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- PDB-5t5o: LECTIN FROM BAUHINIA FORFICATA IN COMPLEX WITH TN-PEPTIDE -

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Basic information

Entry
Database: PDB / ID: 5t5o
TitleLECTIN FROM BAUHINIA FORFICATA IN COMPLEX WITH TN-PEPTIDE
Components
  • Lectin
  • TN-peptide ACE-GLY-VAL-THR-SER-ALA
KeywordsSUGAR BINDING PROTEIN / LEGUME LECTIN / CONCANAVALIN A / GALNAC-SPECIFIC / LIGAND-FREE
Function / homology
Function and homology information


carbohydrate binding / extracellular region / metal ion binding
Similarity search - Function
Legume lectin / 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
2-acetamido-2-deoxy-alpha-D-galactopyranose / Lectin
Similarity search - Component
Biological speciesBauhinia forficata (plant)
Homo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.75 Å
AuthorsLubkowski, J. / Wlodawer, A.
CitationJournal: FEBS J. / Year: 2017
Title: Structural analysis and unique molecular recognition properties of a Bauhinia forficata lectin that inhibits cancer cell growth.
Authors: Lubkowski, J. / Durbin, S.V. / Silva, M.C. / Farnsworth, D. / Gildersleeve, J.C. / Oliva, M.L. / Wlodawer, A.
History
DepositionAug 31, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 28, 2016Provider: repository / Type: Initial release
Revision 1.1Feb 8, 2017Group: Database references
Revision 1.2Feb 15, 2017Group: Database references
Revision 1.3Nov 1, 2017Group: Author supporting evidence / Category: pdbx_struct_assembly_auth_evidence
Revision 2.0Jul 29, 2020Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Derived calculations / Structure summary
Category: atom_site / atom_site_anisotrop ...atom_site / atom_site_anisotrop / chem_comp / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / pdbx_struct_conn_angle / pdbx_validate_close_contact / struct_conn / struct_conn_type / struct_site / struct_site_gen
Item: _atom_site.auth_atom_id / _atom_site.label_atom_id ..._atom_site.auth_atom_id / _atom_site.label_atom_id / _atom_site_anisotrop.pdbx_auth_atom_id / _atom_site_anisotrop.pdbx_label_atom_id / _chem_comp.name / _chem_comp.type / _entity.pdbx_description / _pdbx_entity_nonpoly.name / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.value / _pdbx_validate_close_contact.auth_atom_id_2 / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.pdbx_role / _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_conn.ptnr2_label_seq_id / _struct_conn_type.id
Description: Carbohydrate remediation / Provider: repository / Type: Remediation

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Lectin
a: TN-peptide ACE-GLY-VAL-THR-SER-ALA
B: Lectin
b: TN-peptide ACE-GLY-VAL-THR-SER-ALA
C: Lectin
c: TN-peptide ACE-GLY-VAL-THR-SER-ALA
D: Lectin
d: TN-peptide ACE-GLY-VAL-THR-SER-ALA
E: Lectin
e: TN-peptide ACE-GLY-VAL-THR-SER-ALA
F: Lectin
f: TN-peptide ACE-GLY-VAL-THR-SER-ALA
G: Lectin
g: TN-peptide ACE-GLY-VAL-THR-SER-ALA
H: Lectin
h: TN-peptide ACE-GLY-VAL-THR-SER-ALA
I: Lectin
i: TN-peptide ACE-GLY-VAL-THR-SER-ALA
J: Lectin
j: TN-peptide ACE-GLY-VAL-THR-SER-ALA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)279,04850
Polymers276,03420
Non-polymers3,01430
Water3,837213
1
A: Lectin
a: TN-peptide ACE-GLY-VAL-THR-SER-ALA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,9055
Polymers27,6032
Non-polymers3013
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Lectin
b: TN-peptide ACE-GLY-VAL-THR-SER-ALA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,9055
Polymers27,6032
Non-polymers3013
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Lectin
c: TN-peptide ACE-GLY-VAL-THR-SER-ALA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,9055
Polymers27,6032
Non-polymers3013
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: Lectin
d: TN-peptide ACE-GLY-VAL-THR-SER-ALA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,9055
Polymers27,6032
Non-polymers3013
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
5
E: Lectin
e: TN-peptide ACE-GLY-VAL-THR-SER-ALA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,9055
Polymers27,6032
Non-polymers3013
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
6
F: Lectin
f: TN-peptide ACE-GLY-VAL-THR-SER-ALA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,9055
Polymers27,6032
Non-polymers3013
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
7
G: Lectin
g: TN-peptide ACE-GLY-VAL-THR-SER-ALA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,9055
Polymers27,6032
Non-polymers3013
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
8
H: Lectin
h: TN-peptide ACE-GLY-VAL-THR-SER-ALA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,9055
Polymers27,6032
Non-polymers3013
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
9
I: Lectin
i: TN-peptide ACE-GLY-VAL-THR-SER-ALA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,9055
Polymers27,6032
Non-polymers3013
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
10
J: Lectin
j: TN-peptide ACE-GLY-VAL-THR-SER-ALA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,9055
Polymers27,6032
Non-polymers3013
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)65.081, 187.290, 258.387
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
31C
41D
51E
61F
71G
81H
91I
101J

