.09180.08670.040.275-0.0504-0.1966-0.05160.10430.06880.00530.1140.00420.110927.442-49.261-11.945
101.4837-0.9737-0.01152.6338-0.06760.34790.0630.1102-0.0163-0.07-0.05580.0059-0.0397-0.0201-0.00730.12730.0580.00220.1083-0.00380.088538.106-50.641-18.2
114.25851.8143-2.04297.8588-2.66583.60320.0196-0.2376-0.25580.629-0.1938-0.1439-0.14310.1160.17420.1460.0585-0.01080.1346-0.00820.125146.327-61.157-9.328
122.1512-2.69930.19173.4045-0.09882.18390.08910.06120.3683-0.1408-0.0513-0.4563-0.10760.0367-0.03780.21230.06210.02570.18390.02690.216746.857-46.703-22.6
1354.38284.6016-19.029521.0818.847311.95240.834-0.28841.2286-1.62610.3951-1.7366-1.1420.3199-1.2290.51630.03530.10690.30970.31060.694743.046-34.124-27.065
141.6056-1.1792-0.23531.8837-0.2911.18430.06530.0646-0.091-0.1079-0.07030.11540.0818-0.12590.0050.13090.0518-0.02260.1356-0.01650.135.025-52.526-19.474
151.10090.5305-0.08531.6579-0.1580.7693-0.07670.11980.0033-0.12140.07820.07510.064-0.0794-0.00140.1163-0.0654-0.00470.10390.00820.0915-20.642-50.163-54.499
162.38251.66560.00023.49390.0031.3231-0.02550.0182-0.2327-0.0759-0.0054-0.20660.09760.07620.03090.1494-0.0256-0.01470.1135-0.00520.1449-5.423-47.153-48.463
171.54831.1491-0.00992.0197-0.09871.06920.0424-0.0541-0.06160.0641-0.0647-0.0246-0.0009-0.07940.02230.1395-0.05330.00260.12840.0120.1188-16.836-49.161-47.274
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 113
2X-RAY DIFFRACTION2A114 - 139
3X-RAY DIFFRACTION3A140 - 180
4X-RAY DIFFRACTION4A181 - 204
5X-RAY DIFFRACTION5A205 - 237
6X-RAY DIFFRACTION6B1 - 113
7X-RAY DIFFRACTION7B114 - 163
8X-RAY DIFFRACTION8B164 - 237
9X-RAY DIFFRACTION9C1 - 84
10X-RAY DIFFRACTION10C85 - 113
11X-RAY DIFFRACTION11C114 - 137
12X-RAY DIFFRACTION12C138 - 157
13X-RAY DIFFRACTION13C158 - 166
14X-RAY DIFFRACTION14C167 - 237
15X-RAY DIFFRACTION15D1 - 113
16X-RAY DIFFRACTION16D114 - 163
17X-RAY DIFFRACTION17D164 - 237

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