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- PDB-3id3: Crystal Structure of RseP PDZ2 I304A domain -

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Basic information

Entry
Database: PDB / ID: 3id3
TitleCrystal Structure of RseP PDZ2 I304A domain
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 / MOLECULAR REPLACEMENT / Resolution: 2.01 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 10, 2021Group: Database references / Category: database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details
Revision 1.3Nov 1, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Regulator of sigma E protease
B: Regulator of sigma E protease


Theoretical massNumber of molelcules
Total (without water)18,8562
Polymers18,8562
Non-polymers00
Water2,540141
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1750 Å2
ΔGint-7 kcal/mol
Surface area8820 Å2
MethodPISA
Unit cell
Length a, b, c (Å)47.411, 38.147, 51.265
Angle α, β, γ (deg.)90.00, 102.84, 90.00
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B

NCS domain segments:
Dom-IDComponent-IDEns-IDSelection detailsAuth asym-IDAuth seq-ID
111chain A and (resseq 0:88 )A0 - 88
211chain B and (resseq 0:88 )B0 - 88

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Components

#1: Protein Regulator of sigma E protease


Mass: 9427.877 Da / Num. of mol.: 2 / Fragment: PDZ2 domain, residues 222-309 / Mutation: I304A
Source method: isolated from a genetically manipulated source
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.: 141 / 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: 2.4 Å3/Da / Density % sol: 48.69 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 4M Sodium Formate, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 291K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: BRUKER AXS MICROSTAR-H / Wavelength: 1.5418 Å
DetectorType: BRUKER SMART 6000 / Detector: CCD / Date: Oct 16, 2008
RadiationMonochromator: mirror / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.01→49.983 Å / Num. all: 18873 / Num. obs: 10330 / % possible obs: 85.2 % / Redundancy: 1.55 % / Biso Wilson estimate: 10.4 Å2 / Rsym value: 0.094 / Net I/σ(I): 9.85
Reflection shellResolution: 2.01→2.11 Å / Redundancy: 0.61 % / Mean I/σ(I) obs: 3.21 / Num. unique all: 10330 / Rsym value: 0.335 / % possible all: 85.2

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Processing

Software
NameVersionClassification
PROTEUM PLUSPLUSdata collection
PHASERphasing
PHENIX(phenix.refine)refinement
SAINTdata reduction
PROTEUM PLUSPLUSdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2ZPM

2zpm


Resolution: 2.01→49.983 Å / Occupancy max: 1 / Occupancy min: 1 / FOM work R set: 0.854 / SU ML: 0.3 / Isotropic thermal model: Isotropic / σ(F): 0.05 / Phase error: 22.05 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2223 491 4.92 %Thin Shell
Rwork0.1965 9497 --
obs0.1978 9988 82.44 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 41.306 Å2 / ksol: 0.375 e/Å3
Displacement parametersBiso max: 77.38 Å2 / Biso mean: 20.716 Å2 / Biso min: 4.66 Å2
Baniso -1Baniso -2Baniso -3
1--7.644 Å20 Å2-4.65 Å2
2---7.08 Å2-0 Å2
3---1.98 Å2
Refinement stepCycle: LAST / Resolution: 2.01→49.983 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1322 0 0 141 1463
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0071344
X-RAY DIFFRACTIONf_angle_d0.9361824
X-RAY DIFFRACTIONf_chiral_restr0.061214
X-RAY DIFFRACTIONf_plane_restr0.005240
X-RAY DIFFRACTIONf_dihedral_angle_d17.633516
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDTypeRms dev position (Å)
11A661X-RAY DIFFRACTIONPOSITIONAL0.032
12B661X-RAY DIFFRACTIONPOSITIONAL0.032
LS refinement shell

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

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.0104-2.21270.213810.2046154054
2.2127-2.53290.2277960.2079269793
2.5329-3.19110.25351500.2037268793
3.1911-49.99870.19691640.1776257389
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.30520.32690.26420.55620.52450.3240.0383-0.0009-0.04250.041-0.08180.03720.0021-0.00920.01970.21170.01120.06160.14650.01420.00111.5992-2.7351-9.1415
20.66470.68680.12660.34040.34080.36950.052300.0499-0.02950.01620.0087-0.02880.03840.00520.20120.02230.04270.15020.0070.0456-8.845-11.8635-23.5445
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain AA0 - 88
2X-RAY DIFFRACTION2chain BB0 - 88

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