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- PDB-5tg3: Crystal Structure of Dioclea reflexa seed lectin (DrfL) in comple... -

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Basic information

Entry
Database: PDB / ID: 5tg3
TitleCrystal Structure of Dioclea reflexa seed lectin (DrfL) in complex with X-Man
ComponentsDioclea reflexa lectin
KeywordsSUGAR BINDING PROTEIN / Lectin / Dioclea Reflexa / DrfL / X-Man
Function / homology
Function and homology information


mannose binding / manganese ion binding / calcium ion binding
Similarity search - Function
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-XMM / Lectin
Similarity search - Component
Biological speciesDioclea reflexa (plant)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.765 Å
AuthorsSantiago, M.Q. / Correia, J.L.A. / Pinto-Junior, V.R. / Osterne, V.J.S. / Pereira, R.I. / Silva-Filho, J.C. / Lossio, C.F. / Rocha, B.A.M. / Delatorre, P. / Neco, A.H.B. ...Santiago, M.Q. / Correia, J.L.A. / Pinto-Junior, V.R. / Osterne, V.J.S. / Pereira, R.I. / Silva-Filho, J.C. / Lossio, C.F. / Rocha, B.A.M. / Delatorre, P. / Neco, A.H.B. / Araripe, D.A. / Nascimento, K.S. / Cavada, B.S.
CitationJournal: Int. J. Biol. Macromol. / Year: 2017
Title: Structural studies of a vasorelaxant lectin from Dioclea reflexa Hook seeds: Crystal structure, molecular docking and dynamics.
Authors: Pinto-Junior, V.R. / Osterne, V.J. / Santiago, M.Q. / Correia, J.L. / Pereira-Junior, F.N. / Leal, R.B. / Pereira, M.G. / Chicas, L.S. / Nagano, C.S. / Rocha, B.A. / Silva-Filho, J.C. / ...Authors: Pinto-Junior, V.R. / Osterne, V.J. / Santiago, M.Q. / Correia, J.L. / Pereira-Junior, F.N. / Leal, R.B. / Pereira, M.G. / Chicas, L.S. / Nagano, C.S. / Rocha, B.A. / Silva-Filho, J.C. / Ferreira, W.P. / Rocha, C.R. / Nascimento, K.S. / Assreuy, A.M. / Cavada, B.S.
History
DepositionSep 27, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 15, 2017Provider: repository / Type: Initial release
Revision 1.1Sep 27, 2017Group: Data collection / Category: diffrn_detector / Item: _diffrn_detector.detector
Revision 1.2Jul 29, 2020Group: Derived calculations / Structure summary
Category: chem_comp / entity ...chem_comp / entity / pdbx_entity_nonpoly / pdbx_struct_conn_angle / struct_conn / struct_site / struct_site_gen
Item: _chem_comp.mon_nstd_flag / _chem_comp.name ..._chem_comp.mon_nstd_flag / _chem_comp.name / _entity.pdbx_description / _pdbx_entity_nonpoly.name / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_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
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.3Oct 4, 2023Group: Data collection / Database references ...Data collection / Database references / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Dioclea reflexa lectin
B: Dioclea reflexa lectin
C: Dioclea reflexa lectin
D: Dioclea reflexa lectin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)104,36016
Polymers102,3454
Non-polymers2,01512
Water12,953719
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8970 Å2
ΔGint-99 kcal/mol
Surface area34410 Å2
MethodPISA
Unit cell
Length a, b, c (Å)72.460, 85.180, 174.580
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein
Dioclea reflexa lectin


Mass: 25586.289 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Source: (natural) Dioclea reflexa (plant) / Tissue: Seed / References: UniProt: C0HK81*PLUS
#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: Sugar
ChemComp-XMM / 5-bromo-4-chloro-1H-indol-3-yl alpha-D-mannopyranoside / (2R,3S,4S,5S,6R)-2-(5-BROMO-4-CHLORO-1H-INDOL-3-YLOXY)-TETRAHYDRO-6-(HYDROXYMETHYL)-2H-PYRAN-3,4,5-TRIOL / (5-BROMO-4-CHLORO-3-INDOLYL)-Alpha-D-MANNOSE / 5-bromo-4-chloro-1H-indol-3-yl alpha-D-mannoside / 5-bromo-4-chloro-1H-indol-3-yl D-mannoside / 5-bromo-4-chloro-1H-indol-3-yl mannoside


