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- PDB-1gkb: CONCANAVALIN A, NEW CRYSTAL FORM -

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Basic information

Entry
Database: PDB / ID: 1gkb
TitleCONCANAVALIN A, NEW CRYSTAL FORM
ComponentsCONCANAVALIN A
KeywordsLECTIN-BINDING PROTEIN
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
Biological speciesCANAVALIA ENSIFORMIS (jack bean)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.56 Å
AuthorsKantardjieff, K. / Rupp, B. / Hoechtl, P. / Segelke, B.
CitationJournal: Acta Crystallogr.,Sect.D / Year: 2002
Title: Concanavalin a in a Dimeric Crystal Form: Revisiting Structural Accuracy and Molecular Flexibility
Authors: Kantardjieff, K. / Hochtl, P. / Segelke, B. / Tao, F. / Rupp, B.
History
DepositionAug 10, 2001Deposition site: PDBE / Processing site: PDBE
SupersessionAug 20, 2001ID: 1E0I
Revision 1.0Aug 20, 2001Provider: repository / Type: Initial release
Revision 1.1Aug 22, 2012Group: Atomic model / Database references ...Atomic model / Database references / Other / Structure summary / Version format compliance
Revision 1.2Jun 28, 2017Group: Data collection / Category: diffrn_source / Item: _diffrn_source.type
Revision 1.3May 8, 2019Group: Data collection / Experimental preparation
Category: database_PDB_rev / database_PDB_rev_record / exptl_crystal_grow
Item: _exptl_crystal_grow.method
Revision 1.4Dec 13, 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_sheet / 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_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_conn.ptnr2_label_seq_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_sheet.number_strands / _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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)51,4838
Polymers51,2452
Non-polymers2396
Water12,394688
1
A: CONCANAVALIN A
B: CONCANAVALIN A
hetero molecules

A: CONCANAVALIN A
B: CONCANAVALIN A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)102,96716
Polymers102,4904
Non-polymers47712
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_555-x,y,-z+1/21
MethodPQS
Unit cell
Length a, b, c (Å)118.700, 101.380, 111.970
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
11A-2130-

HOH

21A-2143-

HOH

31A-2326-

HOH

41B-2122-

HOH

Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B

NCS domain segments:

Ens-ID: 1 / Refine code: 5

Dom-IDComponent-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11ALAALAGLYGLYAA1 - 261 - 26
21ALAALAGLYGLYBB1 - 261 - 26
12ASPASPVALVALAA28 - 6528 - 65
22ASPASPVALVALBB28 - 6528 - 65
13TYRTYRASPASPAA67 - 7167 - 71
23TYRTYRASPASPBB67 - 7167 - 71
14ALAALAALAALAAA7373
24ALAALAALAALABB7373
15VALVALALAALAAA75 - 9575 - 95
25VALVALALAALABB75 - 9575 - 95
16THRTHRLEULEUAA97 - 10797 - 107
26THRTHRLEULEUBB97 - 10797 - 107
17TRPTRPTRPTRPAA109109
27TRPTRPTRPTRPBB109109
18PHEPHETHRTHRAA111 - 112111 - 112
28PHEPHETHRTHRBB111 - 112111 - 112
19LYSLYSPHEPHEAA114 - 128114 - 128
29LYSLYSPHEPHEBB114 - 128114 - 128
110PHEPHEPHEPHEAA130 - 133130 - 133
210PHEPHEPHEPHEBB130 - 133130 - 133
111LYSLYSALAALAAA135 - 193135 - 193
211LYSLYSALAALABB135 - 193135 - 193
112PHEPHEASPASPAA195 - 203195 - 203
212PHEPHEASPASPBB195 - 203195 - 203
113PROPROILEILEAA206 - 214206 - 214
213PROPROILEILEBB206 - 214206 - 214
114ASNASNPROPROAA216 - 222216 - 222
214ASNASNPROPROBB216 - 222216 - 222
115GLYGLYASNASNAA224 - 237224 - 237
215GLYGLYASNASNBB224 - 237224 - 237

NCS oper: (Code: given
Matrix: (-0.9481, -0.000706, 0.3181), (0.000772, -1, 0.002078), (0.3181, 0.002216, 0.9481)
Vector: -8.962, 16.6, 1.399)

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Components

#1: Protein CONCANAVALIN A / CON A


Mass: 25622.385 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Details: PURCHASED FROM SIGMA, CONCANAVALIN C7275 / Source: (natural) CANAVALIA ENSIFORMIS (jack bean) / References: UniProt: P02866
#2: Chemical ChemComp-MN / MANGANESE (II) ION


