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- PDB-6x44: High Resolution Crystal Structure Analysis of SERA5 proenzyme fro... -

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Basic information

Entry
Database: PDB / ID: 6x44
TitleHigh Resolution Crystal Structure Analysis of SERA5 proenzyme from plasmodium falciparum
ComponentsSerine repeat antigen 5
KeywordsHYDROLASE / malaria / prodomain / protease
Function / homology
Function and homology information


membrane-bounded organelle / symbiont-containing vacuolar space / exit from host cell / symbiont-containing vacuole / regulation of immune response / serine-type peptidase activity / cysteine-type peptidase activity / kinase binding / peptidase activity / Hydrolases; Acting on peptide bonds (peptidases); Cysteine endopeptidases ...membrane-bounded organelle / symbiont-containing vacuolar space / exit from host cell / symbiont-containing vacuole / regulation of immune response / serine-type peptidase activity / cysteine-type peptidase activity / kinase binding / peptidase activity / Hydrolases; Acting on peptide bonds (peptidases); Cysteine endopeptidases / lysosome / cysteine-type endopeptidase activity / proteolysis / extracellular space / 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 / Papain-like cysteine peptidase superfamily
Similarity search - Domain/homology
DI(HYDROXYETHYL)ETHER / Serine repeat antigen 5 / Serine-repeat antigen protein 5
Similarity search - Component
Biological speciesPlasmodium falciparum (malaria parasite P. falciparum)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.19733954166 Å
AuthorsClarke, O.B. / Smith, N.A. / Lee, M. / Smith, B.J.
CitationJournal: Protein Sci. / Year: 2020
Title: Structure of the Plasmodium falciparum PfSERA5 pseudo-zymogen.
Authors: Smith, N.A. / Clarke, O.B. / Lee, M. / Hodder, A.N. / Smith, B.J.
History
DepositionMay 22, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 7, 2020Provider: repository / Type: Initial release
Revision 1.1Nov 4, 2020Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID
Revision 1.2Oct 18, 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
Revision 1.3Nov 13, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Serine repeat antigen 5
B: Serine repeat antigen 5
hetero molecules


Theoretical massNumber of molelcules
Total (without water)101,8033
Polymers101,6972
Non-polymers1061
Water4,143230
1
A: Serine repeat antigen 5
hetero molecules


Theoretical massNumber of molelcules
Total (without water)50,9542
Polymers50,8481
Non-polymers1061
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Serine repeat antigen 5


Theoretical massNumber of molelcules
Total (without water)50,8481
Polymers50,8481
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)77.665, 78.937, 178.712
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number17
Space group name H-MP2221
Space group name HallP2c2
Symmetry operation#1: x,y,z
#2: x,-y,-z
#3: -x,y,-z+1/2
#4: -x,-y,z+1/2

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Components

#1: Protein Serine repeat antigen 5


Mass: 50848.332 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Plasmodium falciparum (malaria parasite P. falciparum)
Gene: sera5 / Production host: Escherichia coli (E. coli) / Strain (production host): SHuffle T7 pLysY / References: UniProt: I0IYW5, UniProt: Q9TY95*PLUS
#2: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O3
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 230 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN
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: 2.69 Å3/Da / Density % sol: 54.33 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8.1 / Details: LiSO4, Tris-HCl, PEG-4000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 1.0393 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Jul 18, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0393 Å / Relative weight: 1
ReflectionResolution: 2.197→47.55 Å / Num. obs: 56459 / % possible obs: 99.07 % / Redundancy: 7.3 % / Biso Wilson estimate: 34.5665711195 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.1162 / Rpim(I) all: 0.04576 / Rrim(I) all: 0.1252 / Net I/σ(I): 11.56
Reflection shellResolution: 2.197→2.276 Å / Redundancy: 7.5 % / Rmerge(I) obs: 0.9169 / Num. unique obs: 5430 / CC1/2: 0.737 / Rpim(I) all: 0.3555 / Rrim(I) all: 0.9851 / % possible all: 97.12

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Processing

Software
NameVersionClassification
PHENIX1.10.1_2155refinement
Aimlessdata scaling
PHENIXphasing
BUCCANEERmodel building
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2wbf

2wbf


Resolution: 2.19733954166→47.5499422318 Å / SU ML: 0.238223530532 / Cross valid method: FREE R-VALUE / σ(F): 1.34004080654 / Phase error: 21.762703983
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.213692993255 2849 5.05868357038 %
Rwork0.179672721411 53470 -
obs0.181419861428 56319 99.0833919775 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 46.2048237869 Å2
Refinement stepCycle: LAST / Resolution: 2.19733954166→47.5499422318 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6117 0 7 230 6354
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01125066876136308
X-RAY DIFFRACTIONf_angle_d1.03092796378549
X-RAY DIFFRACTIONf_chiral_restr0.0541865431826899
X-RAY DIFFRACTIONf_plane_restr0.006362274125491112
X-RAY DIFFRACTIONf_dihedral_angle_d13.70961000793761
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.1973954166-2.23520.2851547284971400.2522584971312504X-RAY DIFFRACTION94.5636623748
2.2352-2.27590.2774510488381430.2283012867972642X-RAY DIFFRACTION99.6778811739
2.2759-2.31960.2441102179081360.2231882388382665X-RAY DIFFRACTION99.3262411348
2.3196-2.3670.2862601378461410.2170485231532640X-RAY DIFFRACTION99.8205312276
2.367-2.41850.2404309714111490.2105395732952644X-RAY DIFFRACTION99.3950177936
2.4185-2.47470.2594141891861280.2052946379452664X-RAY DIFFRACTION99.2181947406
2.4747-2.53660.2381520449471420.1951425586422658X-RAY DIFFRACTION99.8573466476
2.5366-2.60520.2547956867971500.1953964413782640X-RAY DIFFRACTION99.7497318556
2.6052-2.68180.2584430703161550.1951718978252662X-RAY DIFFRACTION99.4703389831
2.6818-2.76840.248443200281420.1917343584112649X-RAY DIFFRACTION99.4299964375
2.7684-2.86730.2345347090531270.1795072771732683X-RAY DIFFRACTION99.4690265487
2.8673-2.98210.2199551692311230.1848014245192677X-RAY DIFFRACTION99.0449239476
2.9821-3.11780.2253880408791440.1878464237592682X-RAY DIFFRACTION99.6122664787
3.1178-3.28210.2205232939291410.1789022221712693X-RAY DIFFRACTION99.7536078845
3.2821-3.48770.1904597356231400.1669968126082674X-RAY DIFFRACTION99.1543340381
3.4877-3.75690.2348656886141520.1643561161572684X-RAY DIFFRACTION99.1261796575
3.7569-4.13480.1770078193641370.155768794452679X-RAY DIFFRACTION98.392732355
4.1348-4.73260.1679623189381490.1484116842542720X-RAY DIFFRACTION99.583477959
4.7326-5.96080.1926777724771390.1672987421812750X-RAY DIFFRACTION98.3991825613
5.9608-47.54994223180.1982221033081710.1920429101552860X-RAY DIFFRACTION98.6974926734

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