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- PDB-6fhp: DAIP in complex with a C-terminal fragment of thermolysin -

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Basic information

Entry
Database: PDB / ID: 6fhp
TitleDAIP in complex with a C-terminal fragment of thermolysin
Components
  • Dispase autolysis-inducing protein
  • Thermolysin
KeywordsANTIMICROBIAL PROTEIN / Dispase autolysis-inducing protein / neutral metalloproteases / protease twisting / conformation analysis
Function / homology
Function and homology information


post-Golgi vesicle-mediated transport / thermolysin / metalloendopeptidase activity / proteolysis / extracellular region / metal ion binding
Similarity search - Function
: / PepSY domain / Peptidase propeptide and YPEB domain / : / Peptidase M4, C-terminal / FTP domain / Peptidase M4 domain / Peptidase M4 / Thermolysin metallopeptidase, catalytic domain / Thermolysin metallopeptidase, alpha-helical domain ...: / PepSY domain / Peptidase propeptide and YPEB domain / : / Peptidase M4, C-terminal / FTP domain / Peptidase M4 domain / Peptidase M4 / Thermolysin metallopeptidase, catalytic domain / Thermolysin metallopeptidase, alpha-helical domain / Fungalysin/Thermolysin Propeptide Motif / Neutral Protease Domain 2 / Neutral Protease; domain 2 / Peptidase M4/M1, CTD superfamily / Neutral zinc metallopeptidases, zinc-binding region signature. / WD40/YVTN repeat-like-containing domain superfamily / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
Thermolysin / Dispase autolysis-inducing protein
Similarity search - Component
Biological speciesStreptomyces mobaraensis (bacteria)
Geobacillus stearothermophilus (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.703 Å
AuthorsSchmelz, S. / Fiebig, D. / Fuchsbauer, H.L. / Blankenfeldt, W. / Scrima, A.
Funding support Germany, 1items
OrganizationGrant numberCountry
Helmholtz AssociationVH-NG-727 Germany
CitationJournal: FEBS J. / Year: 2018
Title: Destructive twisting of neutral metalloproteases: the catalysis mechanism of the Dispase autolysis-inducing protein from Streptomyces mobaraensis DSM 40487.
Authors: Fiebig, D. / Storka, J. / Roeder, M. / Meyners, C. / Schmelz, S. / Blankenfeldt, W. / Scrima, A. / Kolmar, H. / Fuchsbauer, H.L.
History
DepositionJan 15, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 12, 2018Provider: repository / Type: Initial release
Revision 1.1Nov 28, 2018Group: Data collection / Database references / Category: citation / pdbx_database_proc
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.2Jan 17, 2024Group: 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
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.3Nov 20, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Dispase autolysis-inducing protein
B: Dispase autolysis-inducing protein
C: Thermolysin
D: Thermolysin


Theoretical massNumber of molelcules
Total (without water)84,3374
Polymers84,3374
Non-polymers00
Water16,718928
1
A: Dispase autolysis-inducing protein
C: Thermolysin


Theoretical massNumber of molelcules
Total (without water)42,1682
Polymers42,1682
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1410 Å2
ΔGint-4 kcal/mol
Surface area16110 Å2
MethodPISA
2
B: Dispase autolysis-inducing protein
D: Thermolysin


Theoretical massNumber of molelcules
Total (without water)42,1682
Polymers42,1682
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1360 Å2
ΔGint-4 kcal/mol
Surface area16740 Å2
MethodPISA
Unit cell
Length a, b, c (Å)64.070, 90.050, 69.070
Angle α, β, γ (deg.)90.000, 99.040, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Dispase autolysis-inducing protein


Mass: 35536.938 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptomyces mobaraensis (bacteria) / Gene: daip / Production host: Escherichia coli (E. coli) / References: UniProt: P84908
#2: Protein Thermolysin / Neutral protease


