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- PDB-2wbf: Crystal Structure Analysis of SERA5E from plasmodium falciparum w... -

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Basic information

Entry
Database: PDB / ID: 2wbf
TitleCrystal Structure Analysis of SERA5E from plasmodium falciparum with loop 690-700 ordered
ComponentsSERINE-REPEAT ANTIGEN PROTEIN
KeywordsHYDROLASE / SERINE REPEAT ANTIGEN / SERA / MALARIA / VACUOLE / PROTEASE / CATHEPSIN / PLASMODIUM / GLYCOPROTEIN / THIOL PROTEASE
Function / homology
Function and homology information


symbiont-containing vacuolar space / cysteine-type peptidase activity / Hydrolases; Acting on peptide bonds (peptidases); Cysteine endopeptidases / proteolysis / plasma membrane
Similarity search - Function
Cysteine peptidase, asparagine active site / Eukaryotic thiol (cysteine) proteases asparagine active site. / Cysteine peptidase, histidine active site / Eukaryotic thiol (cysteine) proteases histidine active site. / : / Peptidase C1A, papain C-terminal / Papain family cysteine protease / Papain family cysteine protease / Cysteine proteinases / Cathepsin B; Chain A ...Cysteine peptidase, asparagine active site / Eukaryotic thiol (cysteine) proteases asparagine active site. / Cysteine peptidase, histidine active site / Eukaryotic thiol (cysteine) proteases histidine active site. / : / Peptidase C1A, papain C-terminal / Papain family cysteine protease / Papain family cysteine protease / Cysteine proteinases / Cathepsin B; Chain A / Papain-like cysteine peptidase superfamily / Alpha-Beta Complex / Alpha Beta
Similarity search - Domain/homology
Serine-repeat antigen protein 5
Similarity search - Component
Biological speciesPLASMODIUM FALCIPARUM (malaria parasite P. falciparum)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.6 Å
AuthorsSmith, B.J. / Malby, R.L. / Colman, P.M. / Clarke, O.B.
CitationJournal: J. Mol. Biol. / Year: 2009
Title: Structural insights into the protease-like antigen Plasmodium falciparum SERA5 and its noncanonical active-site serine.
Authors: Hodder, A.N. / Malby, R.L. / Clarke, O.B. / Fairlie, W.D. / Colman, P.M. / Crabb, B.S. / Smith, B.J.
History
DepositionFeb 27, 2009Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 31, 2009Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 2.0Apr 25, 2018Group: Atomic model / Data collection ...Atomic model / Data collection / Database references / Source and taxonomy
Category: atom_site / citation ...atom_site / citation / citation_author / entity_src_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_atom_id / _atom_site.label_atom_id / _citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _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 / _entity_src_gen.pdbx_host_org_scientific_name / _entity_src_gen.pdbx_host_org_strain
Revision 2.1May 29, 2019Group: Data collection / Experimental preparation / Category: exptl_crystal_grow / Item: _exptl_crystal_grow.method
Revision 2.2Dec 13, 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_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_alt_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_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_alt_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.pdbx_ptnr1_label_alt_id / _struct_conn.pdbx_ptnr2_label_alt_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_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
Revision 2.3Oct 9, 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
X: SERINE-REPEAT ANTIGEN PROTEIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,35713
Polymers30,6661
Non-polymers69112
Water4,468248
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)102.360, 102.360, 71.400
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number146
Space group name H-MH3

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Components

#1: Protein SERINE-REPEAT ANTIGEN PROTEIN / 111 KDA ANTIGEN / P126 / SERA5


Mass: 30666.279 Da / Num. of mol.: 1 / Fragment: SERINE-PROTEASE DOMAIN, RESIDUES 555-819
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) PLASMODIUM FALCIPARUM (malaria parasite P. falciparum)
Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P69193
#2: Chemical
ChemComp-DMS / DIMETHYL SULFOXIDE


Mass: 78.133 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C2H6OS / Comment: DMSO, precipitant*YM
#3: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ca
#4: Chemical
ChemComp-CL / CHLORIDE ION


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


Mass: 18.015 Da / Num. of mol.: 248 / 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 / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.5 Å3/Da / Density % sol: 50 % / Description: NONE
Crystal growMethod: vapor diffusion, sitting drop / pH: 6.5
Details: 17% PEG3350,0.2M CACL2, 5% DMSO, 10MM BIS-TRIS PH 6.5, 10MM NACL, SITTING-DROP VAPOUR-DIFFUSION

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 0.95667
DetectorType: MARRESEARCH / Detector: CCD / Date: Jun 21, 2008
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.95667 Å / Relative weight: 1
ReflectionResolution: 1.6→30 Å / Num. obs: 36811 / % possible obs: 99.7 % / Observed criterion σ(I): 0 / Redundancy: 5.5 % / Biso Wilson estimate: 16.63 Å2 / Rmerge(I) obs: 0.07 / Net I/σ(I): 24.6
Reflection shellResolution: 1.6→1.66 Å / Redundancy: 5.1 % / Rmerge(I) obs: 0.67 / Mean I/σ(I) obs: 2.6 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX(PHENIX.REFINE)refinement
DENZOdata reduction
SCALEPACKdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3CH2

3ch2


Resolution: 1.6→29.55 Å / SU ML: 0.67 / σ(F): 1.96 / Phase error: 16.78 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.18 1841 5 %
Rwork0.152 --
obs0.153 36700 99.7 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 56.89 Å2 / ksol: 0.43 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-0.0003 Å2-0 Å2-0 Å2
2--0.0003 Å20 Å2
3----0.0007 Å2
Refinement stepCycle: LAST / Resolution: 1.6→29.55 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2091 0 30 248 2369
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0064160
X-RAY DIFFRACTIONf_angle_d0.8337433
X-RAY DIFFRACTIONf_dihedral_angle_d14.826986
X-RAY DIFFRACTIONf_chiral_restr0.076302
X-RAY DIFFRACTIONf_plane_restr0.004670
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.6-1.64330.23841190.2392632X-RAY DIFFRACTION98
1.6433-1.69160.25621470.23452683X-RAY DIFFRACTION100
1.6916-1.74620.24151400.20822664X-RAY DIFFRACTION100
1.7462-1.80860.20771350.19212728X-RAY DIFFRACTION100
1.8086-1.8810.2171410.16842682X-RAY DIFFRACTION100
1.881-1.96660.1741640.15242657X-RAY DIFFRACTION100
1.9666-2.07030.17851670.14162661X-RAY DIFFRACTION100
2.0703-2.19990.18611190.1362732X-RAY DIFFRACTION100
2.1999-2.36970.17571360.13112712X-RAY DIFFRACTION100
2.3697-2.60810.15991350.13632663X-RAY DIFFRACTION100
2.6081-2.98520.17611650.13812654X-RAY DIFFRACTION100
2.9852-3.75980.14341540.1242707X-RAY DIFFRACTION100
3.7598-29.55380.16251190.14312684X-RAY DIFFRACTION100
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)
10.56020.0948-0.43260.2-0.34730.92350.03780.140.0659-0.07940.00310.0667-0.0169-0.13060.00270.0260.0097-0.00430.0360.00730.031525.8707-5.84463.9337
20.38470.0242-0.0170.81660.17460.78-0.0535-0.0453-0.05880.0939-0.00150.00850.17180.0043-0.00160.05810.00680.020.00760.00710.024631.3736-18.068716.8156
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1CHAIN X AND RESID 563:685
2X-RAY DIFFRACTION2CHAIN X AND RESID 686:827

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