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- PDB-4wvi: Crystal structure of the Type-I signal peptidase from Staphylococ... -

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Basic information

Entry
Database: PDB / ID: 4wvi
TitleCrystal structure of the Type-I signal peptidase from Staphylococcus aureus (SpsB) in complex with a substrate peptide (pep2).
Components
  • Maltose-binding periplasmic protein,Signal peptidase IB
  • substrate peptide (pep2)
KeywordsHYDROLASE / SpsB Type-I signal peptidase / Peptide complex / Cell secretion / MBP fusion
Function / homology
Function and homology information


signal peptidase I / signal peptide processing / carbohydrate transmembrane transporter activity / outer membrane-bounded periplasmic space / serine-type endopeptidase activity / plasma membrane
Similarity search - Function
Peptidase S26A, signal peptidase I, lysine active site / Signal peptidases I lysine active site. / Peptidase S26A, signal peptidase I / Signal peptidase, peptidase S26 / Peptidase S26A, signal peptidase I, conserved site / Signal peptidases I signature 3. / Peptidase S26A, signal peptidase I, serine active site / Signal peptidases I serine active site. / Peptidase S26 / LexA/Signal peptidase-like superfamily ...Peptidase S26A, signal peptidase I, lysine active site / Signal peptidases I lysine active site. / Peptidase S26A, signal peptidase I / Signal peptidase, peptidase S26 / Peptidase S26A, signal peptidase I, conserved site / Signal peptidases I signature 3. / Peptidase S26A, signal peptidase I, serine active site / Signal peptidases I serine active site. / Peptidase S26 / LexA/Signal peptidase-like superfamily / Maltose/Cyclodextrin ABC transporter, substrate-binding protein / Solute-binding family 1, conserved site / Bacterial extracellular solute-binding proteins, family 1 signature. / Bacterial extracellular solute-binding protein / Bacterial extracellular solute-binding protein
Similarity search - Domain/homology
alpha-maltose / Maltose/maltodextrin-binding periplasmic protein / Signal peptidase IB
Similarity search - Component
Biological speciesEscherichia coli K-12 (bacteria)
Staphylococcus aureus subsp. aureus str. Newman (bacteria)
Staphylococcus aureus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsYoung, P.G. / Ting, Y.T. / Baker, E.N.
Funding support New Zealand, 1items
OrganizationGrant numberCountry
Health Research Council (HRC) New Zealand
CitationJournal: IUCrJ / Year: 2016
Title: Peptide binding to a bacterial signal peptidase visualized by peptide tethering and carrier-driven crystallization.
Authors: Ting, Y.T. / Harris, P.W. / Batot, G. / Brimble, M.A. / Baker, E.N. / Young, P.G.
History
DepositionNov 5, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 23, 2015Provider: repository / Type: Initial release
Revision 1.1Feb 17, 2016Group: Database references
Revision 1.2Sep 20, 2017Group: Author supporting evidence / Data collection ...Author supporting evidence / Data collection / Derived calculations / Refinement description
Category: diffrn_source / pdbx_audit_support ...diffrn_source / pdbx_audit_support / pdbx_struct_oper_list / software
Item: _diffrn_source.pdbx_synchrotron_site / _pdbx_audit_support.funding_organization / _pdbx_struct_oper_list.symmetry_operation
Revision 1.3Apr 25, 2018Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.journal_abbrev / _citation.pdbx_database_id_PubMed ..._citation.journal_abbrev / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.name
Revision 1.4Jun 13, 2018Group: Data collection / Category: diffrn_radiation / Item: _diffrn_radiation.pdbx_diffrn_protocol
Revision 1.5Jan 23, 2019Group: Data collection / Source and taxonomy / Category: entity_src_gen
Item: _entity_src_gen.gene_src_strain / _entity_src_gen.pdbx_gene_src_ncbi_taxonomy_id / _entity_src_gen.pdbx_gene_src_scientific_name
Revision 1.6Jan 1, 2020Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 2.0Jul 29, 2020Group: Atomic model / Data collection ...Atomic model / Data collection / Derived calculations / Non-polymer description / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / entity / entity_name_com / 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_molecule_features / pdbx_nonpoly_scheme / 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_atom_id / _atom_site.label_comp_id / _chem_comp.formula / _chem_comp.formula_weight / _chem_comp.id / _chem_comp.mon_nstd_flag / _chem_comp.name / _chem_comp.type / _entity.formula_weight / _entity.pdbx_description / _entity.type
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Sep 27, 2023Group: Data collection / Database references ...Data collection / Database references / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 2.2Oct 23, 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

Downloads & links

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Assembly

Deposited unit
A: Maltose-binding periplasmic protein,Signal peptidase IB
D: substrate peptide (pep2)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)60,4183
Polymers60,0762
Non-polymers3421
Water6,684371
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1790 Å2
ΔGint-5 kcal/mol
Surface area23870 Å2
MethodPISA
Unit cell
Length a, b, c (Å)63.989, 80.232, 119.879
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Maltose-binding periplasmic protein,Signal peptidase IB / MBP / MMBP / Maltodextrin-binding protein / SPase IB / Leader peptidase IB


