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- PDB-2wea: ACID PROTEINASE (PENICILLOPEPSIN) (E.C.3.4.23.20) COMPLEX WITH PH... -

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Basic information

Entry
Database: PDB / ID: 2wea
TitleACID PROTEINASE (PENICILLOPEPSIN) (E.C.3.4.23.20) COMPLEX WITH PHOSPHONATE INHIBITOR: METHYL[CYCLO-7[(2R)-((N-VALYL) AMINO)-2-(HYDROXYL-(1S)-1-METHYOXYCARBONYL-2-PHENYLETHOXY) PHOSPHINYLOXY-ETHYL]-1-NAPHTHALENEACETAMIDE], SODIUM SALT
ComponentsPENICILLOPEPSIN
KeywordsHYDROLASE / PENICILLOPEPSIN / PHOSPHONATE INHIBITOR
Function / homology
Function and homology information


penicillopepsin / aspartic-type endopeptidase activity / proteolysis / extracellular region
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
alpha-D-mannopyranose / Chem-PP6 / Penicillopepsin-1
Similarity search - Component
Biological speciesPenicillium janthinellum (fungus)
MethodX-RAY DIFFRACTION / DIFFERENCE FOURIER METHOD / Resolution: 1.25 Å
AuthorsDing, J. / Fraser, M.E. / James, M.N.G.
Citation
Journal: J.Am.Chem.Soc. / Year: 1998
Title: Macrocyclic Inhibitors of Penicillopepsin. II. X-Ray Crystallographic Analyses of Penicillopepsin Complexed with a P3-P1 Macrocyclic Peptidyl Inhibitor and with its Two Acyclic Analogues
Authors: Ding, J. / Fraser, M.E. / Meyer, J.H. / Bartlett, P.A. / James, M.N.G.
#1: Journal: To be Published
Title: Macrocyclic Inhibitors of Penicillopepsin. I. Design, Synthesis, and Evaluation of an Inhibitor Bridged between P1 and P3
Authors: Meyer, J.H. / Bartlett, P.A.
#2: Journal: Biochemistry / Year: 1992
Title: Crystallographic Analysis of Transition-State Mimics Bound to Penicillopepsin: Phosphorus-Containing Peptide Analogues
Authors: Fraser, M.E. / Strynadka, N.C. / Bartlett, P.A. / Hanson, J.E. / James, M.N.
#3: Journal: Biochemistry / Year: 1992
Title: Crystallographic Analysis of Transition State Mimics Bound to Penicillopepsin: Difluorostatine-and Difluorostatone-Containing Peptides
Authors: James, M.N. / Sielecki, A.R. / Hayakawa, K. / Gelb, M.H.
History
DepositionFeb 3, 1998Processing site: BNL
SupersessionMay 27, 1998ID: 1WEA
Revision 1.0May 27, 1998Provider: repository / Type: Initial release
Revision 1.1Mar 3, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Apr 4, 2018Group: Data collection / Other / Category: diffrn_source / pdbx_database_status
Item: _diffrn_source.type / _pdbx_database_status.process_site
Revision 1.4Jul 29, 2020Group: Data collection / Derived calculations / Structure summary
Category: chem_comp / entity ...chem_comp / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / struct_conn / struct_site / struct_site_gen
Item: _chem_comp.name / _chem_comp.type ..._chem_comp.name / _chem_comp.type / _entity.pdbx_description / _pdbx_entity_nonpoly.name / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.pdbx_role / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id
Description: Carbohydrate remediation / Provider: repository / Type: Remediation

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: PENICILLOPEPSIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,4775
Polymers33,4691
Non-polymers1,0084
Water9,224512
1
A: PENICILLOPEPSIN
hetero molecules

A: PENICILLOPEPSIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)68,95310
Polymers66,9382
Non-polymers2,0168
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_656-x+1,y,-z+11
Unit cell
Length a, b, c (Å)96.330, 46.270, 64.590
Angle α, β, γ (deg.)90.00, 115.10, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-863-

HOH

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Components

#1: Protein PENICILLOPEPSIN /


Mass: 33468.809 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Penicillium janthinellum (fungus) / References: UniProt: P00798, penicillopepsin
#2: Sugar ChemComp-MAN / alpha-D-mannopyranose / Mannose