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


Mass: 40.078 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ca
#4: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 688 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsCONCANAVALIN A COMPLEXED WITH ALPHA-METHYL-D THE SWS ENTRY P81461 IS THE MATURE CHAIN. THE SWS ...CONCANAVALIN A COMPLEXED WITH ALPHA-METHYL-D THE SWS ENTRY P81461 IS THE MATURE CHAIN. THE SWS ENTRY P02866 IS THE PRECURSOR PROTEIN. THE MATURE C CONSISTS OF RESIDUES 164-281 FOLLOWED BY 30-148. TO FORM A MATURE CHAIN THE PRECURSOR UNDERGOES FURTHER POST-TRANSLATIONAL MODIFICATION AFTER REMOVAL OF THE SIGNAL SEQUENCE; CLEAVAGE AFTER ASN AT POSITIONS 148, 163, AND 281 FOLLOWED BY TRANSPOSITION AND LIGATION (BY FORMATION OF A N PEPTIDE BOND) OF RESIDUES 164-281 AND 30-148. THERE ARE 3 DIFFERENCES BETWEEN THE DEPOSITORS' DATA AND THE GENETIC SEQUENCE(S) : (1) RESIDUE ASP 58 (GLY IN THE P81461 ENTRY): FROM THE ELECTRON DENSITY IT APPEARS HIGHLY UNLIKELY THAT THIS RESIDUE IS GLYCINE. ASP (OR ASN) IS THE PROPER RESIDUE IN THIS X-RAY STRUCTURE. COMPARE ENTRIES 1JBC, 1NLS AND P02866 CONA_CANEN. (2) RESIDUE ASP 151 (GLU IN THE GENETIC ENTRY): ALTHOUGH NOT AS CLEARLY DEFINED AS IN GLU 155, WARP AND THE FO-FC OMIT MAPS SUGGEST THAT THIS RESIDUE IS PROBABLY ASP IN AGREEMENT WITH ENTRIES 1JBC, 1NLS. (3) RESIDUE ASP 155 (ARG IN THE PROSITE ENTRY): FROM THE ELECTRON DENSITY IT APPEARS HIGHLY UNLIKELY THAT THIS RESIDUE IS ARGININE. GLU (OR GLN) IS THE PROPER RESIDUE IN THE X-RAY STRUCTURE. COMPARE ENTRIES 1JBC AND 1NLS.

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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: 3.37 Å3/Da / Density % sol: 63.53 %
Crystal growMethod: vapor diffusion, hanging drop / pH: 8
Details: HANGING DROP, 30MG/ML, 10+10 UL 1 ML WELL, TRIS/HCL PH 8.0, 25%
Crystal grow
*PLUS
Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
130 mg/mlprotein1dropin water
2100 mMTris-HCl1reservoir
325 %(v/v)ethanol1reservoir

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Data collection

DiffractionMean temperature: 120 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.54178
DetectorType: ADSC AREA DETECTOR / Date: Jul 15, 1995 / Details: COLLIMATOR 0.5 MM
RadiationMonochromator: SUPPER GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54178 Å / Relative weight: 1
ReflectionResolution: 1.564→38.63 Å / Num. obs: 73179 / % possible obs: 77 % / Redundancy: 3.2 % / Rmerge(I) obs: 0.035 / Net I/σ(I): 16
Reflection shellResolution: 1.56→1.6 Å / Redundancy: 2.5 % / Rmerge(I) obs: 0.249 / Mean I/σ(I) obs: 2.1 / % possible all: 46
Reflection
*PLUS
Num. measured all: 234173
Reflection shell
*PLUS
Num. unique obs: 2920 / Num. measured obs: 7300

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Processing

Software
NameVersionClassification
REFMAC5refinement
ADSCdata reduction
DATAMANdata scaling
FCALCdata scaling
EPMRphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1JBC

1jbc


Resolution: 1.56→38.63 Å / Cor.coef. Fo:Fc: 0.97 / Cor.coef. Fo:Fc free: 0.961 / SU B: 3.903 / SU ML: 0.125 / Cross valid method: THROUGHOUT / ESU R: 0.095 / ESU R Free: 0.094 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. SOME DISORDERED OR POORLY DEFINED SOLVENT ATOMS ARE MODELLED WITH PARTIALLY OCCUPIED (N=0.5) WATERS. THOSE ATOMS DO NOT HAVE AN ASSOCIATED ...Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. SOME DISORDERED OR POORLY DEFINED SOLVENT ATOMS ARE MODELLED WITH PARTIALLY OCCUPIED (N=0.5) WATERS. THOSE ATOMS DO NOT HAVE AN ASSOCIATED SECOND CONFORMER AND CAN BE IN CLOSE CONTACT (~2.1 A) TO EACH OTHER.
RfactorNum. reflection% reflectionSelection details
Rfree0.206 7385 10.1 %RANDOM
Rwork0.178 ---
obs0.18 65794 76.9 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Refinement stepCycle: LAST / Resolution: 1.56→38.63 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3618 0 6 688 4312
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0190.0213761
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg
X-RAY DIFFRACTIONr_angle_other_deg1.8491.9345127
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.5663472
X-RAY DIFFRACTIONr_dihedral_angle_2_deg
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.79815641
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.1530.2599
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.022827
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.210.31757
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1290.5696
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2110.347
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2320.532
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.1822376
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.99333879
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it1.97331385
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it2.91541248
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Dom-ID: 1 / Auth asym-ID: A / Ens-ID: 1 / Refine-ID: X-RAY DIFFRACTION

NumberTypeRms dev position (Å)Weight position
112tight positional0.210.05
826medium positional0.130.5
771loose positional0.315
112tight thermal0.810.5
826medium thermal1.512
771loose thermal2.0610
LS refinement shellResolution: 1.56→1.58 Å / Total num. of bins used: 40 /
RfactorNum. reflection
Rfree0.273 124
Rwork0.275 1070
Software
*PLUS
Name: REFMAC / Version: 5 / Classification: refinement
Refinement
*PLUS
Rfactor all: 0.18048 / Rfactor obs: 0.178
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONp_bond_d0.02
X-RAY DIFFRACTIONp_angle_d
X-RAY DIFFRACTIONp_angle_deg1.85
X-RAY DIFFRACTIONp_mcbond_it1.182
X-RAY DIFFRACTIONp_scbond_it1.9733
X-RAY DIFFRACTIONp_mcangle_it1.9933
X-RAY DIFFRACTIONp_scangle_it2.9154
LS refinement shell
*PLUS
Highest resolution: 1.564 Å / Lowest resolution: 1.584 Å / Num. reflection Rwork: 1070

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