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- PDB-4ii0: Crystal structure of CrataBL, a trypsin inhibitor from Crataeva tapia -

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Basic information

Entry
Database: PDB / ID: 4ii0
TitleCrystal structure of CrataBL, a trypsin inhibitor from Crataeva tapia
ComponentsCrataBL
KeywordsHYDROLASE INHIBITOR / beta-trefoil / Serine protease inhibitor
Function / homology
Function and homology information


serine-type endopeptidase inhibitor activity / toxin activity / carbohydrate binding
Similarity search - Function
Proteinase inhibitor I3, Kunitz legume / Trypsin and protease inhibitor / Soybean trypsin inhibitor (Kunitz) family of protease inhibitors / Kunitz inhibitor STI-like superfamily / Trefoil (Acidic Fibroblast Growth Factor, subunit A) - #50 / Trefoil (Acidic Fibroblast Growth Factor, subunit A) / Trefoil / Mainly Beta
Similarity search - Domain/homology
Bark lectin isoform 1
Similarity search - Component
Biological speciesCrataeva tapia (garlic-pear)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.75 Å
AuthorsZhou, D. / Wlodawer, A.
CitationJournal: Plos One / Year: 2013
Title: Crystal Structure of Crataeva tapia Bark Protein (CrataBL) and Its Effect in Human Prostate Cancer Cell Lines.
Authors: Ferreira, R.D. / Zhou, D. / Ferreira, J.G. / Silva, M.C. / Silva-Lucca, R.A. / Mentele, R. / Paredes-Gamero, E.J. / Bertolin, T.C. / Dos Santos Correia, M.T. / Paiva, P.M. / Gustchina, A. / ...Authors: Ferreira, R.D. / Zhou, D. / Ferreira, J.G. / Silva, M.C. / Silva-Lucca, R.A. / Mentele, R. / Paredes-Gamero, E.J. / Bertolin, T.C. / Dos Santos Correia, M.T. / Paiva, P.M. / Gustchina, A. / Wlodawer, A. / Oliva, M.L.
History
DepositionDec 19, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 24, 2013Provider: repository / Type: Initial release
Revision 2.0Jul 29, 2020Group: Atomic model / Data collection ...Atomic model / Data collection / Derived calculations / Structure summary
Category: atom_site / atom_site_anisotrop ...atom_site / atom_site_anisotrop / chem_comp / entity / pdbx_branch_scheme / pdbx_chem_comp_identifier / pdbx_entity_branch / pdbx_entity_branch_descriptor / pdbx_entity_branch_link / pdbx_entity_branch_list / pdbx_entity_nonpoly / pdbx_nonpoly_scheme / pdbx_struct_assembly_gen / struct_asym / struct_conn / struct_site / struct_site_gen
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_asym_id / _atom_site.auth_atom_id / _atom_site.auth_comp_id / _atom_site.auth_seq_id / _atom_site.label_asym_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _atom_site.label_entity_id / _atom_site.occupancy / _atom_site.type_symbol / _atom_site_anisotrop.U[1][1] / _atom_site_anisotrop.U[1][2] / _atom_site_anisotrop.U[1][3] / _atom_site_anisotrop.U[2][2] / _atom_site_anisotrop.U[2][3] / _atom_site_anisotrop.U[3][3] / _atom_site_anisotrop.pdbx_auth_asym_id / _atom_site_anisotrop.pdbx_auth_atom_id / _atom_site_anisotrop.pdbx_auth_comp_id / _atom_site_anisotrop.pdbx_auth_seq_id / _atom_site_anisotrop.pdbx_label_asym_id / _atom_site_anisotrop.pdbx_label_atom_id / _atom_site_anisotrop.pdbx_label_comp_id / _atom_site_anisotrop.type_symbol / _chem_comp.name / _chem_comp.type / _entity.formula_weight / _entity.pdbx_description / _entity.pdbx_number_of_molecules / _entity.src_method / _entity.type / _pdbx_struct_assembly_gen.asym_id_list / _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
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: CrataBL
B: CrataBL
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,05120
Polymers36,4882
Non-polymers2,56318
Water5,350297
1
A: CrataBL
hetero molecules

A: CrataBL
hetero molecules

B: CrataBL
hetero molecules

B: CrataBL
hetero molecules


Theoretical massNumber of molelcules
Total (without water)78,10240
Polymers72,9764
Non-polymers5,12636
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_455-x-1,y,-z1
crystal symmetry operation1_556x,y,z+11
crystal symmetry operation2_454-x-1,y,-z-11
Buried area11310 Å2
ΔGint-233 kcal/mol
Surface area31220 Å2
MethodPISA
2
A: CrataBL
hetero molecules