Type: D-saccharide, alpha linking / Mass: 180.156 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Formula: C6H12O6
IdentifierTypeProgram
DManpaCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
a-D-mannopyranoseCOMMON NAMEGMML 1.0
a-D-ManpIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
ManSNFG CARBOHYDRATE SYMBOLGMML 1.0
#3: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#4: Chemical ChemComp-PP6 / METHYL[CYCLO-7[(2R)-((N-VALYL)AMINO)-2-(HYDROXYL-(1S)-1-METHYLOXYCARBONYL-2-PHENYLETHOXY)PHOSPHINYLOXY-ETHYL]-1-NAPHTHALENEACETAMIDE]


Mass: 551.547 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C29H32N2O7P
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 512 / 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: 1.95 Å3/Da / Density % sol: 36.81 %
Crystal growpH: 4.4 / Details: 0.1M NAC2H3O2 PH=4.4 35-40% SATURATED (NH4)2SO4
Crystal grow
*PLUS
Temperature: 18-22 ℃ / Method: vapor diffusion, hanging drop
Details: used macroseeding, Fraser, M.E., (1992) Biochemistry, 31, 5201.
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
134-40 %satammonium sulfate1drop
20.1 M1dropNaC2H3O2
310 mg/mlcomplex1drop

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Data collection

DiffractionMean temperature: 110 K
Diffraction sourceSource: ROTATING ANODE / Type: OTHER / Wavelength: 1.5418
DetectorType: SIEMENS-NICOLET X100 / Detector: AREA DETECTOR / Date: Mar 22, 1997
RadiationMonochromator: GRAPHITE(002) / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.25→40 Å / Num. obs: 58629 / % possible obs: 82.22 % / Observed criterion σ(I): 0 / Redundancy: 3.47 % / Biso Wilson estimate: 10.427 Å2 / Rmerge(I) obs: 0.0595 / Net I/σ(I): 41.28
Reflection shellResolution: 1.25→1.29 Å / Redundancy: 2.05 % / Rmerge(I) obs: 0.148 / Mean I/σ(I) obs: 5.18 / % possible all: 40.47
Reflection
*PLUS
Observed criterion σ(I): 2 / Num. measured all: 203415
Reflection shell
*PLUS
% possible obs: 40.47 %

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Processing

Software
NameClassification
XENGENdata collection
XENGENdata reduction
X-PLORmodel building
TNTrefinement
X-PLORrefinement
XENGENdata scaling
X-PLORphasing
RefinementMethod to determine structure: DIFFERENCE FOURIER METHOD / Resolution: 1.25→40 Å
Isotropic thermal model: CSDX_PROTGEO.DAT, OTHERGEO.DAT, CPPP6GEO.DAT, SEMTHMGEO.DAT
σ(F): 2
Stereochemistry target values: CSDX_PROTGEO.DAT, OTHERGEO.DAT, CPPP6GEO.DAT, SEMTHMGEO.DAT, CONTACT.DAT
Details: X-PLOR AND TNT ESD FROM SIGMAA (A) : 0.138904 UNCERTAINTY IN RMS ERROR SQUARED : 0.001516
RfactorNum. reflection% reflection
Rfree0.19 -10 %
Rwork0.145 --
obs0.149 55829 78 %
all-58629 -
Solvent computationSolvent model: TNT / Bsol: 441.6 Å2 / ksol: 1.002 e/Å3
Refinement stepCycle: LAST / Resolution: 1.25→40 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2376 0 66 512 2954
Refine LS restraints
Refine-IDTypeDev idealNumberWeight
X-RAY DIFFRACTIONt_bond_d0.01425011.1
X-RAY DIFFRACTIONt_angle_deg1.45433921.1
X-RAY DIFFRACTIONt_dihedral_angle_d15.71214085
X-RAY DIFFRACTIONt_incorr_chiral_ct0
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes0.016682
X-RAY DIFFRACTIONt_gen_planes0.0263663
X-RAY DIFFRACTIONt_it1.3725010.75
X-RAY DIFFRACTIONt_nbd0.03599
Software
*PLUS
Name: TNT / Version: 5E / Classification: refinement
Refinement
*PLUS
Rfactor all: 0.155 / Rfactor Rfree: 0.192
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev idealWeight
X-RAY DIFFRACTIONt_planar_d0.0162
X-RAY DIFFRACTIONt_plane_restr0.0263

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