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- PDB-5p6d: Automated refinement of diffraction data obtained from an endothi... -

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Basic information

Entry
Database: PDB / ID: 5p6d
TitleAutomated refinement of diffraction data obtained from an endothiapepsin crystal treated with fragment 274
Componentsendothiapepsin
KeywordsHYDROLASE / fragment screening / method development / aspartic protease
Function / homology
Function and homology information


endothiapepsin / aspartic-type endopeptidase activity / proteolysis
Similarity search - Function
Aspergillopepsin-like catalytic domain / Eukaryotic aspartyl protease / Aspartic peptidase A1 family / Peptidase family A1 domain / Peptidase family A1 domain profile. / Cathepsin D, subunit A; domain 1 / Acid Proteases / Aspartic peptidase, active site / Eukaryotic and viral aspartyl proteases active site. / Aspartic peptidase domain superfamily ...Aspergillopepsin-like catalytic domain / Eukaryotic aspartyl protease / Aspartic peptidase A1 family / Peptidase family A1 domain / Peptidase family A1 domain profile. / Cathepsin D, subunit A; domain 1 / Acid Proteases / Aspartic peptidase, active site / Eukaryotic and viral aspartyl proteases active site. / Aspartic peptidase domain superfamily / Beta Barrel / Mainly Beta
Similarity search - Domain/homology
Biological speciesCryphonectria parasitica (chestnut blight fungus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.439 Å
Model detailsAll 364 structures of this series were generated by an automated refinement pipeline and, thus, not ...All 364 structures of this series were generated by an automated refinement pipeline and, thus, not refined to full convergence (e.g. since no manual (re-)building was performed, fragments are missing in the structural model even when present as indicated by the electron density)
AuthorsSchiebel, J. / Heine, A. / Klebe, G.
CitationJournal: Structure / Year: 2016
Title: High-Throughput Crystallography: Reliable and Efficient Identification of Fragment Hits.
Authors: Schiebel, J. / Krimmer, S.G. / Rower, K. / Knorlein, A. / Wang, X. / Park, A.Y. / Stieler, M. / Ehrmann, F.R. / Fu, K. / Radeva, N. / Krug, M. / Huschmann, F.U. / Glockner, S. / Weiss, M.S. ...Authors: Schiebel, J. / Krimmer, S.G. / Rower, K. / Knorlein, A. / Wang, X. / Park, A.Y. / Stieler, M. / Ehrmann, F.R. / Fu, K. / Radeva, N. / Krug, M. / Huschmann, F.U. / Glockner, S. / Weiss, M.S. / Mueller, U. / Klebe, G. / Heine, A.
History
DepositionJun 28, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 3, 2016Provider: repository / Type: Initial release
Revision 1.1Aug 10, 2016Group: Database references
Revision 1.2Jan 11, 2017Group: Database references
Revision 1.3Feb 21, 2018Group: Structure summary / Category: pdbx_deposit_group / Item: _pdbx_deposit_group.group_type
Revision 1.4Nov 17, 2021Group: Data collection / Database references / Structure summary
Category: database_2 / diffrn_radiation_wavelength / pdbx_deposit_group
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_deposit_group.group_description
Revision 1.5Nov 6, 2024Group: Data collection / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: endothiapepsin


Theoretical massNumber of molelcules
Total (without water)33,8141
Polymers33,8141
Non-polymers00
Water3,855214
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)45.306, 73.232, 52.845
Angle α, β, γ (deg.)90.000, 109.410, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein endothiapepsin


Mass: 33813.855 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Cryphonectria parasitica (chestnut blight fungus)
References: UniProt: P11838, endothiapepsin
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 214 / 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: 2.45 Å3/Da / Density % sol: 49.7 %
Crystal growTemperature: 290 K / Method: vapor diffusion, sitting drop / pH: 4.6
Details: 0.1 M ammonium acetate, 0.1 M sodium acetate, 24-30% PEG 4000; crystal obtained by streak-seeding and soaked with 90 mM of fragment 274 with the SMILES code NC[C@@H](O)C1=CC=C(F)C=C1

