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

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Basic information

Entry
Database: PDB / ID: 4wvg
TitleCrystal structure of the Type-I signal peptidase from Staphylococcus aureus (SpsB).
ComponentsMaltose-binding periplasmic protein,Signal peptidase IB
KeywordsHYDROLASE / SpsB Type-I signal peptidase / Cell secretion / MBP fusion protein
Function / homology
Function and homology information


signal peptidase I / signal peptide processing / carbohydrate transmembrane transporter activity / maltose binding / maltose transport / maltodextrin transmembrane transport / ATP-binding cassette (ABC) transporter complex, substrate-binding subunit-containing / 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 / Periplasmic binding protein-like II / D-Maltodextrin-Binding Protein; domain 2 / 3-Layer(aba) Sandwich / Alpha Beta
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)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.05 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 1.2Nov 22, 2017Group: Data collection / Derived calculations / Refinement description
Category: diffrn_source / pdbx_struct_oper_list / software
Item: _diffrn_source.pdbx_synchrotron_site / _pdbx_struct_oper_list.symmetry_operation / _software.classification
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.gene_src_strain / _entity_src_gen.pdbx_gene_src_ncbi_taxonomy_id / _entity_src_gen.pdbx_gene_src_scientific_name / _entity_src_gen.pdbx_host_org_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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)60,6442
Polymers60,3021
Non-polymers3421
Water6,413356
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)57.683, 63.565, 79.892
Angle α, β, γ (deg.)90.000, 92.590, 90.000
Int Tables number4
Space group name H-MP1211

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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: 60301.949 Da / Num. of mol.: 1 / Fragment: UNP RESIDUES 33-393, UNP RESIDUES 26-191 / Mutation: S36A, 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 / Production host: Escherichia coli K-12 (bacteria) / Strain (production host): K12
References: UniProt: P0AEY0, UniProt: Q5HHB9, signal peptidase I
#2: 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
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 356 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsTHIS MUTATION IS A RESULT OF PCR REACTION. THE MUTATION R393N HAS BEEN INTRODUCED TO STABILIZE THE ...THIS MUTATION IS A RESULT OF PCR REACTION. THE MUTATION R393N HAS BEEN 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: 2.43 Å3/Da / Density % sol: 49.31 % / Description: Needles
Crystal growTemperature: 296 K / Method: vapor diffusion, hanging drop
Details: 12 % PEG 8000, 20 % ethylene glycol, 0.2 M amino acids mix (0.2 M sodium-L-glutamate, 0.2 M DL-alanine, 0.2 M glycine, 0.2 M DL-lysine, 0.2 M DL-serine), 100 mM Tris.Cl pH 8.5
PH range: 8.0 - 8.5

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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: Mar 25, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9537 Å / Relative weight: 1
ReflectionResolution: 2.05→19.44 Å / Num. obs: 36318 / % possible obs: 99.8 % / Redundancy: 7.6 % / CC1/2: 0.994 / Rmerge(I) obs: 0.211 / Rpim(I) all: 0.082 / Net I/σ(I): 10.1 / Num. measured all: 275184
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
2.05-2.117.61.5771.42109527790.5280.60899.8
8.94-19.446.90.02759.229374260.9990.01191.1

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
XDSdata scaling
Aimlessdata scaling
PHASER2.5.2phasing
REFMAC5.8.0071refinement
PDB_EXTRACT3.15data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1ANF

1anf


Resolution: 2.05→19.44 Å / Cor.coef. Fo:Fc: 0.954 / Cor.coef. Fo:Fc free: 0.923 / WRfactor Rfree: 0.1901 / WRfactor Rwork: 0.1481 / FOM work R set: 0.7898 / SU B: 5.971 / SU ML: 0.151 / SU R Cruickshank DPI: 0.2001 / SU Rfree: 0.1796 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.2 / ESU R Free: 0.18 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.242 1839 5.1 %RANDOM
Rwork0.1896 34468 --
obs0.1921 34468 99.72 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 64.54 Å2 / Biso mean: 29.325 Å2 / Biso min: 14.23 Å2
Baniso -1Baniso -2Baniso -3
1--0.72 Å2-0 Å2-0.32 Å2
2---0.51 Å2-0 Å2
3---1.26 Å2
Refinement stepCycle: final / Resolution: 2.05→19.44 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3977 0 23 356 4356
Biso mean--18.84 35.13 -
Num. residues----513
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.024092
X-RAY DIFFRACTIONr_bond_other_d0.0010.023889
X-RAY DIFFRACTIONr_angle_refined_deg1.161.9695556
X-RAY DIFFRACTIONr_angle_other_deg0.71738984
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.3315510
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.68725.722180
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.96915680
X-RAY DIFFRACTIONr_dihedral_angle_4_deg8.2411510
X-RAY DIFFRACTIONr_chiral_restr0.0660.2612
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.0214637
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02879
X-RAY DIFFRACTIONr_mcbond_it1.2962.8422049
X-RAY DIFFRACTIONr_mcbond_other1.2962.8412048
X-RAY DIFFRACTIONr_mcangle_it2.2114.2542556
LS refinement shellResolution: 2.05→2.103 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.353 126 -
Rwork0.304 2525 -
all-2651 -
obs--99.81 %

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