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- PDB-4akd: High resolution structure of Mannose Binding lectin from Champeda... -

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Basic information

Entry
Database: PDB / ID: 4akd
TitleHigh resolution structure of Mannose Binding lectin from Champedak (CMB)
ComponentsMANNOSE-SPECIFIC LECTIN KM+
KeywordsSUGAR BINDING PROTEIN
Function / homology
Function and homology information


carbohydrate binding
Similarity search - Function
Jacalin-like lectin domain, plant / Jacalin-like lectin domain / Jacalin-like lectin domain / Jacalin-type lectin domain profile. / Aligned Prism / Vitelline Membrane Outer Layer Protein I, subunit A / Jacalin-like lectin domain / Jacalin-like lectin domain / Jacalin-like lectin domain superfamily / Mainly Beta
Similarity search - Domain/homology
: / Mannose-specific lectin KM+
Similarity search - Component
Biological speciesARTOCARPUS INTEGER (chempedak)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å
AuthorsGabrielsen, M. / Abdul-Rahman, P.S. / Othman, S. / Hashim, O.H. / Cogdell, R.J.
Citation
Journal: Acta Crystallogr.,Sect.F / Year: 2014
Title: Structures and Binding Specificity of Galactose- and Mannose-Binding Lectins from Champedak: Differences from Jackfruit Lectins
Authors: Gabrielsen, M. / Abdul-Rahman, P.S. / Othman, S. / Hashim, O.H. / Cogdell, R.J.
#1: Journal: Acta Crystallogr.,Sect.F / Year: 2010
Title: Crystallization and Initial X-Ray Diffraction Analysis of a Mannose-Binding Lectin from Champedak.
Authors: Gabrielsen, M. / Abdul-Rahman, P.S. / Isaacs, N.W. / Hashim, O.H. / Cogdell, R.J.
History
DepositionFeb 22, 2012Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 27, 2013Provider: repository / Type: Initial release
Revision 1.1Jun 11, 2014Group: Database references
Revision 1.2Jun 18, 2014Group: Database references
Revision 1.3Dec 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _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.ptnr1_symmetry / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_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.ptnr3_symmetry / _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.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 / _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: MANNOSE-SPECIFIC LECTIN KM+
B: MANNOSE-SPECIFIC LECTIN KM+
C: MANNOSE-SPECIFIC LECTIN KM+
D: MANNOSE-SPECIFIC LECTIN KM+
hetero molecules


Theoretical massNumber of molelcules
Total (without water)65,84819
Polymers64,7014
Non-polymers1,14715
Water4,990277
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7760 Å2
ΔGint-76.2 kcal/mol
Surface area23680 Å2
MethodPISA
Unit cell
Length a, b, c (Å)76.887, 86.222, 95.373
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein
MANNOSE-SPECIFIC LECTIN KM+ / CHAMPEDAK MANNOSE BINDING LECTIN


Mass: 16175.169 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Source: (natural) ARTOCARPUS INTEGER (chempedak) / References: UniProt: Q7M1T4
#2: Chemical
ChemComp-CD / CADMIUM ION


Mass: 112.411 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: Cd
#3: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: Cl
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 277 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsCROSS-REFERENCE IS TO NEAREST UNIPROT BUT SEQUENCE IS VARIANT WITH GENBANK REFERENCE GB FR728241.

