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- PDB-3id2: Crystal Structure of RseP PDZ2 domain -

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Basic information

Entry
Database: PDB / ID: 3id2
TitleCrystal Structure of RseP PDZ2 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
IODIDE ION / Regulator of sigma-E protease RseP
Similarity search - Component
Biological speciesEscherichia coli K-12 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.089 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 ...Data collection / Database references / Derived calculations / 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 / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)20,48512
Polymers19,2162
Non-polymers1,26910
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2860 Å2
ΔGint-17 kcal/mol
Surface area9420 Å2
MethodPISA
Unit cell
Length a, b, c (Å)108.961, 108.961, 58.335
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212

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Components

#1: Protein Regulator of sigma E protease


Mass: 9608.105 Da / Num. of mol.: 2 / Fragment: PDZ2 domain, residues 222-309
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: Chemical
ChemComp-IOD / IODIDE ION


Mass: 126.904 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: I

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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: 4.51 Å3/Da / Density % sol: 72.7 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 4M Sodium Formate, 4% Methanol, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 291K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL38B1 / Wavelength: 1.5418 Å
DetectorType: RIGAKU JUPITER 210 / Detector: CCD / Date: Oct 24, 2008
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 3.089→39.82 Å / Num. obs: 6668 / % possible obs: 97.6 % / Redundancy: 3.7 % / Biso Wilson estimate: 67.8 Å2 / Rsym value: 0.1 / Net I/σ(I): 19.8
Reflection shellResolution: 3.089→3.2 Å / Redundancy: 3.2 % / Mean I/σ(I) obs: 3.24 / Num. unique all: 6696 / Rsym value: 0.393 / % possible all: 90.4

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Processing

Software
NameVersionClassification
BSSdata collection
PHASERphasing
PHENIX(phenix.refine)refinement
HKL-2000data reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2ZPM

2zpm


Resolution: 3.089→39.817 Å / Occupancy max: 1 / Occupancy min: 0.48 / FOM work R set: 0.805 / SU ML: 0.5 / Isotropic thermal model: Isotropic / σ(F): 0.01 / Phase error: 25.94 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2698 533 4.67 %Thin shell
Rwork0.2049 10873 --
all0.2078 ---
obs0.2078 6668 92.73 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 63.998 Å2 / ksol: 0.383 e/Å3
Displacement parametersBiso max: 212.29 Å2 / Biso mean: 69.08 Å2 / Biso min: 11.79 Å2
Baniso -1Baniso -2Baniso -3
1--8.573 Å2-0 Å20 Å2
2---8.573 Å2-0 Å2
3---13.809 Å2
Refinement stepCycle: LAST / Resolution: 3.089→39.817 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1368 0 10 0 1378
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0111394
X-RAY DIFFRACTIONf_angle_d1.4091892
X-RAY DIFFRACTIONf_dihedral_angle_d16.978532
X-RAY DIFFRACTIONf_chiral_restr0.078220
X-RAY DIFFRACTIONf_plane_restr0.008248
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 (%)
3.089-3.40.3581790.2752355253483
3.4-3.8920.3151190.2072786290594
3.892-4.9020.21010.1742871297297
4.902-39.820.2451340.2052861299597
Refinement TLS params.

S31: -0.1667 Å ° / 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 °)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)
11.60390.51330.52111.9484-1.41390.0751-0.0649-0.2650.31880.39660.1120.1884-0.19430.0610.080.03260.00320.1051-0.08740.042-9.1734-43.3491-3.1868
22.0328-0.5835-0.01840.734-0.6031-0.3206-0.3592-0.4548-0.00250.64070.31740.41510.02540.01910.37440.22820.55070.2135-0.10490.3826-26.4749-42.288810.7808
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain AA220 - 309
2X-RAY DIFFRACTION2chain BB220 - 309

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