NCS domain segments:
Dom-IDComponent-IDEns-IDRefine codeAuth asym-IDAuth seq-ID
1111A1 - 229
2111B1 - 229
3111C1 - 229
4111D1 - 229
5111E1 - 229
6111F1 - 229
7111G1 - 229
8111H1 - 229
9111I1 - 229
10111J1 - 229

NCS oper:
IDCodeMatrixVector
1given(1), (1), (1)
2given(-0.858173, -0.511906, 0.038617), (-0.512347, 0.849329, -0.127048), (0.032238, -0.128814, -0.991145)19.018761, 16.60815, 164.352081
3given(-0.338245, -0.923564, -0.180608), (0.929813, -0.298411, -0.215402), (0.145043, -0.240791, 0.959678)49.923611, -39.606529, 79.649757
4given(-0.195157, 0.933664, 0.300308), (0.937676, 0.267388, -0.221962), (-0.287537, 0.238274, -0.927657)0.37954, -52.674591, 92.906471
5given(-0.810043, 0.584067, 0.051919), (0.582996, 0.792733, 0.178015), (0.062815, 0.174468, -0.982657)57.623119, -29.389351, 118.396507
6given(0.370753, -0.91538, -0.156915), (0.913712, 0.32925, 0.238171), (-0.166352, -0.231678, 0.958464)-9.97941, -52.994259, 52.990452
7given(-0.234579, -0.920407, 0.312766), (-0.920509, 0.313739, 0.232875), (-0.312467, -0.233277, -0.92084)16.6576, -8.57273, 206.964523
8given(0.664118, 0.606612, -0.437), (-0.630216, 0.76869, 0.109288), (0.402213, 0.202824, 0.892798)19.07052, -20.277269, -39.73737
9given(-0.894315, 0.032114, 0.446284), (0.036642, 0.999327, 0.001517), (-0.445935, 0.01771, -0.89489)26.04808, -47.073471, 153.452393
10given(0.739136, -0.526861, -0.419637), (0.528946, 0.839747, -0.122646), (0.417006, -0.131313, 0.899368)26.114071, -55.295502, 18.63879
DetailsDIMER AS DETERMINED BY ANALYTICAL ULTRACENTRIFUGATION

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Components

#1: Protein
Lectin / / BfL


Mass: 27143.914 Da / Num. of mol.: 10
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bauhinia forficata (plant) / Production host: Escherichia coli (E. coli) / References: UniProt: P86993
#2: Protein/peptide
TN-peptide ACE-GLY-VAL-THR-SER-ALA


Mass: 459.495 Da / Num. of mol.: 10 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human)
#3: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 20 / Source method: obtained synthetically / Formula: Ca
#4: Sugar
ChemComp-A2G / 2-acetamido-2-deoxy-alpha-D-galactopyranose / N-Acetylgalactosamine


