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- PDB-6orm: Crystal Structure of Peruvianin-I (Cysteine peptidase from Thevet... -

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Basic information

Entry
Database: PDB / ID: 6orm
TitleCrystal Structure of Peruvianin-I (Cysteine peptidase from Thevetia peruviana latex)
ComponentsPeruvianin-I
KeywordsHYDROLASE / Laticifer
Function / homology
Function and homology information


apoplast / manganese ion binding / hydrolase activity
Similarity search - Function
Germin / Cupin / Cupin 1 / Cupin / RmlC-like cupin domain superfamily / Jelly Rolls / RmlC-like jelly roll fold / Jelly Rolls / Sandwich / Mainly Beta
Similarity search - Domain/homology
Biological speciesThevetia peruviana (plant)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.15 Å
AuthorsCruz, W.T. / Bezerra, E.H.S. / da Silva, F.M.S. / Freire, V.N. / Ramos, M.V. / Rocha, B.A.M. / Freitas, C.D.T.
Funding support Brazil, 1items
OrganizationGrant numberCountry
Coordination for the Improvement of Higher Education Personnel Brazil
CitationJournal: Plant Sci. / Year: 2020
Title: Crystal structure and specific location of a germin-like protein with proteolytic activity from Thevetia peruviana.
Authors: Cruz, W.T. / Bezerra, E.H.S. / Ramos, M.V. / Rocha, B.A.M. / Medina, M.C. / Demarco, D. / Carvalho, C.P.S. / Oliveira, J.S. / Sousa, J.S. / Souza, P.F.N. / Freire, V.N. / da Silva, F.M.S. / Freitas, C.D.T.
History
DepositionApr 30, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 6, 2020Provider: repository / Type: Initial release
Revision 2.0Jul 29, 2020Group: Atomic model / Data collection ...Atomic model / Data collection / Derived calculations / Structure summary
Category: atom_site / chem_comp ...atom_site / 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 / pdbx_struct_special_symmetry / struct_asym / struct_conn / struct_site / struct_site_gen
Item: _atom_site.auth_asym_id / _atom_site.auth_seq_id ..._atom_site.auth_asym_id / _atom_site.auth_seq_id / _atom_site.label_asym_id / _atom_site.label_entity_id / _chem_comp.name / _entity.formula_weight / _entity.pdbx_description / _entity.pdbx_number_of_molecules / _entity.type / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_struct_special_symmetry.label_asym_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_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_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_comp_id
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Aug 26, 2020Group: Database references / Derived calculations / Structure summary
Category: chem_comp / citation ...chem_comp / citation / citation_author / struct_conn
Item: _chem_comp.pdbx_synonyms / _citation.country ..._chem_comp.pdbx_synonyms / _citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _struct_conn.pdbx_leaving_atom_flag
Revision 2.2Oct 11, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
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: Peruvianin-I
B: Peruvianin-I
C: Peruvianin-I
hetero molecules


Theoretical massNumber of molelcules
Total (without water)69,0859
Polymers65,5973
Non-polymers3,4876
Water4,107228
1
A: Peruvianin-I
B: Peruvianin-I
C: Peruvianin-I
hetero molecules

A: Peruvianin-I
B: Peruvianin-I
C: Peruvianin-I
hetero molecules


Theoretical massNumber of molelcules
Total (without water)138,16918
Polymers131,1956
Non-polymers6,97512
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation8_554-y,-x,-z-1/21
Buried area31340 Å2
ΔGint-9 kcal/mol
Surface area34700 Å2
MethodPISA
Unit cell
Length a, b, c (Å)88.642, 88.642, 179.094
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212
Components on special symmetry positions
IDModelComponents
11A-425-

