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- PDB-3hgn: Structure of porcine pancreatic elastase complexed with a potent ... -

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Basic information

Entry
Database: PDB / ID: 3hgn
TitleStructure of porcine pancreatic elastase complexed with a potent peptidyl inhibitor FR130180 determined by neutron crystallography
ComponentsElastase-1
KeywordsHYDROLASE / Chymotrypsin Family / Serine Protease / Disulfide bond / Metal-binding / Protease / Secreted / Zymogen
Function / homology
Function and homology information


pancreatic elastase / serine-type endopeptidase activity / proteolysis / extracellular space / metal ion binding
Similarity search - Function
Serine proteases, trypsin family, histidine active site / Serine proteases, trypsin family, serine active site / Peptidase S1A, chymotrypsin family / Serine proteases, trypsin family, histidine active site. / Serine proteases, trypsin domain profile. / Serine proteases, trypsin family, serine active site. / Trypsin-like serine protease / Serine proteases, trypsin domain / Trypsin / Trypsin-like serine proteases ...Serine proteases, trypsin family, histidine active site / Serine proteases, trypsin family, serine active site / Peptidase S1A, chymotrypsin family / Serine proteases, trypsin family, histidine active site. / Serine proteases, trypsin domain profile. / Serine proteases, trypsin family, serine active site. / Trypsin-like serine protease / Serine proteases, trypsin domain / Trypsin / Trypsin-like serine proteases / Thrombin, subunit H / Peptidase S1, PA clan, chymotrypsin-like fold / Peptidase S1, PA clan / Beta Barrel / Mainly Beta
Similarity search - Domain/homology
DEUTERATED WATER / Chem-FRW / Chymotrypsin-like elastase family member 1
Similarity search - Component
Biological speciesSus scrofa (pig)
MethodNEUTRON DIFFRACTION / X-RAY DIFFRACTION / NUCLEAR REACTOR / SYNCHROTRON / Resolution: 1.65 Å
AuthorsTamada, T. / Kinoshita, T. / Kuroki, R. / Tada, T.
Citation
Journal: J.Am.Chem.Soc. / Year: 2009
Title: Combined High-Resolution Neutron and X-ray Analysis of Inhibited Elastase Confirms the Active-Site Oxyanion Hole but Rules against a Low-Barrier Hydrogen Bond
Authors: Tamada, T. / Kinoshita, T. / Kurihara, K. / Adachi, M. / Ohhara, T. / Imai, K. / Kuroki, R. / Tada, T.
#1: Journal: Acta Crystallogr.,Sect.F / Year: 2007
Title: Crystallization of porcine pancreatic elastase and a preliminary neutron diffraction experiment
Authors: Kinoshita, T. / Tamada, T. / Imai, K. / Kurihara, K. / Ohhara, T. / Tada, T. / Kuroki, R.
History
DepositionMay 14, 2009Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Jul 28, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Data collection / Non-polymer description / Version format compliance
Revision 1.2Nov 1, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Elastase-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,5794
Polymers25,9291
Non-polymers6503
Water3,423190
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)50.937, 57.464, 75.180
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 Elastase-1 /


Mass: 25929.016 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: Porcine Pancreatic / Source: (natural) Sus scrofa (pig) / References: UniProt: P00772, pancreatic elastase
#2: Chemical ChemComp-FRW / 4-[[(2S)-3-methyl-1-oxo-1-[(2S)-2-[[(3S)-1,1,1-trifluoro-4-methyl-2-oxo-pentan-3-yl]carbamoyl]pyrrolidin-1-yl]butan-2-yl]carbamoyl]benzoic acid


Mass: 513.507 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C24H30F3N3O6
#3: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca
#4: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#5: Chemical ChemComp-DOD / water / Heavy water


Mass: 18.015 Da / Num. of mol.: 190 / Source method: isolated from a natural source / Formula: D2O