Type: D-saccharide, alpha linking / Mass: 221.208 Da / Num. of mol.: 10
Source method: isolated from a genetically manipulated source
Formula: C8H15NO6
IdentifierTypeProgram
DGalpNAcaCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
N-acetyl-a-D-galactopyranosamineCOMMON NAMEGMML 1.0
a-D-GalpNAcIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GalNAcSNFG CARBOHYDRATE SYMBOLGMML 1.0
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 213 / 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: 2.85 Å3/Da / Density % sol: 56.88 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: PROTEIN CONCENTRATION 5-8 MG/ML IN 0.05 M HEPES BUFFER (pH 7.5) AND 0.15 M NACL, PRECIPITANT: 24% (W/W) PEG1500, 0.2 M L-PROLINE, 0.1 M HEPES (pH 7.5), DROPLETS RATIO: 1:1

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1 Å
DetectorType: RAYONIX MX300-HS / Detector: CCD / Date: Oct 12, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.75→50 Å / Num. obs: 85387 / % possible obs: 98.4 % / Redundancy: 5.7 % / Rmerge(I) obs: 0.113 / Rpim(I) all: 0.05 / Rrim(I) all: 0.124 / Χ2: 0.904 / Net I/av σ(I): 14.45 / Net I/σ(I): 5.5 / Num. measured all: 489032
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsCC1/2Diffraction-ID% possible all
2.75-2.85.20.8640.814188.8
2.8-2.855.40.8570.848192.4
2.85-2.95.50.7380.884194.5
2.9-2.965.60.6140.911196.9
2.96-3.035.70.5550.924198.3
3.03-3.15.80.470.94199.5
3.1-3.175.80.3820.964199.8
3.17-3.265.80.3250.971199.9
3.26-3.365.90.2630.98199.8
3.36-3.465.90.2160.984199.9
3.46-3.595.90.1860.989199.9
3.59-3.735.90.1450.991199.9
3.73-3.95.80.1260.993199.9
3.9-4.115.80.1050.994199.9
4.11-4.365.80.0890.9951100
4.36-4.75.80.0710.994199.9
4.7-5.175.80.0630.9961100
5.17-5.925.80.060.9961100
5.92-7.465.70.0520.9961100
7.46-505.40.040.996199

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Processing

Software
NameVersionClassification
HKL-3000data collection
HKL-3000data scaling
REFMAC5.8.0107refinement
PDB_EXTRACT3.2data extraction
HKL-3000data reduction
PHASERphasing
RefinementResolution: 2.75→49.384 Å / Cor.coef. Fo:Fc: 0.932 / Cor.coef. Fo:Fc free: 0.904 / SU B: 27.98 / SU ML: 0.258 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.357 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.2296 3493 4.9 %RANDOM
Rwork0.2014 ---
obs0.2028 67604 79.7 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 117.13 Å2 / Biso mean: 58.07 Å2 / Biso min: 10.92 Å2
Baniso -1Baniso -2Baniso -3
1-1.83 Å20 Å20 Å2
2--2.13 Å2-0 Å2
3----3.96 Å2
Refinement stepCycle: final / Resolution: 2.75→49.384 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms18430 0 160 213 18803
Biso mean--52.02 39.17 -
Num. residues----2350
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0190.01919100
X-RAY DIFFRACTIONr_bond_other_d0.0040.0217090
X-RAY DIFFRACTIONr_angle_refined_deg1.8541.92826070
X-RAY DIFFRACTIONr_angle_other_deg1.239339190
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.76352320
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.24523.172930
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.723152690
X-RAY DIFFRACTIONr_dihedral_angle_4_deg8.40815120
X-RAY DIFFRACTIONr_chiral_restr0.10.22880
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.02122020
X-RAY DIFFRACTIONr_gen_planes_other0.0050.024850
X-RAY DIFFRACTIONr_mcbond_it0.2640.6439360
X-RAY DIFFRACTIONr_mcbond_other0.2640.6439359
X-RAY DIFFRACTIONr_mcangle_it0.4790.96311660
Refine LS restraints NCS

