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- PDB-4g9m: Crystal structure of the Rhizoctonia solani agglutinin -

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Basic information

Entry
Database: PDB / ID: 4g9m
TitleCrystal structure of the Rhizoctonia solani agglutinin
Componentsagglutinin
KeywordsSUGAR BINDING PROTEIN / Lectin / carbohydrate-binding specificity
Function / homologyRicin-type beta-trefoil lectin domain-like / Ricin B, lectin domain / Ricin B-like lectins / Trefoil (Acidic Fibroblast Growth Factor, subunit A) - #50 / Trefoil (Acidic Fibroblast Growth Factor, subunit A) / Trefoil / carbohydrate binding / Mainly Beta / Ricin-type beta-trefoil lectin domain-containing protein
Function and homology information
Biological speciesRhizoctonia solani (fungus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.601 Å
AuthorsSkamnaki, V.T. / Kantsadi, A.L. / Leonidas, D.D.
CitationJournal: Febs J. / Year: 2013
Title: Structural analysis of the Rhizoctonia solani agglutinin reveals a domain-swapping dimeric assembly.
Authors: Skamnaki, V.T. / Peumans, W.J. / Kantsadi, A.L. / Cubeta, M.A. / Plas, K. / Pakala, S. / Zographos, S.E. / Smagghe, G. / Nierman, W.C. / Van Damme, E.J. / Leonidas, D.D.
History
DepositionJul 24, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 5, 2013Provider: repository / Type: Initial release
Revision 1.1Mar 7, 2018Group: Data collection / Category: diffrn_source / Item: _diffrn_source.pdbx_synchrotron_site
Revision 1.2Sep 13, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _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: agglutinin
B: agglutinin


Theoretical massNumber of molelcules
Total (without water)30,9662
Polymers30,9662
Non-polymers00
Water4,450247
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2310 Å2
ΔGint-13 kcal/mol
Surface area11580 Å2
MethodPISA
Unit cell
Length a, b, c (Å)121.979, 61.091, 32.793
Angle α, β, γ (deg.)90.00, 93.00, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein agglutinin


Mass: 15483.156 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Rhizoctonia solani (fungus) / References: UniProt: L8WGI4*PLUS
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 247 / 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: 1.97 Å3/Da / Density % sol: 37.57 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 4.2
Details: 0.1 M sodium acetate, pH 4.2, 20% v/v PEG8000, 0.2 M sodium chloride, 10 mM sodium citrate, VAPOR DIFFUSION, SITTING DROP, temperature 289K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: MAX II / Beamline: I911-2 / Wavelength: 1.03954 Å
DetectorType: MAR CCD 165 mm / Detector: CCD / Date: Oct 20, 2011
RadiationMonochromator: bent Si(111) crystal, horizontally focusing / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.03954 Å / Relative weight: 1
ReflectionResolution: 1.6→20.734 Å / Num. all: 27436 / Num. obs: 27436 / % possible obs: 86.4 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 14.63 % / Biso Wilson estimate: 21.05 Å2 / Rsym value: 0.09 / Net I/σ(I): 4.9
Reflection shellResolution: 1.6→1.66 Å / Mean I/σ(I) obs: 1.5 / Rsym value: 0.342 / % possible all: 37.5

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Processing

Software
NameVersionClassification
DNAdata collection
MrBUMPphasing
PHENIX(phenix.refine: 1.7.3_928)refinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2X2S

