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

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Basic information

Entry
Database: PDB / ID: 4wvh
TitleCrystal structure of the Type-I signal peptidase from Staphylococcus aureus (SpsB) in complex with a substrate peptide (pep1).
Components
  • Maltose-binding periplasmic protein,Signal peptidase IB
  • substrate peptide (pep1)
KeywordsSIGNALING PROTEIN / SpsB Type-I signal peptidase / Peptide complex / Cell secretion / MBP fusion protein
Function / homology
Function and homology information


signal peptidase I / signal peptide processing / detection of maltose stimulus / maltose transport complex / maltose binding / carbohydrate transport / maltose transport / maltodextrin transmembrane transport / carbohydrate transmembrane transporter activity / ATP-binding cassette (ABC) transporter complex, substrate-binding subunit-containing ...signal peptidase I / signal peptide processing / detection of maltose stimulus / maltose transport complex / maltose binding / carbohydrate transport / maltose transport / maltodextrin transmembrane transport / carbohydrate transmembrane transporter activity / ATP-binding cassette (ABC) transporter complex, substrate-binding subunit-containing / ATP-binding cassette (ABC) transporter complex / cell chemotaxis / outer membrane-bounded periplasmic space / periplasmic space / serine-type endopeptidase activity / DNA damage response / membrane / 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 / 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: 2.1 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

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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
C: substrate peptide (pep1)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)60,1993
Polymers59,8562
Non-polymers3421
Water4,432246
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1540 Å2
ΔGint-1 kcal/mol
Surface area23760 Å2
MethodPISA
Unit cell
Length a, b, c (Å)63.661, 80.193, 119.426
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 33-382, unp reisdues 26-175 / Mutation: K143G, Q78C,K143G, Q78C
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, UniProt: P0AEX9*PLUS, signal peptidase I
#2: Protein/peptide substrate peptide (pep1)


Mass: 666.640 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.: 246 / 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: 2.62 Å3/Da / Density % sol: 53.11 %
Crystal growTemperature: 296 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: MX1 / Wavelength: 0.9537 Å
DetectorType: ADSC QUANTUM 210r / Detector: CCD / Date: Jun 10, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9537 Å / Relative weight: 1
ReflectionResolution: 2.1→66.58 Å / Num. obs: 36431 / % possible obs: 99.9 % / CC1/2: 0.994 / Rmerge(I) obs: 0.319 / Rpim(I) all: 0.086 / Net I/σ(I): 10 / Num. measured all: 534471
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
2.1-2.1614.82.6221.64356029450.5890.703100
8.91-19.7712.40.04644.462445040.9990.01391.4

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Processing

Software
NameVersionClassification
REFMACrefinement
XDSdata scaling
Aimless0.3.3data scaling
PHASERphasing
PDB_EXTRACT3.15data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4WVG

4wvg


Resolution: 2.1→66.58 Å / Cor.coef. Fo:Fc: 0.944 / Cor.coef. Fo:Fc free: 0.917 / WRfactor Rfree: 0.2021 / WRfactor Rwork: 0.1666 / FOM work R set: 0.783 / SU B: 6.427 / SU ML: 0.161 / SU R Cruickshank DPI: 0.2238 / SU Rfree: 0.1883 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.224 / ESU R Free: 0.188 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2485 1799 4.9 %RANDOM
Rwork0.2083 ---
obs0.2103 34573 99.81 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 67.86 Å2 / Biso mean: 29.051 Å2 / Biso min: 14.87 Å2
Baniso -1Baniso -2Baniso -3
1-0.29 Å2-0 Å2-0 Å2
2---0.88 Å20 Å2
3---0.59 Å2
Refinement stepCycle: final / Resolution: 2.1→66.58 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4075 0 23 246 4344
Biso mean--19.82 33.51 -
Num. residues----525
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0194198
X-RAY DIFFRACTIONr_bond_other_d0.0010.023959
X-RAY DIFFRACTIONr_angle_refined_deg1.1741.9645701
X-RAY DIFFRACTIONr_angle_other_deg0.72539145
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.6355521
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.39625.585188
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.30815687
X-RAY DIFFRACTIONr_dihedral_angle_4_deg7.9551510
X-RAY DIFFRACTIONr_chiral_restr0.0660.2623
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0214768
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02916
X-RAY DIFFRACTIONr_mcbond_it1.2272.8312096
X-RAY DIFFRACTIONr_mcbond_other1.2272.8312095
X-RAY DIFFRACTIONr_mcangle_it2.0284.2362613
LS refinement shellResolution: 2.1→2.154 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.329 144 -
Rwork0.296 2523 -
all-2667 -
obs--99.96 %

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