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- PDB-8fxq: The Crystal Sturucture of Rhizopuspepsin with a bound modified pe... -

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Basic information

Entry
Database: PDB / ID: 8fxq
TitleThe Crystal Sturucture of Rhizopuspepsin with a bound modified peptide inhibitor generated by de novo drug design.
Components
  • ALA-CYS-VAL-LYS
  • Rhizopuspepsin
KeywordsHYDROLASE / Rhizopuspepsin / de novo drug design / peptide inhibitors
Function / homology
Function and homology information


rhizopuspepsin / 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
CYCLOHEXANE / Rhizopuspepsin
Similarity search - Component
Biological speciesRhizopus microsporus var. chinensis (fungus)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.21 Å
AuthorsSatyshur, K.A. / Rich, D.H. / Ripka, A.S.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM50113 United States
Citation
Journal: Org Lett / Year: 2001
Title: Aspartic protease inhibitors designed from computer-generated templates bind as predicted.
Authors: Ripka, A.S. / Satyshur, K.A. / Bohacek, R.S. / Rich, D.H.
#1: Journal: Org Lett / Year: 2001
Title: Design and synthesis of unsymmetrical peptidyl urea inhibitors of aspartic peptidases.
Authors: Dales, N.A. / Bohacek, R.S. / Satyshur, K.A. / Rich, D.H.
#2: Journal: Protein Expr Purif / Year: 1999
Title: Purification and crystallization of rhizopuspepsin: the use of nickel chelation chromatography to select for catalytically active species.
Authors: Flentke, G.R. / Glinski, J. / Satyshur, K. / Rich, D.H.
History
DepositionJan 25, 2023Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 8, 2023Provider: repository / Type: Initial release
Revision 1.1Oct 9, 2024Group: Data collection / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_entry_details / pdbx_modification_feature
Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Rhizopuspepsin
B: Rhizopuspepsin
W: ALA-CYS-VAL-LYS
Y: ALA-CYS-VAL-LYS
hetero molecules


Theoretical massNumber of molelcules
Total (without water)70,4037
Polymers70,2124
Non-polymers1913
Water13,421745
1
A: Rhizopuspepsin
W: ALA-CYS-VAL-LYS
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,1903
Polymers35,1062
Non-polymers841
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1190 Å2
ΔGint0 kcal/mol
Surface area12780 Å2
MethodPISA
2
B: Rhizopuspepsin
Y: ALA-CYS-VAL-LYS
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,2134
Polymers35,1062
Non-polymers1072
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1290 Å2
ΔGint-9 kcal/mol
Surface area13270 Å2
MethodPISA
Unit cell
Length a, b, c (Å)69.873, 71.696, 120.736
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Space group name HallP2ac2ab
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x,y+1/2,-z+1/2
#4: -x+1/2,-y,z+1/2

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Components

#1: Protein Rhizopuspepsin


Mass: 34685.270 Da / Num. of mol.: 2 / Mutation: I230V
Source method: isolated from a genetically manipulated source
Details: IVPD residual N-term tag, -3, -2, -1, 0. Numbering above is wrong. It should be the same as Mol A.
Source: (gene. exp.) Rhizopus microsporus var. chinensis (fungus)
Plasmid: pET16b-RPN / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): plysS / References: UniProt: P06026, rhizopuspepsin
#2: Protein/peptide ALA-CYS-VAL-LYS


Mass: 420.546 Da / Num. of mol.: 2 / Source method: obtained synthetically
Details: This is the peptide inhibitor with A alanine as -1 and Cys as zero, and only the carbonyl and a methyl on the C alpha of A. Lysine and cystine are covalently linked to a cyclohexyl ring to ...Details: This is the peptide inhibitor with A alanine as -1 and Cys as zero, and only the carbonyl and a methyl on the C alpha of A. Lysine and cystine are covalently linked to a cyclohexyl ring to link the sidechains together.
Source: (synth.) synthetic construct (others)
#3: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-CHX / CYCLOHEXANE


Mass: 84.159 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H12 / Feature type: SUBJECT OF INVESTIGATION
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 745 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
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: 2.21 Å3/Da / Density % sol: 44.25 % / Description: Long Prisms.
Crystal growTemperature: 273 K / Method: vapor diffusion, sitting drop
Details: Dissolve hydrolyzed powder in water and adjust the pH with acetic acid until slight precipitate is formed (about pH 6).
PH range: 6 - 7 / Temp details: Constant room temperature.