Ens-ID: 1 / Number: 3478 / Refine-ID: X-RAY DIFFRACTION / Type: TIGHT THERMAL / Weight position: 0.5

Dom-IDAuth asym-IDRms dev position (Å)
1A2.18
2B2.66
3C1.5
4D1.59
5E1.74
6F2
7G1.91
8H2.43
9I1.64
10J1.81
LS refinement shellResolution: 2.75→2.774 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.376 101 -
Rwork0.322 2338 -
all-2439 -
obs--38.59 %
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)
12.6962-0.0843-0.58651.3136-0.41232.5684-0.09350.1933-0.0578-0.07750.08760.03660.0384-0.17010.00590.0141-0.06420.01270.53410.03230.4809-3.5332-4.272385.5201
22.85020.4241-0.5781.68730.24313.01940.004-0.02240.0697-0.03960.0155-0.0315-0.17920.0559-0.01950.0176-0.05130.03120.5059-0.0030.486327.51383.966279.9199
30.95710.48880.40292.630.74843.3090.08690.11560.18470.003-0.2338-0.0703-0.66340.14990.14690.6747-0.1034-0.06620.39930.03940.543851.777637.41467.6695
41.7399-0.08630.39582.61410.93253.4141-0.0210.0461-0.12520.365-0.0609-0.1275-0.00270.18740.0820.174-0.0506-0.08780.3773-0.01170.519148.27777.5293-5.0597
51.8405-0.7419-0.55631.7670.40873.2514-0.0108-0.0934-0.14390.2276-0.0121-0.12210.86740.4140.02290.59670.1318-0.00740.7494-0.0110.534762.1253-21.542933.5976
62.1073-0.4922-0.77182.18310.21553.80880.04880.23390.0694-0.2739-0.0317-0.0033-0.0373-0.0976-0.01710.1388-0.08470.0250.58270.02440.4941.49922.609641.7652
70.94330.3881-0.4072.6163-1.32631.9191-0.0743-0.17570.20730.34980.0038-0.0477-0.8250.09080.07050.99770.0164-0.15590.5771-0.07710.613738.728748.2621106.5142
81.92180.3665-0.38531.98-1.14693.5173-0.0418-0.0926-0.0080.15750.11340.237-0.5624-0.6451-0.07160.4280.204-0.04050.74750.00350.575425.274723.9886123.4466
91.8346-0.3165-1.07571.59170.68992.8065-0.0732-0.15170.10930.18790.0243-0.2196-0.78950.6580.04890.9597-0.3105-0.18630.61140.0070.591258.319340.613947.6613
101.1598-0.6722-1.15251.65280.44833.5281-0.03470.17320.1491-0.2092-0.00810.1871-0.75-0.33690.04281.11440.0132-0.20670.5467-0.00740.632932.964549.68466.321
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 229
2X-RAY DIFFRACTION1a100 - 105
3X-RAY DIFFRACTION2B1 - 229
4X-RAY DIFFRACTION2b100 - 105
5X-RAY DIFFRACTION3C1 - 229
6X-RAY DIFFRACTION3c100 - 105
7X-RAY DIFFRACTION4D1 - 229
8X-RAY DIFFRACTION4d100 - 105
9X-RAY DIFFRACTION5E1 - 229
10X-RAY DIFFRACTION5e100 - 105
11X-RAY DIFFRACTION6F1 - 229
12X-RAY DIFFRACTION6f100 - 105
13X-RAY DIFFRACTION7G1 - 229
14X-RAY DIFFRACTION7g100 - 105
15X-RAY DIFFRACTION8H1 - 229
16X-RAY DIFFRACTION8h100 - 105
17X-RAY DIFFRACTION9I1 - 229
18X-RAY DIFFRACTION9i100 - 105
19X-RAY DIFFRACTION10J1 - 229
20X-RAY DIFFRACTION10j100 - 105

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