Mass: 6631.481 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Geobacillus stearothermophilus (bacteria) / Plasmid details: Sigma T7902 / References: UniProt: P43133, thermolysin
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 928 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 2.33 Å3/Da / Density % sol: 47.28 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 5.6
Details: 117 mM ammonium sulfate, 83.3 mM sodium acetate pH 5.6 and 25.3 % (w/v) PEG 1500

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.54187 Å
DetectorType: RIGAKU SATURN 944+ / Detector: CCD / Date: Sep 26, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54187 Å / Relative weight: 1
ReflectionResolution: 1.7→31.148 Å / Num. obs: 82461 / % possible obs: 96.9 % / Redundancy: 2.778 % / Biso Wilson estimate: 20.71 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.035 / Rrim(I) all: 0.043 / Χ2: 1.021 / Net I/σ(I): 17.95 / Num. measured all: 229037 / Scaling rejects: 25
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. possibleNum. unique obsCC1/2Rrim(I) all% possible all
1.7-1.81.6840.4461.811995613315118470.670.63189
1.8-1.91.9670.2523.512024810684102920.880.34396.3
1.9-22.3470.1436.5519862867084620.9610.18797.6
2-2.52.9620.07813.687440225465251150.9920.09598.6
2.5-33.5430.04325.333981611297112370.9980.05199.5
3-43.5530.02442.0631739898389320.9990.02899.4
4-63.5430.01854.5916338465446110.9990.02299.1
6-103.4480.01854.935324155915440.9990.02199
10-31.1483.2110.01563.17135244942110.01793.8

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Phasing

PhasingMethod: molecular replacement
Phasing MR
Highest resolutionLowest resolution
Rotation3.66 Å37.56 Å
Translation3.66 Å37.56 Å

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Processing

Software
NameVersionClassificationNB
PHENIXrefinement
XDSdata reduction
XSCALEdata scaling
PHASER2.8.0phasing
PDB_EXTRACT3.24data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5fzp

5fzp


Resolution: 1.703→31.148 Å / SU ML: 0.21 / Cross valid method: THROUGHOUT / σ(F): 1.37 / Phase error: 24.83 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2263 4123 5 %
Rwork0.1857 78331 -
obs0.1877 82454 97.44 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 68.23 Å2 / Biso mean: 24.9945 Å2 / Biso min: 9.9 Å2
Refinement stepCycle: final / Resolution: 1.703→31.148 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5920 0 0 934 6854
Biso mean---33.73 -
Num. residues----805
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 29

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.7031-1.72320.31951290.32172459258888
1.7232-1.74420.36581310.29232495262692
1.7442-1.76620.30581360.27772586272293
1.7662-1.78950.30041380.27582611274995
1.7895-1.8140.31041380.26192618275695
1.814-1.83990.29221390.24732652279196
1.8399-1.86740.25651400.24272665280597
1.8674-1.89650.24481400.22832655279597
1.8965-1.92760.26131410.2182675281697
1.9276-1.96090.27051430.21532718286198
1.9609-1.99650.31081420.22082700284298
1.9965-2.03490.26241440.21862725286998
2.0349-2.07640.27861400.21012673281398
2.0764-2.12160.2411450.20432745289099
2.1216-2.17090.25891430.20362720286398
2.1709-2.22520.27771440.2062738288299
2.2252-2.28530.25171420.20052706284898
2.2853-2.35260.24871460.19762764291099
2.3526-2.42850.28181440.21012732287699
2.4285-2.51520.26391450.20332761290699
2.5152-2.61590.21591440.19592737288199
2.6159-2.73490.24051450.188127462891100
2.7349-2.8790.22961460.188727862932100
2.879-3.05920.20811460.18227672913100
3.0592-3.29520.21211450.17362766291199
3.2952-3.62630.20681460.15722768291499
3.6263-4.150.18651460.144827732919100
4.15-5.22460.14661460.13052772291899
5.2246-31.15270.18141490.16152818296799

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