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- PDB-3w0d: Structure of elastase inhibitor AFUEI (cyrstal form I) -

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Basic information

Entry
Database: PDB / ID: 3w0d
TitleStructure of elastase inhibitor AFUEI (cyrstal form I)
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 / SAD / Resolution: 2.3 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 6, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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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
Water1,874104
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1350 Å2
ΔGint-11 kcal/mol
Surface area7480 Å2
MethodPISA
Unit cell
Length a, b, c (Å)40.710, 40.710, 135.530
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number170
Space group name H-MP65

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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.: 104 / 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: 2.15 Å3/Da / Density % sol: 42.85 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 1.5M NaCl, 10%(v/v) ethanol, 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: May 25, 2010
RadiationMonochromator: Double-crystal monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.3→35.2 Å / Num. all: 5612 / Num. obs: 5612 / % possible obs: 99.2 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4 % / Biso Wilson estimate: 31 Å2 / Rmerge(I) obs: 0.107 / Net I/σ(I): 9.5
Reflection shellResolution: 2.3→2.42 Å / Redundancy: 4 % / Rmerge(I) obs: 0.3 / Mean I/σ(I) obs: 4.4 / Num. unique all: 825 / % possible all: 99.2

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Processing

Software
NameVersionClassification
SPring-8BBSdata collection
PHENIXmodel building
CNS1.2refinement
MOSFLMdata reduction
SCALAdata scaling
PHENIXphasing
RefinementMethod to determine structure: SAD / Resolution: 2.3→31.28 Å / Rfactor Rfree error: 0.011 / Data cutoff high absF: 1071549.15 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber / Details: BULK SOLVENT MODEL USED
RfactorNum. reflection% reflectionSelection details
Rfree0.252 544 9.7 %RANDOM
Rwork0.205 ---
obs0.205 5612 99.1 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 34.9725 Å2 / ksol: 0.35 e/Å3
Displacement parametersBiso mean: 27.2 Å2
Baniso -1Baniso -2Baniso -3
1-2.37 Å20 Å20 Å2
2--2.37 Å20 Å2
3----4.73 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.35 Å0.26 Å
Luzzati d res low-5 Å
Luzzati sigma a0.34 Å0.25 Å
Refinement stepCycle: LAST / Resolution: 2.3→31.28 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1052 0 0 104 1156
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.009
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.6
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d26.8
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d1.25
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it1.321.5
X-RAY DIFFRACTIONc_mcangle_it2.232
X-RAY DIFFRACTIONc_scbond_it2.132
X-RAY DIFFRACTIONc_scangle_it3.212.5
Refine LS restraints NCSNCS model details: NONE
LS refinement shellResolution: 2.3→2.44 Å / Rfactor Rfree error: 0.031 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.296 94 10 %
Rwork0.251 843 -
obs-825 100 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2water_rep.paramwater.top
X-RAY DIFFRACTION3cis_peptide_mar30r2g2.param

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