2x2s


Resolution: 1.601→20.734 Å / SU ML: 0.19 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 24.88 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.232 1386 5.05 %RANDOM
Rwork0.1813 ---
obs0.184 27436 86.43 %-
all-27436 --
Solvent computationShrinkage radii: 0.6 Å / VDW probe radii: 0.9 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 80.942 Å2 / ksol: 0.438 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-4.3207 Å2-0 Å21.6549 Å2
2--1.4573 Å20 Å2
3----5.7779 Å2
Refinement stepCycle: LAST / Resolution: 1.601→20.734 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2178 0 0 247 2425
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0062244
X-RAY DIFFRACTIONf_angle_d1.0973065
X-RAY DIFFRACTIONf_dihedral_angle_d12.422800
X-RAY DIFFRACTIONf_chiral_restr0.081348
X-RAY DIFFRACTIONf_plane_restr0.004399
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.601-1.65840.2667610.27261120X-RAY DIFFRACTION37
1.6584-1.72480.30261070.25011989X-RAY DIFFRACTION66
1.7248-1.80320.29061440.2252572X-RAY DIFFRACTION86
1.8032-1.89820.25441510.20152845X-RAY DIFFRACTION95
1.8982-2.01710.25441490.18562894X-RAY DIFFRACTION97
2.0171-2.17260.24531500.17462928X-RAY DIFFRACTION97
2.1726-2.3910.20291570.17842912X-RAY DIFFRACTION97
2.391-2.73630.26911440.18732983X-RAY DIFFRACTION98
2.7363-3.44490.23861650.182946X-RAY DIFFRACTION98
3.4449-20.73530.20341580.1662861X-RAY DIFFRACTION93
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)
10.5730.1709-0.52930.0873-0.0370.7439-0.48090.2905-0.2357-0.25390.18930.16350.515-0.3661-0.01190.3408-0.0670.04670.1221-0.03490.243339.914234.90362.0898
21.07140.4546-1.30761.4378-0.33181.2393-0.1677-0.217-0.2633-0.075-0.1178-0.23720.23770.209-0.020.20730.02280.03220.14670.04820.203441.252732.040310.8552
30.61081.0393-0.63551.9657-0.9750.977-0.2175-1.0213-0.5155-0.1696-0.0293-0.93840.11950.7028-0.21480.18040.0559-0.00450.49770.06060.281152.272734.733511.4085
40.5816-0.0169-0.34760.50450.26040.4057-0.21270.0906-0.3046-0.60380.0711-0.19660.2292-0.008-0.03540.25910.01060.09750.19890.01430.278149.106333.73383.6116
50.1313-0.1779-0.05740.11660.00130.0305-0.0370.23750.1461-0.2817-0.06220.08560.0526-0.53260.01270.2175-0.0353-0.00080.2475-0.01390.140940.73154.44482.4618
60.1202-0.098-0.03570.0391-0.02470.06390.17070.01670.49260.26450.02090.2536-0.2757-0.0848-0.00020.2165-0.00690.00150.1462-0.00580.208340.636768.551812.188
70.06560.1216-0.09940.1809-0.12850.11860.01450.06090.4083-0.0170.05560.0452-0.1963-0.09950.00010.17880.0101-0.02230.19370.0210.189544.581971.593110.7422
80.0316-0.0735-0.00080.06190.0302-0.0080.23780.1409-0.0028-0.4841-0.1183-0.0427-0.115-0.14380.00020.20040.01950.0010.20330.02830.181147.033162.48853.2852
90.20910.0528-0.05530.0684-0.10110.0376-0.02520.0296-0.0061-0.0505-0.03680.079-0.14410.053100.18370.0035-0.00890.15650.02160.172353.242360.04847.0509
100.4316-0.3564-0.2670.36520.16280.15550.268-0.4760.16560.3062-0.1904-0.2618-0.201-0.1240.0150.1577-0.0061-0.02480.30310.0170.144352.624662.34124.2917
110.01320.1922-0.09370.0863-0.1770.03530.0113-0.0069-0.08150.0308-0.0731-0.0916-0.021-0.029800.1407-0.0083-0.00830.1899-0.00990.182347.463255.61412.8938
120.230.13610.07990.1561-0.13470.2658-0.05020.1926-0.04450.1781-0.1474-0.0289-0.1039-0.0416-0.00030.21670.0138-0.01160.22320.01420.173546.493956.844920.5886
130.0738-0.0886-0.15230.15140.1140.356-0.077-0.08560.10360.06820.08260.0619-0.0082-0.154600.15070.0059-0.02970.1982-0.01360.154840.108160.929120.4384
140.12650.0882-0.02280.0067-0.00650.00730.02870.1293-0.0358-0.1621-0.0986-0.12210.3971-0.0458-0.00010.1963-0.0017-0.01660.23450.00580.149938.89958.10633.3828
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resseq 1:26)
2X-RAY DIFFRACTION2chain 'A' and (resseq 27:103)
3X-RAY DIFFRACTION3chain 'A' and (resseq 104:116)
4X-RAY DIFFRACTION4chain 'A' and (resseq 117:142)
5X-RAY DIFFRACTION5chain 'B' and (resseq 1:14)
6X-RAY DIFFRACTION6chain 'B' and (resseq 15:26)
7X-RAY DIFFRACTION7chain 'B' and (resseq 27:42)
8X-RAY DIFFRACTION8chain 'B' and (resseq 43:51)
9X-RAY DIFFRACTION9chain 'B' and (resseq 52:71)
10X-RAY DIFFRACTION10chain 'B' and (resseq 72:80)
11X-RAY DIFFRACTION11chain 'B' and (resseq 81:103)
12X-RAY DIFFRACTION12chain 'B' and (resseq 104:116)
13X-RAY DIFFRACTION13chain 'B' and (resseq 117:136)
14X-RAY DIFFRACTION14chain 'B' and (resseq 137:143)

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