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- PDB-5duy: Structure of lectin from the sea mussel Crenomytilus grayanus -

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Basic information

Entry
Database: PDB / ID: 5duy
TitleStructure of lectin from the sea mussel Crenomytilus grayanus
ComponentsGalNAc/Gal-specific lectin
KeywordsSUGAR BINDING PROTEIN / lectin / sea vertebrate / recombinant / trefoil
Function / homologyTrefoil (Acidic Fibroblast Growth Factor, subunit A) - #50 / Trefoil (Acidic Fibroblast Growth Factor, subunit A) / Trefoil / carbohydrate binding / Mainly Beta / Galactose-binding lectin
Function and homology information
Biological speciesCrenomytilus grayanus (invertebrata)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.12 Å
AuthorsLubkowski, J. / Jakob, M. / O'Keefe, B. / Wlodawer, A.
CitationJournal: Acta Crystallogr.,Sect.F / Year: 2015
Title: Structure of a lectin from the sea mussel Crenomytilus grayanus (CGL).
Authors: Jakob, M. / Lubkowski, J. / O'Keefe, B.R. / Wlodawer, A.
History
DepositionSep 21, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 11, 2015Provider: repository / Type: Initial release
Revision 1.1Nov 18, 2015Group: Database references
Revision 1.2Dec 23, 2015Group: Structure summary
Revision 1.3Nov 1, 2017Group: Author supporting evidence / Derived calculations
Category: pdbx_struct_assembly_auth_evidence / pdbx_struct_oper_list
Item: _pdbx_struct_oper_list.symmetry_operation
Revision 1.4Mar 6, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
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: GalNAc/Gal-specific lectin
B: GalNAc/Gal-specific lectin
C: GalNAc/Gal-specific lectin
D: GalNAc/Gal-specific lectin
E: GalNAc/Gal-specific lectin
F: GalNAc/Gal-specific lectin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)125,82424
Polymers124,1666
Non-polymers1,65818
Water13,385743
1
A: GalNAc/Gal-specific lectin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)20,9714
Polymers20,6941
Non-polymers2763
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: GalNAc/Gal-specific lectin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)20,9714
Polymers20,6941
Non-polymers2763
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: GalNAc/Gal-specific lectin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)20,9714
Polymers20,6941
Non-polymers2763
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
4
D: GalNAc/Gal-specific lectin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)20,9714
Polymers20,6941
Non-polymers2763
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
5
E: GalNAc/Gal-specific lectin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)20,9714
Polymers20,6941
Non-polymers2763
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
6
F: GalNAc/Gal-specific lectin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)20,9714
Polymers20,6941
Non-polymers2763
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)137.289, 68.337, 131.694
Angle α, β, γ (deg.)90.00, 110.55, 90.00
Int Tables number5
Space group name H-MC121
DetailsMonomer confirmed by gel filtration and X-ray analysis

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Components

#1: Protein
GalNAc/Gal-specific lectin


Mass: 20694.383 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Details: The synthetic gene was cloned in the Gateway (R) system with the N-TERMINAL HIS6-TAG
Source: (gene. exp.) Crenomytilus grayanus (invertebrata)
Description: Non-optimized sequence synthesized by BioiBasic
Production host: Escherichia coli (E. coli) / References: UniProt: H2FH31
#2: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 18 / Source method: obtained synthetically / Formula: C3H8O3
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 743 / 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: 2.33 Å3/Da / Density % sol: 47.2 % / Description: needles
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 0.1 M HEPES pH 7.0, 18% (w/v) PEG4000, 0.1 M SODIUM ACETATE, 0.1 M LITHIUM SUFFATE
Temp details: incubator

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1 Å
DetectorType: RAYONIX MX300HS / Detector: CCD / Date: Oct 10, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.12→50 Å / Num. obs: 63465 / % possible obs: 97.7 % / Redundancy: 5.3 % / Rmerge(I) obs: 0.07 / Net I/σ(I): 21.2
Reflection shellResolution: 2.12→2.16 Å / Redundancy: 4.7 % / Rmerge(I) obs: 0.421 / Mean I/σ(I) obs: 3.9 / % possible all: 80.2

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Processing

Software
NameVersionClassification
REFMAC5.5.0104refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
MR-Rosettaphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: Model was an electron density calculated for the assembly of 39 homologous structures

Resolution: 2.12→38 Å / Cor.coef. Fo:Fc: 0.972 / Cor.coef. Fo:Fc free: 0.946 / SU B: 7.428 / SU ML: 0.09 / Cross valid method: THROUGHOUT / ESU R: 0.16 / ESU R Free: 0.145 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.18422 1922 3 %RANDOM
Rwork0.13937 ---
obs0.14072 61539 97.58 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 29.068 Å2
Baniso -1Baniso -2Baniso -3
1-0.74 Å20 Å2-0.05 Å2
2--0.76 Å20 Å2
3----1.54 Å2
Refinement stepCycle: 1 / Resolution: 2.12→38 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7210 0 108 743 8061
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0190.0217631
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.6321.93510297
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.1055914
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.37423.874382
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.807151234
X-RAY DIFFRACTIONr_dihedral_angle_4_deg23.4591533
X-RAY DIFFRACTIONr_chiral_restr0.1240.21025
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.0215931
X-RAY DIFFRACTIONr_gen_planes_other
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_it0.811.54519
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.38527312
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it2.53833112
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it3.7184.52973
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.12→2.175 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.194 133 -
Rwork0.168 3736 -
obs--81.44 %
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)
11.33660.06880.06461.06090.47792.55850.0192-0.1094-0.03070.1579-0.02740.06240.1531-0.24390.00830.063-0.01910.00870.05770.01230.01628.7020.05221.69
21.49540.07810.21990.8651-0.1122.7230.06990.1654-0.0333-0.0691-0.071-0.05050.07730.34540.00110.08030.037-0.00840.08770.00160.00951.72111.47147.073
33.0912-1.3166-1.36092.17210.70892.10410.21220.45180.3306-0.2406-0.0865-0.2044-0.148-0.2265-0.12560.1050.01120.04420.09920.07820.099627.28635.42746.188
42.15960.407-1.29562.2413-0.03172.4352-0.16580.13810.0746-0.17060.1447-0.0330.14110.00020.0210.0519-0.03430.01190.0437-0.02750.058412.2784.96451.186
51.1883-0.1514-0.04552.297-1.15532.3806-0.031-0.1452-0.01080.2860.18450.2474-0.2571-0.2558-0.15340.05910.05280.03010.06670.02290.040125.71430.3986.333
63.8906-0.6333-0.80311.3971-0.16512.1021-0.2038-0.58490.2930.210.1993-0.14960.11320.20460.00450.09280.0461-0.08770.1359-0.0510.104859.02824.68812.592
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A2 - 150
2X-RAY DIFFRACTION1A201
3X-RAY DIFFRACTION2B2 - 150
4X-RAY DIFFRACTION2B201
5X-RAY DIFFRACTION3C1 - 150
6X-RAY DIFFRACTION3C201
7X-RAY DIFFRACTION4D2 - 150
8X-RAY DIFFRACTION4D201
9X-RAY DIFFRACTION5E3 - 150
10X-RAY DIFFRACTION5E201
11X-RAY DIFFRACTION6F2 - 150
12X-RAY DIFFRACTION6F201

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