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- PDB-3u4x: Crystal structure of a lectin from Camptosema pedicellatum seeds ... -

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Basic information

Entry
Database: PDB / ID: 3u4x
TitleCrystal structure of a lectin from Camptosema pedicellatum seeds in complex with 5-bromo-4-chloro-3-indolyl-alpha-D-mannose
ComponentsCamptosema pedicellatum lectin (CPL)
Keywordscarbohydrate-binding protein / jelly-roll domain / lectin
Function / homology
Function and homology information


glucose binding / 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 CPL
Similarity search - Component
Biological speciesCamptosema pedicellatum (plant)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.16 Å
AuthorsRocha, B.A.M. / Teixeira, C.S. / Moura, T.R. / Silva, H.C. / Pereira-Junior, F.N. / Nagano, C.S. / Delatorre, P. / Cavada, B.S.
CitationJournal: J.Biochem. / Year: 2012
Title: Crystal structure of the lectin of Camptosema pedicellatum: implications of a conservative substitution at the hydrophobic subsite.
Authors: Souza Teixeira, C. / Colares da Silva, H. / Rocha de Moura, T. / Pereira-Junior, F.N. / Santiago do Nascimento, K. / Shiniti Nagano, C. / Holanda Sampaio, A. / Delatorre, P. / Matias Rocha, ...Authors: Souza Teixeira, C. / Colares da Silva, H. / Rocha de Moura, T. / Pereira-Junior, F.N. / Santiago do Nascimento, K. / Shiniti Nagano, C. / Holanda Sampaio, A. / Delatorre, P. / Matias Rocha, B.A. / Sousa Cavada, B.
History
DepositionOct 10, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 12, 2012Provider: repository / Type: Initial release
Revision 1.1Jul 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_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.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_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_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 1.2Feb 28, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Camptosema pedicellatum lectin (CPL)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,8234
Polymers25,3201
Non-polymers5043
Water1,38777
1
A: Camptosema pedicellatum lectin (CPL)
hetero molecules

A: Camptosema pedicellatum lectin (CPL)
hetero molecules

A: Camptosema pedicellatum lectin (CPL)
hetero molecules

A: Camptosema pedicellatum lectin (CPL)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)103,29416
Polymers101,2794
Non-polymers2,01512
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_545-x,-y-1,z1
crystal symmetry operation3_555-x,y,-z1
crystal symmetry operation4_545x,-y-1,-z1
Buried area10480 Å2
ΔGint-112 kcal/mol
Surface area32830 Å2
MethodPISA
Unit cell
Length a, b, c (Å)65.940, 66.780, 107.700
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number23
Space group name H-MI222

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Components

#1: Protein Camptosema pedicellatum lectin (CPL)


Mass: 25319.854 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: Seeds / Source: (natural) Camptosema pedicellatum (plant) / References: UniProt: J9PBR3*PLUS
#2: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca
#3: Chemical ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 1 / 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.: 1
Source method: isolated from a genetically manipulated source
Formula: C14H15BrClNO6
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 77 / 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: 2.34 Å3/Da / Density % sol: 47.47 %
Crystal growTemperature: 310 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: Hepes, Ammonium sulfate, PEG 400, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 310K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: LNLS / Beamline: D03B-MX1 / Wavelength: 1.42 Å
DetectorType: MAR CCD 165 mm / Detector: CCD / Date: Mar 18, 2008
RadiationMonochromator: Elastically bent silicon single crystal monochromator, Asymmetric angle 7.25, condensed mode, X-ray energy photons - 6 keV-12 keV (1 -2 A).
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.42 Å / Relative weight: 1
Reflection twin
Crystal-IDIDOperatorDomain-IDFraction
11H, K, L10.944
11K, H, -L20.056
ReflectionResolution: 2.16→21.51 Å / Num. obs: 12708 / % possible obs: 94.7 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Biso Wilson estimate: 18.012 Å2 / Rmerge(I) obs: 0.147 / Rsym value: 0.147
Reflection shellResolution: 2.16→2.215 Å / % possible all: 94.7

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Phasing

PhasingMethod: molecular replacement
Phasing MR
Highest resolutionLowest resolution
Rotation2.25 Å28.38 Å
Translation2.25 Å28.38 Å

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Processing

Software
NameVersionClassificationNB
MOLREPphasing
REFMACrefinement
PDB_EXTRACT3.1data extraction
MOSFLMdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.16→21.51 Å / Cor.coef. Fo:Fc: 0.923 / Cor.coef. Fo:Fc free: 0.865 / Occupancy max: 1 / Occupancy min: 0.5 / SU B: 5.149 / SU ML: 0.131 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.045 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.2368 636 5 %RANDOM
Rwork0.1902 ---
all0.1925 16817 --
obs0.1925 11436 96.96 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso max: 55.9 Å2 / Biso mean: 17.2771 Å2 / Biso min: 2 Å2
Baniso -1Baniso -2Baniso -3
1-0.03 Å20 Å20 Å2
2---0.36 Å20 Å2
3---0.33 Å2
Refinement stepCycle: LAST / Resolution: 2.16→21.51 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1790 0 25 77 1892
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.020.0221852
X-RAY DIFFRACTIONr_angle_refined_deg1.9241.952534
X-RAY DIFFRACTIONr_dihedral_angle_1_deg9.5335235
X-RAY DIFFRACTIONr_dihedral_angle_2_deg39.28624.8179
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.4415271
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.129157
X-RAY DIFFRACTIONr_chiral_restr0.130.2292
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.0211419
X-RAY DIFFRACTIONr_mcbond_it1.0751.51174
X-RAY DIFFRACTIONr_mcangle_it1.89421899
X-RAY DIFFRACTIONr_scbond_it2.673678
X-RAY DIFFRACTIONr_scangle_it4.0874.5635
LS refinement shellResolution: 2.16→2.215 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.348 25 -
Rwork0.226 558 -
all-583 -
obs--61.76 %

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