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- PDB-3id4: Crystal Structure of RseP PDZ2 domain fused GKASPV peptide -

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Basic information

Entry
Database: PDB / ID: 3id4
TitleCrystal Structure of RseP PDZ2 domain fused GKASPV peptide
ComponentsRegulator of sigma E protease
KeywordsHYDROLASE / Cell inner membrane / Cell membrane / Membrane / Metal-binding / Metalloprotease / Protease / Transmembrane / Zinc
Function / homology
Function and homology information


anti-sigma factor antagonist activity / Hydrolases; Acting on peptide bonds (peptidases); Metalloendopeptidases / cellular response to cell envelope stress / metalloendopeptidase activity / positive regulation of DNA-templated transcription / proteolysis / metal ion binding / plasma membrane
Similarity search - Function
Peptidase M50, putative membrane-associated zinc metallopeptidase / Peptidase M50 / Peptidase family M50 / PDZ domain 6 / PDZ domain / PDZ domain / Pdz3 Domain / PDZ domain profile. / Domain present in PSD-95, Dlg, and ZO-1/2. / PDZ domain ...Peptidase M50, putative membrane-associated zinc metallopeptidase / Peptidase M50 / Peptidase family M50 / PDZ domain 6 / PDZ domain / PDZ domain / Pdz3 Domain / PDZ domain profile. / Domain present in PSD-95, Dlg, and ZO-1/2. / PDZ domain / PDZ superfamily / Neutral zinc metallopeptidases, zinc-binding region signature. / Roll / Mainly Beta
Similarity search - Domain/homology
Regulator of sigma-E protease RseP
Similarity search - Component
Biological speciesEscherichia coli K-12 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.604 Å
AuthorsLi, X. / Wang, B. / Feng, L. / Wang, J. / Shi, Y.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2009
Title: Cleavage of RseA by RseP requires a carboxyl-terminal hydrophobic amino acid following DegS cleavage
Authors: Li, X. / Wang, B. / Feng, L. / Kang, H. / Qi, Y. / Wang, J. / Shi, Y.
History
DepositionJul 20, 2009Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Aug 11, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 1, 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 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Regulator of sigma E protease


Theoretical massNumber of molelcules
Total (without water)9,7981
Polymers9,7981
Non-polymers00
Water1,26170
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)35.094, 35.094, 62.373
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number144
Space group name H-MP31

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Components

#1: Protein Regulator of sigma E protease


Mass: 9798.302 Da / Num. of mol.: 1 / Fragment: PDZ2 domain, residues 222-307
Source method: isolated from a genetically manipulated source
Details: Carboxy-terminally fused GKASPV peptide / Source: (gene. exp.) Escherichia coli K-12 (bacteria) / Strain: K12 / Gene: rseP / Plasmid: pET15b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)
References: UniProt: P0AEH1, Hydrolases; Acting on peptide bonds (peptidases); Metalloendopeptidases
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 70 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsTHE FUSED PEPTIDE OF GLY308 TO VAL313 IS CARBOXT-TERMINUS OF RSEA BY DEGS CLEAVAGE. THE DEPOSITORS ...THE FUSED PEPTIDE OF GLY308 TO VAL313 IS CARBOXT-TERMINUS OF RSEA BY DEGS CLEAVAGE. THE DEPOSITORS FUSED THIS PEPTIDE TO VERIFY THAT RSEA V148 CAN BIND TO RSEP PDZ2 DOMAIN.

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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: 2.26 Å3/Da / Density % sol: 45.65 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 5.5
Details: 0.2M (NH4)2SO4, 30%(w/v) Polyethylene Glycol 4000, pH 5.5, VAPOR DIFFUSION, HANGING DROP, temperature 291K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 0.96386 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: May 28, 2009
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.96386 Å / Relative weight: 1
ReflectionResolution: 1.6→30 Å / Num. obs: 10945 / % possible obs: 97.5 % / Redundancy: 3 % / Biso Wilson estimate: 22.6 Å2 / Rsym value: 0.06 / Net I/σ(I): 33.1
Reflection shellResolution: 1.6→1.63 Å / Redundancy: 1.8 % / Mean I/σ(I) obs: 2.8 / Num. unique all: 469 / Rsym value: 0.246 / % possible all: 85

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Processing

Software
NameVersionClassification
MAR345dtbdata collection
PHASERphasing
PHENIX(phenix.refine)refinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3ID2

3id2


Resolution: 1.604→21.766 Å / Occupancy max: 1 / Occupancy min: 0.5 / FOM work R set: 0.849 / SU ML: 0.2 / Isotropic thermal model: Isotropic / σ(F): 0.09 / Phase error: 22.61 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2187 498 4.73 %Random
Rwork0.1919 10041 --
obs0.1932 10539 93.82 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 56.077 Å2 / ksol: 0.405 e/Å3
Displacement parametersBiso max: 124.79 Å2 / Biso mean: 30.269 Å2 / Biso min: 12.25 Å2
Baniso -1Baniso -2Baniso -3
1-2.743 Å2-0 Å2-0 Å2
2--2.743 Å20 Å2
3----5.485 Å2
Refinement stepCycle: LAST / Resolution: 1.604→21.766 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms703 0 0 70 773
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.004718
X-RAY DIFFRACTIONf_angle_d0.883979
X-RAY DIFFRACTIONf_chiral_restr0.056113
X-RAY DIFFRACTIONf_plane_restr0.004131
X-RAY DIFFRACTIONf_dihedral_angle_d15.026284
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 4

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.604-1.7660.2731060.2342273237985
1.766-2.0210.2121280.22543267195
2.021-2.5460.2191410.1792643278498
2.546-21.7680.2091230.1882582270597
Refinement TLS params.Method: refined / Origin x: 3.0364 Å / Origin y: 6.5931 Å / Origin z: 8.3741 Å
111213212223313233
T0.1409 Å2-0.0107 Å20.0122 Å2-0.1418 Å2-0.0063 Å2--0.1673 Å2
L1.2288 °2-0.532 °2-0.5126 °2-0.8241 °20.6489 °2--1.3787 °2
S0.1034 Å °-0.0819 Å °0.0673 Å °0.0288 Å °-0.1073 Å °0.0794 Å °-0.0814 Å °-0.0548 Å °0.0093 Å °
Refinement TLS groupSelection details: chain A

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