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- PDB-3w0e: Structure of elastase inhibitor AFUEI (crystal form II) -

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Basic information

Entry
Database: PDB / ID: 3w0e
TitleStructure of elastase inhibitor AFUEI (crystal form II)
ComponentsElastase inhibitor AFUEI
KeywordsHYDROLASE INHIBITOR / elastase inhibitor / secreted protein
Function / homology
Function and homology information


enzyme inhibitor activity / serine-type endopeptidase inhibitor activity / extracellular region
Similarity search - Function
Proteinase inhibitor I78 / Peptidase inhibitor I78 family / Trypsin Inhibitor V, subunit A / Trypsin Inhibitor V; Chain A / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Elastase inhibitor AFUEI
Similarity search - Component
Biological speciesAspergillus fumigatus Af293 (mold)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsImada, K. / Sakuma, M. / Okumura, Y. / Ogawa, K. / Nikai, T. / Homma, M.
CitationJournal: J.Biol.Chem. / Year: 2013
Title: X-ray Structure Analysis and Characterization of AFUEI, an Elastase Inhibitor from Aspergillus fumigatus
Authors: Sakuma, M. / Imada, K. / Okumura, Y. / Uchiya, K. / Yamashita, N. / Ogawa, K. / Hijikata, A. / Shirai, T. / Homma, M. / Nikai, T.
History
DepositionOct 29, 2012Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0May 15, 2013Provider: repository / Type: Initial release
Revision 1.1Jul 3, 2013Group: Database references
Revision 1.2Nov 8, 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 1.3Oct 30, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Elastase inhibitor AFUEI
B: Elastase inhibitor AFUEI


Theoretical massNumber of molelcules
Total (without water)15,0632
Polymers15,0632
Non-polymers00
Water3,135174
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1420 Å2
ΔGint-10 kcal/mol
Surface area7230 Å2
MethodPISA
Unit cell
Length a, b, c (Å)77.499, 77.499, 115.224
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number155
Space group name H-MH32
Components on special symmetry positions
IDModelComponents
11A-119-

HOH

21A-176-

HOH

31B-105-

HOH

41B-183-

HOH

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Components

#1: Protein Elastase inhibitor AFUEI


Mass: 7531.449 Da / Num. of mol.: 2 / Fragment: Mature AFUEI, UNP residues 20-87 / Source method: isolated from a natural source / Source: (natural) Aspergillus fumigatus Af293 (mold) / Strain: ATCC MYA-4609 / Af293 / CBS 101355 / FGSC A1100 / References: UniProt: Q4WZ11
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 174 / 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: 2.21 Å3/Da / Density % sol: 44.36 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 4
Details: 0.8M Sodium Sulfate, 0.1M Sodium acetate, pH 4.0, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 90 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL41XU / Wavelength: 1 Å
DetectorType: RAYONIX MX225HE / Detector: CCD / Date: Jan 26, 2012
RadiationMonochromator: Double-crystal monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.8→32.22 Å / Num. all: 12564 / Num. obs: 12564 / % possible obs: 99.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 9.1 % / Biso Wilson estimate: 22.9 Å2 / Rmerge(I) obs: 0.08 / Net I/σ(I): 17.4
Reflection shellResolution: 1.8→1.9 Å / Redundancy: 8.9 % / Rmerge(I) obs: 0.401 / Mean I/σ(I) obs: 5.2 / Num. unique all: 1813 / % possible all: 100

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Processing

Software
NameVersionClassification
SPring-8BBSdata collection
PHENIXmodel building
PHENIX(phenix.refine: 1.7.1_743)refinement
MOSFLMdata reduction
SCALAdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3W0D

3w0d


Resolution: 1.8→32.219 Å / SU ML: 0.45 / Isotropic thermal model: isotropic / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 25.56 / Stereochemistry target values: ML / Details: BULK SOLVENT MODEL USED
RfactorNum. reflection% reflectionSelection details
Rfree0.2559 1241 9.89 %Random
Rwork0.2108 ---
obs0.2152 12549 99.65 %-
Solvent computationShrinkage radii: 0.72 Å / VDW probe radii: 1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 33.688 Å2 / ksol: 0.353 e/Å3
Displacement parametersBiso mean: 26.8 Å2
Baniso -1Baniso -2Baniso -3
1-0.6781 Å20 Å2-0 Å2
2--0.6781 Å20 Å2
3----1.3562 Å2
Refinement stepCycle: LAST / Resolution: 1.8→32.219 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1052 0 0 174 1226
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0091070
X-RAY DIFFRACTIONf_angle_d1.0641454
X-RAY DIFFRACTIONf_dihedral_angle_d14.738402
X-RAY DIFFRACTIONf_chiral_restr0.074168
X-RAY DIFFRACTIONf_plane_restr0.006198
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 9

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
1.8-1.87230.30821640.2751199100
1.8723-1.95760.33611580.262123199
1.9576-2.06070.291230.21791241100
2.0607-2.18980.28221360.21681256100
2.1898-2.35890.32231370.24261257100
2.3589-2.59610.27981170.24181268100
2.5961-2.97160.26541170.22661285100
2.9716-3.7430.2221610.18551251100
3.743-32.22440.2141280.1811132098

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