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- PDB-4y9w: Aspartic Proteinase Sapp2 Secreted from Candida Parapsilosis at 0... -

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Basic information

Entry
Database: PDB / ID: 4y9w
TitleAspartic Proteinase Sapp2 Secreted from Candida Parapsilosis at 0.82 A Resolution.
Components
  • Aspartic acid endopeptidase Sapp2
  • PEPTIDE
KeywordsHYDROLASE / Candidapepsin / Aspartic Acid Endopeptidase
Function / homology
Function and homology information


candidapepsin / aspartic-type endopeptidase activity / proteolysis / extracellular region
Similarity search - Function
Secreted aspartic endopeptidase / 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 ...Secreted aspartic endopeptidase / 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
Pepstatin / candidapepsin
Similarity search - Component
Biological speciesCandida parapsilosis (yeast)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 0.83 Å
AuthorsDostal, J. / Brynda, J. / Hruskova-Heidingsfeldova, O. / Rezacova, P. / Mareckova, L. / Pichova, I.
CitationJournal: Acta Crystallogr.,Sect.D / Year: 2015
Title: Atomic resolution crystal structure of Sapp2p, a secreted aspartic protease from Candida parapsilosis.
Authors: Dostal, J. / Pecina, A. / Hruskova-Heidingsfeldova, O. / Mareckova, L. / Pichova, I. / Rezacova, P. / Lepsik, M. / Brynda, J.
History
DepositionFeb 17, 2015Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 30, 2016Provider: repository / Type: Initial release
Revision 1.1Dec 21, 2016Group: Non-polymer description
Revision 1.2Sep 4, 2019Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Aspartic acid endopeptidase Sapp2
B: PEPTIDE


Theoretical massNumber of molelcules
Total (without water)36,1612
Polymers36,1612
Non-polymers00
Water7,044391
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1350 Å2
ΔGint-9 kcal/mol
Surface area12970 Å2
MethodPISA
Unit cell
Length a, b, c (Å)48.260, 57.660, 54.360
Angle α, β, γ (deg.)90.00, 92.95, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Aspartic acid endopeptidase Sapp2


Mass: 35474.992 Da / Num. of mol.: 1 / Fragment: UNP RESIDUES 72-405 / Source method: isolated from a natural source / Source: (natural) Candida parapsilosis (yeast) / References: UniProt: G8B6Y8
#2: Protein/peptide PEPTIDE


Type: Oligopeptide / Class: Enzyme inhibitor / Mass: 685.891 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others) / References: Pepstatin
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 391 / 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: 2.13 Å3/Da / Density % sol: 42.18 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 6.5 / Details: PEG 400

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.2 / Wavelength: 0.91841 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Jun 1, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.91841 Å / Relative weight: 1
ReflectionResolution: 0.825→11.368 Å / Num. all: 261700 / Num. obs: 261700 / % possible obs: 92.3 % / Redundancy: 8.1 % / Rpim(I) all: 0.032 / Rrim(I) all: 0.096 / Rsym value: 0.087 / Net I/av σ(I): 4.512 / Net I/σ(I): 13.2 / Num. measured all: 2124055
Reflection shell

Diffraction-ID: 1 / Rejects: _

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allRpim(I) allRsym valueNet I/σ(I) obs% possible all
0.82-0.853.10.3781.843021137050.2890.378265.5
0.85-0.874.70.3282.280124171580.1890.3283.184.6
0.87-0.895.90.3012.3102728172870.1460.3014.186.8
0.89-0.927.10.2482.8125889176870.1060.2485.492
0.92-0.957.60.2053.4134284177550.0840.2056.794.9
0.95-0.998.10.1753.9139768172470.0680.1758.195.6
0.99-1.028.40.1514.4141135168020.0580.1519.596.3
1.02-1.078.90.135143641162210.0480.1311.796.8
1.07-1.119.50.1185.4148134156690.0420.11813.697.3
1.11-1.179.50.1095.8142989150490.0380.10915.297.7
1.17-1.239.50.1026.1137472144090.0360.10216.198.2
1.23-1.39.60.1046130937136810.0360.10416.898.7
1.3-1.399.60.1065.8124152129040.0370.10617.899.1
1.39-1.519.70.16.1116732120920.0350.119.699.4
1.51-1.659.70.0986.3108350111650.0340.0982299.7
1.65-1.849.70.0797.698402100990.0270.07925.399.9
1.84-2.139.70.0718.38700689740.0250.0713199.9
2.13-2.619.30.06796991375220.0250.06733.899.1
2.61-3.698.10.0718.73879947820.0290.07132.581.4
3.69-11.3767.10.0738.41057914920.030.07326.644.9

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Processing

Software
NameVersionClassification
REFMAC5.6.0117refinement
MOSFLMdata reduction
SCALA3.3.16data scaling
PDB_EXTRACT3.15data extraction
MOLREPphasing
RefinementResolution: 0.83→11.37 Å / Cor.coef. Fo:Fc: 0.98 / Cor.coef. Fo:Fc free: 0.978 / WRfactor Rfree: 0.128 / WRfactor Rwork: 0.1197 / FOM work R set: 0.949 / SU B: 0.225 / SU ML: 0.007 / SU R Cruickshank DPI: 0.0119 / SU Rfree: 0.012 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.012 / ESU R Free: 0.012 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.1245 13247 5.1 %RANDOM
Rwork0.1169 ---
obs0.1173 248399 92.02 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso max: 120.06 Å2 / Biso mean: 8.509 Å2 / Biso min: 2.95 Å2
Baniso -1Baniso -2Baniso -3
1--0.02 Å20 Å2-0.11 Å2
2--0.1 Å20 Å2
3----0.09 Å2
Refinement stepCycle: final / Resolution: 0.83→11.37 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2496 0 0 365 2861
Biso mean---19.19 -
Num. residues----340
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0170.022801
X-RAY DIFFRACTIONr_bond_other_d0.0020.021826
X-RAY DIFFRACTIONr_angle_refined_deg1.9131.9673861
X-RAY DIFFRACTIONr_angle_other_deg1.5023.0024527
X-RAY DIFFRACTIONr_dihedral_angle_1_deg8.4345393
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.95325.702114
X-RAY DIFFRACTIONr_dihedral_angle_3_deg10.1415427
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.22157
X-RAY DIFFRACTIONr_chiral_restr0.1130.2444
X-RAY DIFFRACTIONr_gen_planes_refined0.0120.0213242
X-RAY DIFFRACTIONr_gen_planes_other0.0040.02538
X-RAY DIFFRACTIONr_rigid_bond_restr6.96832777
X-RAY DIFFRACTIONr_sphericity_free21.367553
X-RAY DIFFRACTIONr_sphericity_bonded9.40552962
LS refinement shellResolution: 0.825→0.846 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.408 688 -
Rwork0.409 12537 -
all-13225 -
obs--63.66 %

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