A: CrataBL
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,40020
Polymers36,4882
Non-polymers2,91318
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,y,-z1
Buried area5420 Å2
ΔGint-120 kcal/mol
Surface area16860 Å2
MethodPISA
3
B: CrataBL
hetero molecules

B: CrataBL
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,70220
Polymers36,4882
Non-polymers2,21418
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_453-x-1,y,-z-21
Buried area4460 Å2
ΔGint-121 kcal/mol
Surface area16160 Å2
MethodPISA
Unit cell
Length a, b, c (Å)95.585, 76.279, 62.335
Angle α, β, γ (deg.)90.00, 120.08, 90.00
Int Tables number5
Space group name H-MC121

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein CrataBL


Mass: 18243.936 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Crataeva tapia (garlic-pear) / References: UniProt: U3KRG0*PLUS

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Sugars , 2 types, 4 molecules

#2: Polysaccharide alpha-L-fucopyranose-(1-3)-[2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)]2-acetamido-2-deoxy-beta- ...alpha-L-fucopyranose-(1-3)-[2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)]2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 570.542 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
LFucpa1-3[DGlcpNAcb1-4]DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/2,3,2/[a2122h-1b_1-5_2*NCC/3=O][a1221m-1a_1-5]/1-2-1/a3-b1_a4-c1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(3+1)][a-L-Fucp]{}[(4+1)][b-D-GlcpNAc]{}}}LINUCSPDB-CARE
#5: Sugar ChemComp-NAG / 2-acetamido-2-deoxy-beta-D-glucopyranose / N-Acetylglucosamine


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Formula: C8H15NO6
IdentifierTypeProgram
DGlcpNAcbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
N-acetyl-b-D-glucopyranosamineCOMMON NAMEGMML 1.0
b-D-GlcpNAcIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcNAcSNFG CARBOHYDRATE SYMBOLGMML 1.0

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Non-polymers , 3 types, 311 molecules

#3: Chemical
ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: SO4
#4: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C3H8O3
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 297 / 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: 2.69 Å3/Da / Density % sol: 54.35 %
Crystal growTemperature: 293 K / pH: 8
Details: 0.2 M Li2SO4, 30% PEG3350, pH 8.0, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-BM / Wavelength: 1
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Dec 2, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.75→20 Å / Num. obs: 38040 / % possible obs: 97 % / Observed criterion σ(I): 3.87 / Rmerge(I) obs: 0.056
Reflection shellResolution: 1.75→1.85 Å / Rmerge(I) obs: 0.358 / % possible all: 96.1

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Processing

Software
NameVersionClassification
HKL-2000data collection
PHASESphasing
REFMAC5.5.0109refinement
HKL-3000data reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.75→19.98 Å / Cor.coef. Fo:Fc: 0.962 / Cor.coef. Fo:Fc free: 0.941 / SU B: 6.556 / SU ML: 0.09 / Cross valid method: THROUGHOUT / ESU R: 0.114 / ESU R Free: 0.117 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.23171 951 2.5 %RANDOM
Rwork0.1851 ---
obs0.18624 37089 100 %-
all-39201 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 29.694 Å2
Baniso -1Baniso -2Baniso -3
1--0.91 Å20 Å2-0.35 Å2
2--2.32 Å20 Å2
3----1.75 Å2
Refinement stepCycle: LAST / Resolution: 1.75→19.98 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2560 0 154 297 3011
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.0222798
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.7162.023816
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.7985326
X-RAY DIFFRACTIONr_dihedral_angle_2_deg26.47420.286105
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.37215424
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.71532
X-RAY DIFFRACTIONr_chiral_restr0.1240.2430
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.0222051
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_it0.9671.51640
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.6822697
X-RAY DIFFRACTIONr_scbond_it2.60931158
X-RAY DIFFRACTIONr_scangle_it4.0814.51119
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.75→1.795 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.323 68 -
Rwork0.318 2675 -
obs--100 %
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)
11.70010.0689-0.71930.4851-0.15672.159-0.00370.08080.00810.082-0.0093-0.02250.0082-0.06080.01310.0634-0.0084-0.00770.0082-0.01410.0831-16.865627.4025-8.896
21.38730.0529-0.84480.5636-0.05511.846-0.0090.20960.02830.03010.064-0.07560.0747-0.2727-0.0550.0459-0.0189-0.00910.09050.01610.0375-10.400930.6067-38.1491
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 164
2X-RAY DIFFRACTION1A201 - 211
3X-RAY DIFFRACTION1A301 - 460
4X-RAY DIFFRACTION1B301
5X-RAY DIFFRACTION2B1 - 164
6X-RAY DIFFRACTION2B201 - 209
7X-RAY DIFFRACTION2B302 - 437

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