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- PDB-3als: Crystal structure of CEL-IV -

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Basic information

Entry
Database: PDB / ID: 3als
TitleCrystal structure of CEL-IV
ComponentsLectin CEL-IV, C-type
KeywordsSUGAR BINDING PROTEIN / CEL-IV / C-type lectin
Function / homology
Function and homology information


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
Lectin CEL-IV, C-type
Similarity search - Component
Biological speciesCucumaria echinata (invertebrata)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3 Å
AuthorsHatakeyama, T. / Hozawa, T. / Ishii, K. / Kamiya, T. / Goda, S. / Kusunoki, M. / Unno, H.
CitationJournal: J.Biol.Chem. / Year: 2011
Title: Galactose recognition by a tetrameric C-type lectin, CEL-IV, containing the EPN carbohydrate recognition motif
Authors: Hatakeyama, T. / Kamiya, T. / Kusunoki, M. / Nakamura-Tsuruta, S. / Hirabayashi, J. / Goda, S. / Unno, H.
History
DepositionAug 7, 2010Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jan 19, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Jan 29, 2014Group: Database references
Revision 1.3Nov 1, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / struct_ncs_dom_lim / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _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.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_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_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 / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Lectin CEL-IV, C-type
B: Lectin CEL-IV, C-type
C: Lectin CEL-IV, C-type
D: Lectin CEL-IV, C-type
hetero molecules


Theoretical massNumber of molelcules
Total (without water)68,5968
Polymers68,4354
Non-polymers1604
Water1,47782
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7760 Å2
ΔGint-60 kcal/mol
Surface area25890 Å2
MethodPISA
Unit cell
Length a, b, c (Å)86.065, 86.065, 375.321
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number170
Space group name H-MP65
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
31C
41D

NCS domain segments:

Component-ID: 1 / Ens-ID: 1 / Beg auth comp-ID: LEU / Beg label comp-ID: LEU / End auth comp-ID: GLU / End label comp-ID: GLU / Refine code: 1 / Auth seq-ID: 2 - 157 / Label seq-ID: 2 - 157

Dom-IDAuth asym-IDLabel asym-ID
1AA
2BB
3CC
4DD

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Components

#1: Protein
Lectin CEL-IV, C-type


Mass: 17108.805 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Source: (natural) Cucumaria echinata (invertebrata) / References: UniProt: Q7M4F9
#2: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Ca
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 82 / 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: 5.86 Å3/Da / Density % sol: 79.02 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 0.1M HEPES, 4.3M NaCl, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 90 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-6A / Wavelength: 0.978 Å
DetectorType: ADSC QUANTUM 4r / Detector: CCD / Date: Oct 12, 2007
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.978 Å / Relative weight: 1
ReflectionResolution: 3→47.9 Å / Num. obs: 31417 / % possible obs: 99.9 % / Redundancy: 11.4 % / Biso Wilson estimate: 63.6 Å2 / Rmerge(I) obs: 0.077 / Net I/σ(I): 29.4
Reflection shellResolution: 3→3.16 Å / Redundancy: 11.1 % / Rmerge(I) obs: 0.298 / Mean I/σ(I) obs: 8.6 / % possible all: 99.5

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Processing

Software
NameVersionClassification
HKL-2000data collection
PHASERphasing
REFMAC5.5.0109refinement
XDSdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1WMY

1wmy


Resolution: 3→43.03 Å / Cor.coef. Fo:Fc: 0.921 / Cor.coef. Fo:Fc free: 0.905 / SU B: 10.668 / SU ML: 0.191 / Cross valid method: THROUGHOUT / ESU R Free: 0.265 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.21475 1575 5 %RANDOM
Rwork0.19565 ---
obs0.1966 29729 99.97 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 39.869 Å2
Baniso -1Baniso -2Baniso -3
1-0.07 Å20.04 Å20 Å2
2--0.07 Å20 Å2
3----0.11 Å2
Refinement stepCycle: LAST / Resolution: 3→43.03 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4788 0 4 82 4874
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0240.0214940
X-RAY DIFFRACTIONr_angle_refined_deg2.1291.9136744
X-RAY DIFFRACTIONr_dihedral_angle_1_deg8.5025620
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.71124.667240
X-RAY DIFFRACTIONr_dihedral_angle_3_deg19.37315688
X-RAY DIFFRACTIONr_dihedral_angle_4_deg24.0931516
X-RAY DIFFRACTIONr_chiral_restr0.1420.2700
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.0213920
X-RAY DIFFRACTIONr_mcbond_it0.9561.53080
X-RAY DIFFRACTIONr_mcangle_it1.91424912
X-RAY DIFFRACTIONr_scbond_it2.55631860
X-RAY DIFFRACTIONr_scangle_it4.314.51832
Refine LS restraints NCS

Ens-ID: 1 / Number: 1197 / Refine-ID: X-RAY DIFFRACTION

Dom-IDAuth asym-IDTypeRms dev position (Å)Weight position
1Atight positional0.090.05
2Btight positional0.090.05
3Ctight positional0.090.05
4Dtight positional0.090.05
1Atight thermal0.120.5
2Btight thermal0.120.5
3Ctight thermal0.120.5
4Dtight thermal0.120.5
LS refinement shellResolution: 3→3.078 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.343 108 -
Rwork0.299 2225 -
obs--99.79 %

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