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- PDB-1flh: CRYSTAL STRUCTURE OF HUMAN UROPEPSIN AT 2.45 A RESOLUTION -

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Basic information

Entry
Database: PDB / ID: 1flh
TitleCRYSTAL STRUCTURE OF HUMAN UROPEPSIN AT 2.45 A RESOLUTION
ComponentsUROPEPSIN
KeywordsHYDROLASE / ACID PROTEINASE
Function / homology
Function and homology information


multivesicular body lumen / pepsin A / Surfactant metabolism / digestion / aspartic-type endopeptidase activity / proteolysis / extracellular exosome
Similarity search - Function
Pepsin catalytic domain / Aspartic peptidase, N-terminal / A1 Propeptide / 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 ...Pepsin catalytic domain / Aspartic peptidase, N-terminal / A1 Propeptide / 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
Pepsin A-5 / Pepsin A-4
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.45 Å
AuthorsCanduri, F. / Teodoro, L.G.V.L. / Fadel, V. / Lorenzi, C.C.B. / Hial, V. / Gomes, R.A.S. / Neto, J.R. / De Azevedo Jr., W.F.
Citation
#1: Journal: BIOCHEM.MOL.BIOL.INT. / Year: 1998
Title: Crystallization, Preliminary X-Ray Analysis and Patterson Search of a New Aspartic Protease Isolate from Human Urine
Authors: Canduri, F. / Teodoro, L.G.V.L. / Lorenzi, C.C.B. / Gomes, R.A.S. / Fontes, M.R.M. / Arni, R.K. / De Azevedo Jr., W.F.
History
DepositionAug 14, 2000Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 31, 2001Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Aug 9, 2023Group: 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 1.4Oct 9, 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: UROPEPSIN


Theoretical massNumber of molelcules
Total (without water)34,6181
Polymers34,6181
Non-polymers00
Water2,576143
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)50.989, 75.557, 89.896
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein UROPEPSIN


Mass: 34617.859 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P00790, UniProt: P0DJD7*PLUS, pepsin A
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 143 / 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: 2.17 Å3/Da / Density % sol: 43.3 %
Crystal growMethod: vapor diffusion / pH: 7
Details: 0.1M HEPES BUFFER (pH 7.0), 2% PEG 400, 2.0M AMMONIUM SULFATE., VAPOR DIFFUSION
Crystal grow
*PLUS
Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
10.1 MHEPES1reservoir
22 %PEG4001reservoir
32.0 Mammonium sulfate1reservoir

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Data collection

Diffraction sourceSource: SYNCHROTRON / Site: LNLS / Beamline: D03B-MX1 / Wavelength: 1.38
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Jul 12, 1998
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.38 Å / Relative weight: 1
ReflectionResolution: 2.45→12 Å / Num. obs: 13134 / % possible obs: 98.9 % / Observed criterion σ(I): 1 / Redundancy: 3.26 % / Rmerge(I) obs: 0.077
Reflection
*PLUS
Num. measured all: 24189
Reflection shell
*PLUS
Highest resolution: 2.45 Å / Lowest resolution: 2.51 Å / % possible obs: 99.1 % / Rmerge(I) obs: 0.303

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Processing

Software
NameClassification
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
X-PLORrefinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1PSN

1psn


Resolution: 2.45→12 Å / σ(F): 2
RfactorNum. reflection% reflection
Rwork0.161 --
obs0.161 24189 99.1 %
Displacement parametersBiso mean: 15.52 Å2
Refine analyzeLuzzati coordinate error obs: 0.19 Å
Refinement stepCycle: LAST / Resolution: 2.45→12 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2437 0 0 143 2580
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.009
X-RAY DIFFRACTIONx_angle_deg1.608
X-RAY DIFFRACTIONx_dihedral_angle_d27.04
X-RAY DIFFRACTIONx_improper_angle_d1.306
Software
*PLUS
Name: X-PLOR / Classification: refinement
Refinement
*PLUS
Lowest resolution: 12 Å / σ(F): 2 / % reflection Rfree: 10 % / Rfactor Rfree: 0.251
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_deg27.04
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg1.306

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