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- PDB-2zpm: Crystal structure analysis of PDZ domain B -

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Basic information

Entry
Database: PDB / ID: 2zpm
TitleCrystal structure analysis of PDZ domain B
ComponentsRegulator of sigma E protease
KeywordsHYDROLASE / metalloproteinase / membrane protein / PDZ domain / Inner 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 (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 0.98 Å
AuthorsInaba, K. / Suzuki, M.
CitationJournal: To be Published
Title: Crystal Structure analysis of PDZ-domain B
Authors: Inaba, K. / Suzuki, M. / Maegawa, K. / Akiyama, Y.
History
DepositionJul 17, 2008Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Oct 21, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Oct 11, 2017Group: Refinement description / Category: software

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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)9,8151
Polymers9,8151
Non-polymers00
Water2,720151
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: Regulator of sigma E protease

A: Regulator of sigma E protease


Theoretical massNumber of molelcules
Total (without water)19,6312
Polymers19,6312
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_656-x+1,y,-z+11
Buried area1150 Å2
ΔGint-10 kcal/mol
Surface area10020 Å2
MethodPISA
Unit cell
Length a, b, c (Å)70.141, 26.867, 42.789
Angle α, β, γ (deg.)90.00, 112.12, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-13-

HOH

21A-51-

HOH

31A-138-

HOH

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Components

#1: Protein Regulator of sigma E protease


Mass: 9815.257 Da / Num. of mol.: 1 / Fragment: PDZ-domain B
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Strain: K12 / Plasmid: pGEX-5X-1 / Production host: Escherichia coli (E. coli)
References: UniProt: P0AEH1, Hydrolases; Acting on peptide bonds (peptidases); Metalloendopeptidases
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 151 / 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: 1.9 Å3/Da / Density % sol: 35.35 %
Crystal growTemperature: 293 K / Method: vapor diffusion / Details: 25% PEG3350, VAPOR DIFFUSION, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL44XU / Wavelength: 0.65 Å
DetectorType: Bruker DIP-6040 / Detector: CCD
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.65 Å / Relative weight: 1
ReflectionResolution: 0.98→21.47 Å / Num. obs: 42333 / % possible obs: 99.4 % / Redundancy: 3.7 % / Biso Wilson estimate: 7.3 Å2 / Rmerge(I) obs: 0.044 / Net I/σ(I): 17.1
Reflection shellResolution: 0.98→1.03 Å / Redundancy: 3.7 % / Rmerge(I) obs: 0.446 / Mean I/σ(I) obs: 2.9 / % possible all: 99

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Processing

Software
NameVersionClassification
REFMAC5.5.0035refinement
HKL-2000data reduction
HKL-2000data scaling
SCALAdata scaling
SHELXCDphasing
SHELXEmodel building
RefinementMethod to determine structure: SAD / Resolution: 0.98→20.75 Å / Cor.coef. Fo:Fc: 0.974 / Cor.coef. Fo:Fc free: 0.964 / Cross valid method: THROUGHOUT / ESU R: 0.025 / ESU R Free: 0.027 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.18043 2140 5.1 %RANDOM
Rwork0.14977 ---
obs0.15135 40180 99.38 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 13.227 Å2
Baniso -1Baniso -2Baniso -3
1--0.07 Å20 Å20.13 Å2
2---0.22 Å20 Å2
3---0.38 Å2
Refinement stepCycle: LAST / Resolution: 0.98→20.75 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms733 0 0 151 884
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0230.022758
X-RAY DIFFRACTIONr_angle_refined_deg2.1422.0761051
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.9225112
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.15925.92627
X-RAY DIFFRACTIONr_dihedral_angle_3_deg10.34715111
X-RAY DIFFRACTIONr_dihedral_angle_4_deg8.869154
X-RAY DIFFRACTIONr_chiral_restr0.1360.2132
X-RAY DIFFRACTIONr_gen_planes_refined0.0120.022552
X-RAY DIFFRACTIONr_mcbond_it2.4931.5472
X-RAY DIFFRACTIONr_mcangle_it3.5642785
X-RAY DIFFRACTIONr_scbond_it4.8643286
X-RAY DIFFRACTIONr_scangle_it6.5064.5252
X-RAY DIFFRACTIONr_rigid_bond_restr2.7753758
X-RAY DIFFRACTIONr_sphericity_free12.0933151
X-RAY DIFFRACTIONr_sphericity_bonded7.0833733
LS refinement shellResolution: 0.981→1.006 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.22 171 -
Rwork0.212 2922 -
obs--98.88 %

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