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- PDB-7ljg: Crystal Structure of Lectin from Dioclea altissima -

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Basic information

Entry
Database: PDB / ID: 7ljg
TitleCrystal Structure of Lectin from Dioclea altissima
ComponentsLectin
KeywordsSUGAR BINDING PROTEIN / Lectin / Dioclea altissima
Function / homology
Function and homology information


D-mannose binding / metal 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 / Concanavalin A-like lectin/glucanase domain superfamily
Similarity search - Domain/homology
Biological speciesDioclea violacea (plant)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.21 Å
AuthorsVieira-Neto, A.E. / Pereira, H.M. / Sousa, F.D. / Goncalves, N.G.G. / Vieira, N.C.G. / Monteiro-Moreira, A.C.O. / Moereira, R.A.
CitationJournal: To Be Published
Title: Crystal Structure of Lectin from Dioclea altissima
Authors: Vieira-Neto, A.E. / Pereira, H.M. / Sousa, F.D. / Goncalves, N.G.G. / Vieira, N.C.G. / Monteiro-Moreira, A.C.O. / Moereira, R.A.
History
DepositionJan 29, 2021Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 9, 2022Provider: repository / Type: Initial release
Revision 1.1Oct 18, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Lectin
B: Lectin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)51,0684
Polymers50,9582
Non-polymers1102
Water1,964109
1
A: Lectin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,5342
Polymers25,4791
Non-polymers551
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Lectin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,5342
Polymers25,4791
Non-polymers551
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)71.958, 71.958, 161.906
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number154
Space group name H-MP3221
Components on special symmetry positions
IDModelComponents
11B-442-

HOH

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Components

#1: Protein Lectin


Mass: 25479.197 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Dioclea violacea (plant) / References: UniProt: I1SB09
#2: Chemical ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mn
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 109 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 2.48 Å3/Da / Density % sol: 50.5 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 4.6
Details: 100mM Sodium acetate pH4.6, 200mM Ammonium sulphate, 25% PEG4000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04-1 / Wavelength: 0.92821 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: May 6, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.92821 Å / Relative weight: 1
ReflectionResolution: 2.21→161.91 Å / Num. obs: 25094 / % possible obs: 100 % / Redundancy: 11.6 % / CC1/2: 0.997 / Rmerge(I) obs: 0.202 / Net I/σ(I): 8.9
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsDiffraction-ID% possible all
2.21-2.279.73.42518421100
9.88-161.919.80.076352199.9

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Processing

Software
NameVersionClassification
PHENIX1.16_3549refinement
Aimless0.5.26data scaling
PDB_EXTRACT3.27data extraction
xia2data reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2JE9

2je9


Resolution: 2.21→62.318 Å / SU ML: 0.26 / Cross valid method: THROUGHOUT / σ(F): 1.33 / Phase error: 25.88 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2492 1290 5.18 %Random seelction
Rwork0.215 23600 --
obs0.2168 24890 99.19 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 99.3 Å2 / Biso mean: 44.7348 Å2 / Biso min: 18.74 Å2
Refinement stepCycle: final / Resolution: 2.21→62.318 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3392 0 2 109 3503
Biso mean--32.24 46.14 -
Num. residues----450
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.2102-2.29870.31271560.2942252498
2.2987-2.40330.29831500.2751255898
2.4033-2.530.32161590.2731253199
2.53-2.68850.31431300.2527260199
2.6885-2.89610.26641420.2211259999
2.8961-3.18750.29151300.21032630100
3.1875-3.64870.19891390.1782650100
3.6487-4.59680.18321510.1732662100
4.5968-62.3180.26441330.22972845100
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)
11.7054-0.2421-0.23282.72510.76132.05320.0118-0.26620.15220.2368-0.0488-0.1454-0.19350.20530.03830.3453-0.0638-0.00670.3707-0.0080.201-10.649431.6644-4.0684
22.0804-0.22470.2623.4550.76373.32420.0544-0.00650.0338-0.2248-0.08710.2907-0.1882-0.26630.07160.2252-0.0647-0.02060.239-0.01570.21-22.964124.2457-13.5988
32.62971.35380.24474.34671.54612.41690.1285-0.14440.4596-0.3312-0.18730.8236-1.0022-1.23540.21210.43860.0905-0.03460.5087-0.14190.429-32.463332.8883-10.412
46.8310.2328-3.90942.59642.67725.291-0.2321-0.2444-1.08120.40880.0343-0.06790.28610.15910.28220.3173-0.0786-0.0210.25820.04310.3107-14.730714.0227-8.9568
59.3798-5.5723-1.20693.57660.40483.30760.3914-0.16140.1624-1.05840.042-0.1441-0.2282-0.0601-0.42440.2323-0.0715-0.00180.2694-0.04840.2351-16.119630.1866-13.4814
62.3314-0.07971.16360.2671-0.76723.171-0.0941-0.3366-0.0360.6392-0.44970.1543-0.2526-0.29040.3920.4373-0.06160.07120.4523-0.05620.245-21.778928.6160.3866
73.8576-1.0130.23972.29961.50322.6759-0.1042-0.5328-0.32060.34050.158-0.64920.19740.5863-0.03330.27370.0218-0.04050.51150.14080.434315.717817.5307-18.2344
82.9380.06550.05490.99141.24223.75780.0164-0.2363-0.2460.25390.0356-0.0501-0.10620.38590.060.2123-0.0569-0.04590.35410.06340.29387.249823.9861-16.6639
92.5285-0.372-0.02772.69430.03933.29690.05020.1813-0.372-0.17990.0003-0.18350.05640.1761-0.02460.1975-0.02640.00020.33570.02460.33457.27417.8052-31.3268
103.2251-1.37030.22412.22760.44693.0803-0.1938-0.109-0.13090.30070.2164-0.6953-0.34310.753-0.0590.2162-0.0230.01840.5850.03770.506520.286920.5307-27.576
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 3 through 90 )A3 - 90
2X-RAY DIFFRACTION2chain 'A' and (resid 91 through 151 )A91 - 151
3X-RAY DIFFRACTION3chain 'A' and (resid 152 through 171 )A152 - 171
4X-RAY DIFFRACTION4chain 'A' and (resid 172 through 189 )A172 - 189
5X-RAY DIFFRACTION5chain 'A' and (resid 190 through 203 )A190 - 203
6X-RAY DIFFRACTION6chain 'A' and (resid 204 through 239 )A204 - 239
7X-RAY DIFFRACTION7chain 'B' and (resid 3 through 57 )B3 - 57
8X-RAY DIFFRACTION8chain 'B' and (resid 58 through 91 )B58 - 91
9X-RAY DIFFRACTION9chain 'B' and (resid 92 through 203 )B92 - 203
10X-RAY DIFFRACTION10chain 'B' and (resid 204 through 239 )B204 - 239

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