Mass: 59189.781 Da / Num. of mol.: 1 / Fragment: unp residues 33-393, unp residues 26-175 / Mutation: K143G, Q78C, R393N
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli K-12 (bacteria), (gene. exp.) Staphylococcus aureus subsp. aureus str. Newman (bacteria)
Strain: K12, Newman / Gene: malE, Z5632, ECs5017, spsB, SACOL0969 / Plasmid: pMBP-pProExHta / Details (production host): MBP fusion protein / Production host: Escherichia coli (E. coli) / Strain (production host): K12
References: UniProt: P0AEY0, UniProt: Q5HHB9, signal peptidase I
#2: Protein/peptide substrate peptide (pep2)


Mass: 885.985 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Staphylococcus aureus (bacteria)
#3: Polysaccharide alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose / alpha-maltose


Type: oligosaccharide, Oligosaccharide / Class: Nutrient / Mass: 342.297 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: oligosaccharide / References: alpha-maltose
DescriptorTypeProgram
DGlcpa1-4DGlcpa1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/1,2,1/[a2122h-1a_1-5]/1-1/a4-b1WURCSPDB2Glycan 1.1.0
[][a-D-Glcp]{[(4+1)][a-D-Glcp]{}}LINUCSPDB-CARE
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 371 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY
Sequence detailsTHESE MUTATIONS ARE CONSEQUENCE OF PCR REACTION. THE MUTATION R393N WAS INTRODUCED TO STABILIZE THE ...THESE MUTATIONS ARE CONSEQUENCE OF PCR REACTION. THE MUTATION R393N WAS INTRODUCED TO STABILIZE THE LINKER REGION

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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: 2.63 Å3/Da / Density % sol: 53.2 % / Description: Needles
Crystal growTemperature: 290 K / Method: batch mode
Details: 12 % PEG 8000, 20 % ethylene glycol, 100 mM sodium acetate pH 5.3 - 5.5
PH range: 5.3 - 5.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX2 / Wavelength: 0.9537 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Apr 1, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9537 Å / Relative weight: 1
ReflectionResolution: 1.9→19.78 Å / Num. obs: 49376 / % possible obs: 99.9 % / Redundancy: 9.5 % / CC1/2: 0.997 / Rmerge(I) obs: 0.19 / Rpim(I) all: 0.064 / Net I/σ(I): 11.1 / Num. measured all: 466776
Reflection shell

Diffraction-ID: 1 / Rejects: _

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allCC1/2Rpim(I) all% possible all
1.9-1.949.52.0771.53117832830.5140.698100
8.91-19.788.10.04237.240585040.9990.01591

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Processing

Software
NameVersionClassification
XDSdata scaling
Aimless0.2.8data scaling
PHASERphasing
REFMAC5.8.0071refinement
PDB_EXTRACT3.15data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4WVG

4wvg


Resolution: 1.9→19.78 Å / Cor.coef. Fo:Fc: 0.955 / Cor.coef. Fo:Fc free: 0.937 / WRfactor Rfree: 0.1953 / WRfactor Rwork: 0.1637 / FOM work R set: 0.8302 / SU B: 3.701 / SU ML: 0.104 / SU R Cruickshank DPI: 0.143 / SU Rfree: 0.1312 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.143 / ESU R Free: 0.131 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2194 2503 5.1 %RANDOM
Rwork0.1879 46809 --
obs0.1895 46809 99.83 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 67.6 Å2 / Biso mean: 24.36 Å2 / Biso min: 10.87 Å2
Baniso -1Baniso -2Baniso -3
1-0.37 Å20 Å2-0 Å2
2---0.6 Å20 Å2
3---0.23 Å2
Refinement stepCycle: final / Resolution: 1.9→19.78 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4075 0 23 371 4469
Biso mean--16.65 33.17 -
Num. residues----532
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0194203
X-RAY DIFFRACTIONr_bond_other_d0.0010.023922
X-RAY DIFFRACTIONr_angle_refined_deg1.2151.9625720
X-RAY DIFFRACTIONr_angle_other_deg0.74139042
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.6335529
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.1525.455187
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.37815658
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.6381511
X-RAY DIFFRACTIONr_chiral_restr0.0720.2628
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0214818
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02929
X-RAY DIFFRACTIONr_mcbond_it1.2752.322122
X-RAY DIFFRACTIONr_mcbond_other1.272.3192121
X-RAY DIFFRACTIONr_mcangle_it2.0743.4662646
LS refinement shellResolution: 1.9→1.949 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.303 182 -
Rwork0.295 3421 -
all-3603 -
obs--99.97 %

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