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- PDB-4wqq: Structure of EPNH mutant of CEL-I -

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Basic information

Entry
Database: PDB / ID: 4wqq
TitleStructure of EPNH mutant of CEL-I
ComponentsLectin CEL-I, N-acetyl-D-galactosamine-specific C-type
KeywordsSUGAR BINDING PROTEIN / CEL-I / EPNH munant / C-type lectin / mannose recognition
Function / homology
Function and homology information


signaling receptor activity / metal ion binding
Similarity search - Function
CEL-1-like C-type lectin-like domain / : / Mannose-Binding Protein A; Chain A / Mannose-Binding Protein A, subunit A / Lectin C-type domain / C-type lectin domain profile. / C-type lectin-like / C-type lectin (CTL) or carbohydrate-recognition domain (CRD) / C-type lectin-like/link domain superfamily / C-type lectin fold ...CEL-1-like C-type lectin-like domain / : / Mannose-Binding Protein A; Chain A / Mannose-Binding Protein A, subunit A / Lectin C-type domain / C-type lectin domain profile. / C-type lectin-like / C-type lectin (CTL) or carbohydrate-recognition domain (CRD) / C-type lectin-like/link domain superfamily / C-type lectin fold / Roll / Alpha Beta
Similarity search - Domain/homology
alpha-D-mannopyranose / Lectin CEL-I, N-acetyl-D-galactosamine-specific C-type
Similarity search - Component
Biological speciesCucumaria echinata (invertebrata)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.7 Å
AuthorsUnno, H. / Hatakeyama, T.
CitationJournal: Biochim.Biophys.Acta / Year: 2015
Title: Mannose-recognition mutant of the galactose/N-acetylgalactosamine-specific C-type lectin CEL-I engineered by site-directed mutagenesis.
Authors: Moriuchi, H. / Unno, H. / Goda, S. / Tateno, H. / Hirabayashi, J. / Hatakeyama, T.
History
DepositionOct 22, 2014Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Apr 29, 2015Provider: repository / Type: Initial release
Revision 1.1May 20, 2015Group: Database references
Revision 1.2Jul 29, 2020Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Source and taxonomy / Structure summary
Category: chem_comp / citation ...chem_comp / citation / entity / entity_src_gen / pdbx_chem_comp_identifier / pdbx_database_status / pdbx_entity_nonpoly / pdbx_struct_assembly / pdbx_struct_assembly_gen / pdbx_struct_assembly_prop / pdbx_struct_conn_angle / pdbx_struct_oper_list / struct_conn / struct_site / struct_site_gen
Item: _chem_comp.name / _chem_comp.type ..._chem_comp.name / _chem_comp.type / _citation.journal_id_CSD / _entity.pdbx_description / _entity_src_gen.pdbx_alt_source_flag / _pdbx_database_status.pdb_format_compatible / _pdbx_entity_nonpoly.name / _pdbx_struct_assembly.oligomeric_details / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_struct_assembly_prop.type / _pdbx_struct_assembly_prop.value / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.value / _pdbx_struct_oper_list.symmetry_operation / _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.ptnr1_symmetry / _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_conn.ptnr2_symmetry
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.3Nov 8, 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: Lectin CEL-I, N-acetyl-D-galactosamine-specific C-type
B: Lectin CEL-I, N-acetyl-D-galactosamine-specific C-type
C: Lectin CEL-I, N-acetyl-D-galactosamine-specific C-type
D: Lectin CEL-I, N-acetyl-D-galactosamine-specific C-type
hetero molecules


Theoretical massNumber of molelcules
Total (without water)65,71920
Polymers64,5184
Non-polymers1,20216
Water13,655758
1
A: Lectin CEL-I, N-acetyl-D-galactosamine-specific C-type
B: Lectin CEL-I, N-acetyl-D-galactosamine-specific C-type
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,86010
Polymers32,2592
Non-polymers6018
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2900 Å2
ΔGint-78 kcal/mol
Surface area12980 Å2
MethodPISA
2
C: Lectin CEL-I, N-acetyl-D-galactosamine-specific C-type
D: Lectin CEL-I, N-acetyl-D-galactosamine-specific C-type
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,86010
Polymers32,2592
Non-polymers6018
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2910 Å2
ΔGint-78 kcal/mol
Surface area12990 Å2
MethodPISA
Unit cell
Length a, b, c (Å)64.290, 61.060, 80.700
Angle α, β, γ (deg.)90.00, 109.39, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
Lectin CEL-I, N-acetyl-D-galactosamine-specific C-type


Mass: 16129.394 Da / Num. of mol.: 4 / Mutation: Q101E, D103N, W105H
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Cucumaria echinata (invertebrata) / Production host: Escherichia coli (E. coli) / References: UniProt: Q7M462
#2: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: Ca
#3: Sugar
ChemComp-MAN / alpha-D-mannopyranose / alpha-D-mannose / D-mannose / mannose


Type: D-saccharide, alpha linking / Mass: 180.156 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C6H12O6
IdentifierTypeProgram
DManpaCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
a-D-mannopyranoseCOMMON NAMEGMML 1.0
a-D-ManpIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
ManSNFG CARBOHYDRATE SYMBOLGMML 1.0
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 758 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.32 Å3/Da / Density % sol: 46.89 %
Crystal growTemperature: 293 K / Method: vapor diffusion / pH: 6.5
Details: 30% polyethyleneglycol 4000, 0.2 M magnesium acetate, 0.1 M sodium cacodylate.

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Dec 16, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.7→30.53 Å / Num. obs: 60007 / % possible obs: 92.6 % / Redundancy: 3.8 % / Rmerge(I) obs: 0.051 / Net I/σ(I): 15.9
Reflection shellResolution: 1.7→1.79 Å / Redundancy: 3.8 % / Rmerge(I) obs: 0.3 / Mean I/σ(I) obs: 3.9 / % possible all: 88.6

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Processing

Software
NameVersionClassification
REFMAC5.8.0073refinement
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1WMY

1wmy


Resolution: 1.7→30 Å / Cor.coef. Fo:Fc: 0.966 / Cor.coef. Fo:Fc free: 0.947 / SU B: 1.899 / SU ML: 0.063 / Cross valid method: THROUGHOUT / ESU R: 0.105 / ESU R Free: 0.104 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.19024 3067 5.1 %RANDOM
Rwork0.15157 ---
obs0.15356 56922 92.25 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 16.434 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refinement stepCycle: 1 / Resolution: 1.7→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4552 0 60 758 5370
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0190.0194776
X-RAY DIFFRACTIONr_bond_other_d0.0010.023947
X-RAY DIFFRACTIONr_angle_refined_deg1.81.8816515
X-RAY DIFFRACTIONr_angle_other_deg0.91939069
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.7615570
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.22624.783276
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.94115669
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.9011516
X-RAY DIFFRACTIONr_chiral_restr0.1180.2637
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.025659
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021293
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.3851.4252262
X-RAY DIFFRACTIONr_mcbond_other1.3811.4242261
X-RAY DIFFRACTIONr_mcangle_it1.9632.1312823
X-RAY DIFFRACTIONr_mcangle_other1.9632.1312824
X-RAY DIFFRACTIONr_scbond_it2.3231.6292514
X-RAY DIFFRACTIONr_scbond_other2.3231.632515
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other3.5372.3643688
X-RAY DIFFRACTIONr_long_range_B_refined5.25213.4416639
X-RAY DIFFRACTIONr_long_range_B_other4.90312.6716215
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.7→1.744 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.29 227 -
Rwork0.279 4002 -
obs--88.09 %

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