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.1 / Wavelength: 0.918409 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jul 18, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.918409 Å / Relative weight: 1
ReflectionResolution: 1.44→42.73 Å / Num. obs: 58762 / % possible obs: 99.4 % / Observed criterion σ(I): -3 / Redundancy: 3.73 % / Biso Wilson estimate: 10.96 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.056 / Rrim(I) all: 0.065 / Χ2: 0.944 / Net I/σ(I): 16.97 / Num. measured all: 219224
Reflection shell

Diffraction-ID: 1 / Rejects: _

Resolution (Å)Highest resolution (Å)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. possibleNum. unique obsCC1/2Rrim(I) all% possible all
1.44-1.530.4383.0135025952194040.8430.51298.8
1.53-1.630.2914.5933104894389130.9250.33999.7
1.63-1.760.1956.7629464834283240.960.22999.8
1.76-1.930.11511.9529852762576060.9870.13399.8
1.93-2.160.06519.5826789701369820.9950.07599.6
2.16-2.490.04824.6521422610760720.9970.05699.4
2.49-3.050.03334.8220306520651750.9980.03899.4
3.05-4.30.02347.1814742404940230.9990.02799.4
4.30.02254.868520228722630.9990.02699

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Phasing

PhasingMethod: molecular replacement
Phasing MRModel details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation4 Å42.73 Å

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Processing

Software
NameVersionClassificationNB
XDSdata scaling
PHENIXrefinement
PHASER2.5.7phasing
PDB_EXTRACT3.2data extraction
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4Y5L

4y5l


Resolution: 1.439→39.587 Å / SU ML: 0.11 / Cross valid method: THROUGHOUT / σ(F): 1.36 / Phase error: 13.98 / Stereochemistry target values: ML
Details: All 364 structures of this series were generated by an automated refinement pipeline and, thus, not refined to full convergence (e.g. since no manual (re-)building was performed, fragments ...Details: All 364 structures of this series were generated by an automated refinement pipeline and, thus, not refined to full convergence (e.g. since no manual (re-)building was performed, fragments are missing in the structural model even when present as indicated by the electron density)
RfactorNum. reflection% reflectionSelection details
Rfree0.1611 2935 4.99 %RANDOM
Rwork0.1345 55824 --
obs0.1359 58759 99.56 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 46.23 Å2 / Biso mean: 13.544 Å2 / Biso min: 6.5 Å2
Refinement stepCycle: final / Resolution: 1.439→39.587 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2369 0 0 214 2583
Biso mean---23.27 -
Num. residues----330
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0072426
X-RAY DIFFRACTIONf_angle_d1.163329
X-RAY DIFFRACTIONf_chiral_restr0.071399
X-RAY DIFFRACTIONf_plane_restr0.005424
X-RAY DIFFRACTIONf_dihedral_angle_d10.397783
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 21

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.4387-1.46230.22241370.16792599273696
1.4623-1.48750.21081370.162126252762100
1.4875-1.51460.19511400.155426762816100
1.5146-1.54370.18351380.133826312769100
1.5437-1.57520.19631410.127926772818100
1.5752-1.60950.15311390.122626372776100
1.6095-1.64690.16561390.115426442783100
1.6469-1.68810.14351410.112626702811100
1.6881-1.73380.16551380.111226492787100
1.7338-1.78480.16471410.108926772818100
1.7848-1.84240.15151400.107726502790100
1.8424-1.90820.13341380.110926562794100
1.9082-1.98460.15721410.110826382779100
1.9846-2.0750.13481400.110826622802100
2.075-2.18430.12651400.114626672807100
2.1843-2.32120.14861380.12382659279799
2.3212-2.50040.15381420.133526762818100
2.5004-2.75190.15261390.137726482787100
2.7519-3.150.14931410.145726802821100
3.15-3.96810.18871410.155826792820100
3.9681-39.60210.17041440.16392724286899

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