HOH

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Components

#1: Protein Peruvianin-I / Cysteine peptidase


Mass: 21865.830 Da / Num. of mol.: 3 / Source method: isolated from a natural source / Source: (natural) Thevetia peruviana (plant) / References: UniProt: A0A5Q2WX04*PLUS, papain
#2: Polysaccharide beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta- ...beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 586.542 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpb1-4DGlcpNAcb1-4DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/2,3,2/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1b_1-5]/1-1-2/a4-b1_b4-c1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{}}}}LINUCSPDB-CARE
#3: Polysaccharide beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1- ...beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-3)]2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 732.682 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpb1-4DGlcpNAcb1-4[LFucpa1-3]DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/3,4,3/[a2122h-1b_1-5_2*NCC/3=O][a1221m-1a_1-5][a1122h-1b_1-5]/1-2-1-3/a3-b1_a4-c1_c4-d1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(3+1)][a-L-Fucp]{}[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{}}}}LINUCSPDB-CARE
#4: Polysaccharide 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 424.401 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGlcpNAcb1-4DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/1,2,1/[a2122h-1b_1-5_2*NCC/3=O]/1-1/a4-b1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{}}}LINUCSPDB-CARE
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 228 / 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: 54.3 %
Crystal growTemperature: 298 K / Method: vapor diffusion / pH: 4.6
Details: 0.1 M Sodium acetate trihydrate pH 4.6, 2.0 M sodium formate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: LNLS / Beamline: W01B-MX2 / Wavelength: 1.45 Å
DetectorType: DECTRIS PILATUS 2M / Detector: PIXEL / Date: May 18, 2017
RadiationMonochromator: SI (111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.45 Å / Relative weight: 1
ReflectionResolution: 2.15→44.32 Å / Num. obs: 39673 / % possible obs: 99.8 % / Redundancy: 22.9 % / Biso Wilson estimate: 27.4 Å2 / CC1/2: 1 / R split: 0.019 / Rmerge(I) obs: 0.055 / Rpim(I) all: 0.016 / Rrim(I) all: 0.058 / Net I/σ(I): 39.7
Reflection shellResolution: 2.15→2.22 Å / Redundancy: 10.8 % / Rmerge(I) obs: 0.928 / Mean I/σ(I) obs: 2.1 / Num. unique obs: 3319 / CC1/2: 0.735 / Rpim(I) all: 0.478 / Rrim(I) all: 1.18 / % possible all: 98.2

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Processing

Software
NameVersionClassification
PHENIX(1.13_2998)refinement
XDSv0.73data reduction
Aimlessv.0.5.1data scaling
PHASERv.2.6.0phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1FI2

1fi2


Resolution: 2.15→39.642 Å / SU ML: 0.22 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 22.17
RfactorNum. reflection% reflectionSelection details
Rfree0.2205 1918 4.85 %Random selection
Rwork0.1986 ---
obs0.1996 39565 99.76 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 56.6 Å2
Refinement stepCycle: LAST / Resolution: 2.15→39.642 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3673 0 232 228 4133
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0124022
X-RAY DIFFRACTIONf_angle_d1.0495525
X-RAY DIFFRACTIONf_dihedral_angle_d5.9372329
X-RAY DIFFRACTIONf_chiral_restr0.058663
X-RAY DIFFRACTIONf_plane_restr0.005708
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.15-2.20380.30641380.28152595X-RAY DIFFRACTION98
2.2038-2.26340.23931330.25642627X-RAY DIFFRACTION99
2.2634-2.32990.26231300.2482651X-RAY DIFFRACTION100
2.3299-2.40510.26871530.24342631X-RAY DIFFRACTION100
2.4051-2.49110.30121340.24532628X-RAY DIFFRACTION100
2.4911-2.59080.25141370.24332670X-RAY DIFFRACTION100
2.5908-2.70870.24651380.22832664X-RAY DIFFRACTION100
2.7087-2.85150.27381360.23442673X-RAY DIFFRACTION100
2.8515-3.03010.27791400.23322682X-RAY DIFFRACTION100
3.0301-3.26390.27141260.22382697X-RAY DIFFRACTION100
3.2639-3.59220.21521420.19682703X-RAY DIFFRACTION100
3.5922-4.11150.18451380.1712729X-RAY DIFFRACTION100
4.1115-5.17830.151210.14712786X-RAY DIFFRACTION100
5.1783-39.64860.21391520.19072911X-RAY DIFFRACTION99
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)
12.25160.25710.31261.34030.53431.93420.0306-0.09970.23180.00950.0483-0.0641-0.18920.1433-0.08830.3072-0.01230.00610.3268-0.03290.3367-8.825623.7811-35.5688
22.37810.78180.94441.27020.72881.95710.196-0.3682-0.08390.35440.0192-0.19470.40730.1544-0.19880.41670.0402-0.0670.4171-0.02760.3349-2.643611.4876-24.447
31.89630.18140.60121.81720.63721.47770.19870.2276-0.51450.45060.3122-0.83710.61350.846-0.3380.59210.2763-0.27910.7458-0.30320.826414.8562-3.7926-40.357
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(chain A and resseq 2:164)
2X-RAY DIFFRACTION2(chain B and resseq 2:161)
3X-RAY DIFFRACTION3(chain C and resseq 2:164)

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