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.9002 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Oct 27, 2006
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9002 Å / Relative weight: 1
ReflectionResolution: 1.205→61.646 Å / Num. obs: 149092 / % possible obs: 90 % / Redundancy: 4.7 % / Biso Wilson estimate: 11.35 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.052 / Rpim(I) all: 0.033 / Rrim(I) all: 0.058 / Net I/σ(I): 16.9
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) all% possible all
3.454-61.6464.80.01958.474550.9990.0130.02388.7
1.205-1.2894.20.8941.674570.5650.6481.10947.1

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
autoPROCdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.21→33.56 Å / SU ML: 0.1284 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 21.9236
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2007 7184 4.82 %
Rwork0.1795 141881 -
obs0.1806 149065 79.78 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 15.38 Å2
Refinement stepCycle: LAST / Resolution: 1.21→33.56 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4907 0 13 745 5665
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00875099
X-RAY DIFFRACTIONf_angle_d1.04666943
X-RAY DIFFRACTIONf_chiral_restr0.091773
X-RAY DIFFRACTIONf_plane_restr0.0069917
X-RAY DIFFRACTIONf_dihedral_angle_d10.3462739
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.21-1.220.3923190.314454X-RAY DIFFRACTION7.75
1.22-1.230.3718360.3135688X-RAY DIFFRACTION11.72
1.23-1.250.3442510.29031043X-RAY DIFFRACTION17.77
1.25-1.260.3038790.27911520X-RAY DIFFRACTION25.83
1.26-1.280.34011040.28972164X-RAY DIFFRACTION36.8
1.28-1.30.3261760.28172797X-RAY DIFFRACTION48.23
1.3-1.320.31751700.26993604X-RAY DIFFRACTION61.24
1.32-1.340.32282280.27434352X-RAY DIFFRACTION74.27
1.34-1.360.28552330.27095176X-RAY DIFFRACTION87.51
1.36-1.380.27683030.25495549X-RAY DIFFRACTION94.4
1.38-1.40.25773000.23775744X-RAY DIFFRACTION97.77
1.4-1.430.25413280.23925793X-RAY DIFFRACTION99
1.43-1.460.24122940.2315854X-RAY DIFFRACTION99.03
1.46-1.490.23832810.21955821X-RAY DIFFRACTION99.03
1.49-1.520.23732890.21255862X-RAY DIFFRACTION98.76
1.52-1.550.24862800.20665802X-RAY DIFFRACTION98.4
1.55-1.590.23363350.20355783X-RAY DIFFRACTION98.25
1.59-1.640.23382880.1945807X-RAY DIFFRACTION98.39
1.64-1.680.23243040.19195740X-RAY DIFFRACTION97.86
1.68-1.740.20723060.19025772X-RAY DIFFRACTION97.36
1.74-1.80.21392690.18695768X-RAY DIFFRACTION96.62
1.8-1.870.21092860.17735663X-RAY DIFFRACTION95.89
1.87-1.960.20452950.17945657X-RAY DIFFRACTION95.25
1.96-2.060.18592830.16775607X-RAY DIFFRACTION94.19
2.06-2.190.20332880.16265626X-RAY DIFFRACTION94.46
2.19-2.360.16022640.16075618X-RAY DIFFRACTION93.96
2.36-2.60.18922700.16545686X-RAY DIFFRACTION94.24
2.6-2.970.15832750.16465687X-RAY DIFFRACTION94.29
2.97-3.740.17192610.15665717X-RAY DIFFRACTION93.49
3.74-33.560.16052890.14035527X-RAY DIFFRACTION87.66

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