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- PDB-4tr2: Crystal structure of PvSUB1 -

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Basic information

Entry
Database: PDB / ID: 4tr2
TitleCrystal structure of PvSUB1
ComponentsSubtilisin-like 1 serine protease
KeywordsHYDROLASE / plasmodium egress protease / calcium-binding
Function / homology
Function and homology information


subtilisin / serine-type endopeptidase activity / proteolysis / metal ion binding
Similarity search - Function
SUB1 protease prodomain ProdP9 / SUB1 protease Prodomain ProdP9 / Subtilisin SUB1-like catalytic domain / : / Peptidase S8/S53 domain / Peptidase S8, subtilisin, His-active site / Serine proteases, subtilase family, histidine active site. / Serine proteases, subtilase family, aspartic acid active site. / Peptidase S8, subtilisin, Asp-active site / Serine proteases, subtilase family, serine active site. ...SUB1 protease prodomain ProdP9 / SUB1 protease Prodomain ProdP9 / Subtilisin SUB1-like catalytic domain / : / Peptidase S8/S53 domain / Peptidase S8, subtilisin, His-active site / Serine proteases, subtilase family, histidine active site. / Serine proteases, subtilase family, aspartic acid active site. / Peptidase S8, subtilisin, Asp-active site / Serine proteases, subtilase family, serine active site. / Peptidase S8, subtilisin, Ser-active site / Peptidase S8, subtilisin-related / Serine proteases, subtilase domain profile. / Peptidase S8/S53 domain superfamily / Subtilase family / Peptidase S8/S53 domain / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
PHOSPHATE ION / Subtilisin-like protease 1
Similarity search - Component
Biological speciesPlasmodium vivax (malaria parasite P. vivax)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.7 Å
AuthorsGiganti, D. / Bouillon, A. / Martinez, M. / Weber, P. / Girard-Blanc, C. / Petres, S. / Haouz, A. / Barale, J.C. / Alzari, P.M.
Funding support France, 1items
OrganizationGrant numberCountry
French National Research AgencyANR-11-RPIB-002 France
CitationJournal: Nat Commun / Year: 2014
Title: A novel Plasmodium-specific prodomain fold regulates the malaria drug target SUB1 subtilase.
Authors: Giganti, D. / Bouillon, A. / Tawk, L. / Robert, F. / Martinez, M. / Crublet, E. / Weber, P. / Girard-Blanc, C. / Petres, S. / Haouz, A. / Hernandez, J.F. / Mercereau-Puijalon, O. / Alzari, P.M. / Barale, J.C.
History
DepositionJun 13, 2014Deposition site: RCSB / Processing site: PDBE
Revision 1.0Sep 17, 2014Provider: repository / Type: Initial release
Revision 1.1Sep 24, 2014Group: Database references
Revision 2.0Aug 30, 2017Group: Atomic model / Author supporting evidence / Derived calculations
Category: atom_site / pdbx_audit_support ...atom_site / pdbx_audit_support / pdbx_struct_conn_angle / struct_conn / 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 / _pdbx_audit_support.funding_organization / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _struct_conn.ptnr2_auth_seq_id / _struct_site_gen.auth_seq_id
Revision 2.1Dec 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_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.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_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.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id
Revision 2.2Nov 20, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Subtilisin-like 1 serine protease
B: Subtilisin-like 1 serine protease
hetero molecules


Theoretical massNumber of molelcules
Total (without water)147,87615
Polymers147,0812
Non-polymers79513
Water27015
1
A: Subtilisin-like 1 serine protease
hetero molecules


Theoretical massNumber of molelcules
Total (without water)73,9868
Polymers73,5401
Non-polymers4457
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Subtilisin-like 1 serine protease
hetero molecules


Theoretical massNumber of molelcules
Total (without water)73,8917
Polymers73,5401
Non-polymers3506
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4990 Å2
ΔGint-87 kcal/mol
Surface area35950 Å2
MethodPISA
Unit cell
Length a, b, c (Å)95.000, 95.000, 287.760
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212

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Components

#1: Protein Subtilisin-like 1 serine protease


Mass: 73540.398 Da / Num. of mol.: 2 / Fragment: Residues 26-630
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Plasmodium vivax (malaria parasite P. vivax)
Gene: sub1 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: E6Y8B9
#2: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: Ca
#3: Chemical
ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: PO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 15 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.21 Å3/Da / Density % sol: 44.27 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 4.2
Details: 1.6 M NaH2PO4, 0.4 M K2HPO4, 0.1 M phosphate citrate

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 1 / Wavelength: 0.9801 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Dec 16, 2010
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9801 Å / Relative weight: 1
ReflectionResolution: 2.7→45 Å / Num. obs: 37100 / % possible obs: 99.4 % / Redundancy: 8.6 % / Biso Wilson estimate: 60.13 Å2 / Rmerge(I) obs: 0.137 / Net I/σ(I): 9.2
Reflection shellResolution: 2.7→2.85 Å / Redundancy: 8.8 % / Rmerge(I) obs: 0.726 / Mean I/σ(I) obs: 2.6 / % possible all: 100

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Processing

SoftwareName: BUSTER / Version: 2.11.4 / Classification: refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entries 2TEC, 1DBI, 1CGI, 1R0R, 1LW6, 1EA7, and 1IC6

2tec

1dbi

1cgi

1r0r

1lw6

1ea7

1ic6


Resolution: 2.7→45.1 Å / Cor.coef. Fo:Fc: 0.9288 / Cor.coef. Fo:Fc free: 0.8957 / SU R Cruickshank DPI: 0.537 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.541 / SU Rfree Blow DPI: 0.29 / SU Rfree Cruickshank DPI: 0.294
RfactorNum. reflection% reflectionSelection details
Rfree0.2441 1853 4.99 %RANDOM
Rwork0.1999 ---
obs0.2021 37100 99.63 %-
Displacement parametersBiso mean: 61.98 Å2
Baniso -1Baniso -2Baniso -3
1--5.2931 Å20 Å20 Å2
2---5.2931 Å20 Å2
3---10.5861 Å2
Refine analyzeLuzzati coordinate error obs: 0.418 Å
Refinement stepCycle: 1 / Resolution: 2.7→45.1 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7362 0 33 15 7410
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.0097505HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.1510166HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d2653SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes229HARMONIC2
X-RAY DIFFRACTIONt_gen_planes1069HARMONIC5
X-RAY DIFFRACTIONt_it7505HARMONIC20
X-RAY DIFFRACTIONt_nbd7SEMIHARMONIC5
X-RAY DIFFRACTIONt_omega_torsion2.89
X-RAY DIFFRACTIONt_other_torsion20.89
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion995SEMIHARMONIC5
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_contact8902SEMIHARMONIC4
LS refinement shellResolution: 2.7→2.77 Å / Total num. of bins used: 19
RfactorNum. reflection% reflection
Rfree0.2799 130 4.6 %
Rwork0.2208 2695 -
all0.2236 2825 -
obs--99.63 %
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)
10.18-0.05660.6440.0156-0.15642.19850.0866-0.0351-0.0358-0.0551-0.0819-0.03520.1392-0.0593-0.00470.07940.03360.0704-0.0276-0.0662-0.3228-4.0353-38.1373-17.3582
20.2772-0.1626-0.02830.3508-0.60242.67110.15030.32390.028-0.3218-0.1945-0.06580.50630.13080.04420.46380.04090.05770.57550.0401-0.09811.2971-48.632916.0393
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1{ A|* }
2X-RAY DIFFRACTION2{ B|* }

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