Type: D-saccharide / Mass: 408.629 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Formula: C14H15BrClNO6
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 719 / 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: 2.72 Å3/Da / Density % sol: 54.74 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8
Details: 100 mM HEPES pH 8.0 50 mM Cadmiun Sulfate 1M Sodium Acetate

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: LNLS / Beamline: W01B-MX2 / Wavelength: 1.47 Å
DetectorType: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Jun 18, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.47 Å / Relative weight: 1
ReflectionResolution: 1.75→33.84 Å / Num. all: 100509 / Num. obs: 100509 / % possible obs: 92.2 % / Redundancy: 6.3 % / Biso Wilson estimate: 22.87 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.064 / Rpim(I) all: 0.026 / Rrim(I) all: 0.069 / Rsym value: 0.064 / Net I/σ(I): 15.8 / Num. measured all: 635999
Reflection shell

Diffraction-ID: 1 / Rejects: 0

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. measured allNum. unique allCC1/2Rpim(I) allRrim(I) allRsym valueNet I/σ(I) obs% possible all
1.75-1.8560.24867014111570.9690.0190.0510.0474.970.8
5.54-33.846.80.0472468436470.9980.020.0530.04927.898

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Processing

Software
NameVersionClassification
PHENIX1.10.1_2155refinement
SCALA3.3.22data scaling
PDB_EXTRACT3.2data extraction
iMOSFLMdata reduction
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4NOT

4not


Resolution: 1.765→33.845 Å / SU ML: 0.23 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 26.88 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2489 4959 4.97 %
Rwork0.2169 94829 -
obs0.2185 99788 93.45 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 138.16 Å2 / Biso mean: 26.2792 Å2 / Biso min: 8.67 Å2
Refinement stepCycle: final / Resolution: 1.765→33.845 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7024 0 100 719 7843
Biso mean--30.49 30.91 -
Num. residues----920
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0117284
X-RAY DIFFRACTIONf_angle_d1.3729936
X-RAY DIFFRACTIONf_chiral_restr0.0671148
X-RAY DIFFRACTIONf_plane_restr0.0051260
X-RAY DIFFRACTIONf_dihedral_angle_d15.9382528
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 30

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.765-1.78510.40311090.32562368247771
1.7851-1.80610.35891580.31332896305486
1.8061-1.82810.39581570.32192897305488
1.8281-1.85130.32361400.28352982312288
1.8513-1.87560.37981410.29612953309489
1.8756-1.90130.34551340.2762958309287
1.9013-1.92850.29141570.2482996315389
1.9285-1.95720.27051470.2493026317390
1.9572-1.98780.30181400.25383029316991
1.9878-2.02040.27761580.24563062322091
2.0204-2.05520.26141690.24153116328593
2.0552-2.09260.30091610.24173140330194
2.0926-2.13290.2691740.23483183335794
2.1329-2.17640.28971800.24223190337095
2.1764-2.22370.26851800.23253166334695
2.2237-2.27540.27961520.22843218337096
2.2754-2.33230.26651860.23113223340995
2.3323-2.39530.27551880.24383179336796
2.3953-2.46580.31711830.24683256343997
2.4658-2.54540.24881730.24193268344197
2.5454-2.63630.27791660.23743265343197
2.6363-2.74180.26461770.23463298347597
2.7418-2.86660.28161740.23993298347297
2.8666-3.01760.26451870.22843279346697
3.0176-3.20650.2581680.21573349351799
3.2065-3.45390.2191970.19433364356199
3.4539-3.8010.18641820.17883392357499
3.801-4.35010.22061690.16913420358999
4.3501-5.47690.18191730.15843486365999
5.4769-33.85110.2111790.21873572375198

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