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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: 47.51 % / Description: NONE
Crystal growpH: 7.6
Details: 0.1 M CADMIUM CHLORIDE, 0.1 M SODIUM ACETATE PH 4.6, 30% POLYETHYLENE GLYCOL 400

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.9763
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Dec 14, 2009
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9763 Å / Relative weight: 1
ReflectionResolution: 2.1→49.17 Å / Num. obs: 37852 / % possible obs: 99.8 % / Observed criterion σ(I): 22.4 / Redundancy: 14.5 % / Biso Wilson estimate: 36.1 Å2 / Rmerge(I) obs: 0.08 / Net I/σ(I): 22.4
Reflection shellResolution: 2.1→2.21 Å / Redundancy: 14.6 % / Rmerge(I) obs: 0.63 / Mean I/σ(I) obs: 4.9 / % possible all: 99.2

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Processing

Software
NameVersionClassification
BUSTER2.10.0refinement
MOSFLMdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1J4U

1j4u


Resolution: 2.1→47.69 Å / Cor.coef. Fo:Fc: 0.9451 / Cor.coef. Fo:Fc free: 0.9231 / SU R Cruickshank DPI: 0.208 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.214 / SU Rfree Blow DPI: 0.178 / SU Rfree Cruickshank DPI: 0.177
Details: IDEAL-DIST CONTACT TERM CONTACT SETUP. RESIDUE TYPES WITHOUT CCP4 ATOM TYPE IN LIBRARY=CD CL. NUMBER OF ATOMS WITH PROPER CCP4 ATOM TYPE=4814. NUMBER WITH APPROX DEFAULT CCP4 ATOM TYPE=0. ...Details: IDEAL-DIST CONTACT TERM CONTACT SETUP. RESIDUE TYPES WITHOUT CCP4 ATOM TYPE IN LIBRARY=CD CL. NUMBER OF ATOMS WITH PROPER CCP4 ATOM TYPE=4814. NUMBER WITH APPROX DEFAULT CCP4 ATOM TYPE=0. NUMBER TREATED BY BAD NON-BONDED CONTACTS=15.
RfactorNum. reflection% reflectionSelection details
Rfree0.2357 1879 4.99 %RANDOM
Rwork0.1934 ---
obs0.1956 37670 99.95 %-
Displacement parametersBiso mean: 48.87 Å2
Baniso -1Baniso -2Baniso -3
1-5.9122 Å20 Å20 Å2
2---4.0715 Å20 Å2
3----1.8407 Å2
Refinement stepCycle: LAST / Resolution: 2.1→47.69 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4519 0 15 277 4811
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.014662HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.196338HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d1514SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes99HARMONIC2
X-RAY DIFFRACTIONt_gen_planes692HARMONIC5
X-RAY DIFFRACTIONt_it4662HARMONIC20
X-RAY DIFFRACTIONt_nbd0SEMIHARMONIC5
X-RAY DIFFRACTIONt_omega_torsion3.53
X-RAY DIFFRACTIONt_other_torsion19.1
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion595SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact5289SEMIHARMONIC4
LS refinement shellResolution: 2.1→2.16 Å / Total num. of bins used: 19
RfactorNum. reflection% reflection
Rfree0.2195 117 4.08 %
Rwork0.2101 2754 -
all0.2105 2871 -
obs--99.95 %
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)
12.1749-0.5063-0.21521.79360.7881.67390.0147-0.4596-0.07980.01210.02350.2921-0.1548-0.0143-0.03830.0945-0.02320.03410.1587-0.00040.0955-11.18713.3433.901
23.1515-0.6778-0.75861.68040.62441.81980.36040.4968-0.2872-0.4916-0.37680.344-0.3848-0.4770.01640.29310.1329-0.11910.2477-0.07880.1604-10.937.477.994
34.2103-0.5756-2.99060.93951.34394.98130.512-1.95390.8492-0.22390.4104-0.4099-0.81292.3684-0.92240.168-0.45650.16141.2923-0.49590.259223.217.9732.477
44.4052-0.2717-2.16910.7230.03082.28420.1694-0.3501-0.1258-0.222-0.1401-0.1379-0.16720.5293-0.02920.1814-0.0320.07040.17480.02090.091223.8464.5399.772
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1CHAIN A
2X-RAY DIFFRACTION2CHAIN B
3X-RAY DIFFRACTION3CHAIN C
4X-RAY DIFFRACTION4CHAIN D

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