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Experimental details

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Experiment

Experiment
MethodNumber of used crystals
NEUTRON DIFFRACTION1
X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.12 Å3/Da / Density % sol: 42.03 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 5
Details: 0.3M sodium sulphate, 0.05M D-substituted sodium acetate, pH5.0, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
12931
22931
Diffraction source
SourceSiteBeamlineIDWavelength (Å)
NUCLEAR REACTOR12.9
SYNCHROTRONPhoton Factory BL-6A21
Detector
TypeIDDetectorDate
NEUTRON IMAGING PLATE1IMAGE PLATESep 19, 2006
ADSC QUANTUM 4r2CCDMay 28, 2008
Radiation
IDMonochromatorProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1ELASTICALLY-BENT PERFECT SI(111)SINGLE WAVELENGTHMneutron1
2TRIANGULAR SI(111)SINGLE WAVELENGTHMx-ray1
Radiation wavelength
IDWavelength (Å)Relative weight
12.91
211
ReflectionResolution: 1.65→42.17 Å / Num. obs: 24296 / % possible obs: 88.9 % / Observed criterion σ(I): -3 / Redundancy: 3 % / Biso Wilson estimate: 10.06 Å2 / Rmerge(I) obs: 0.098 / Net I/σ(I): 11.3
Reflection shellResolution: 1.65→1.71 Å / Redundancy: 2.6 % / Rmerge(I) obs: 0.328 / Mean I/σ(I) obs: 3.9 / Num. unique all: 2065 / % possible all: 77.1

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Processing

Software
NameClassification
PHENIXrefinement
DENZOdata reduction
SCALEPACKdata scaling
Refinement

R Free selection details: RANDOM / Isotropic thermal model: Isotropic / Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Starting model: PDB ENTRY 3HGP

3hgp

/ Stereochemistry target values: ML / Solvent model: FLAT BULK SOLVENT MODEL / Details: perfomed by a joint refinement method using X-ray and neutron diffraction data from the same crystal

Resolution (Å)Refine-IDBiso mean (Å2)Rfactor RfreeRfactor RworkRfactor obsNum. reflection RfreeNum. reflection obs% reflection Rfree (%)% reflection obs (%)SU MLDiffraction-IDPhase errorBsol (Å2)ksol (e/Å3)
1.65-42.169NEUTRON DIFFRACTION15.30.21610.19640.19731127234864.886.30.21118.65200.6
1.201-45.655X-RAY DIFFRACTION0.16250.14870.14943374663195.0995.450.11214.9244.8010.402
Refinement stepCycle: LAST / Resolution: 1.65→42.169 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1822 0 42 190 2054
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0264312
X-RAY DIFFRACTIONf_angle_d3.0667277
X-RAY DIFFRACTIONf_dihedral_angle_d22.449926
X-RAY DIFFRACTIONf_chiral_restr0.171290
X-RAY DIFFRACTIONf_plane_restr0.022831
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.6501-1.72520.30721140.31352336NEUTRON DIFFRACTION74
1.7252-1.81610.28421270.26792563NEUTRON DIFFRACTION80
1.8161-1.92990.24141220.22472654NEUTRON DIFFRACTION83
1.9299-2.07890.22561350.19392726NEUTRON DIFFRACTION85
2.0789-2.28810.18691340.17932839NEUTRON DIFFRACTION88
2.2881-2.61920.18771780.16862849NEUTRON DIFFRACTION89
2.6192-3.29970.20571540.17043072NEUTRON DIFFRACTION94
3.2997-42.18320.18721630.16233320NEUTRON DIFFRACTION97
1.201-1.21810.26621140.21772407X-RAY DIFFRACTION88
1.2181-1.23630.2371230.20982472X-RAY DIFFRACTION91
1.2363-1.25560.24311470.19842496X-RAY DIFFRACTION92
1.2556-1.27620.22151390.19562518X-RAY DIFFRACTION92
1.2762-1.29820.21931400.19012509X-RAY DIFFRACTION93
1.2982-1.32190.20761510.18472517X-RAY DIFFRACTION94
1.3219-1.34730.18441400.17642551X-RAY DIFFRACTION94
1.3473-1.37480.2051220.17132603X-RAY DIFFRACTION94
1.3748-1.40470.18191390.16352553X-RAY DIFFRACTION94
1.4047-1.43740.17131360.15782599X-RAY DIFFRACTION95
1.4374-1.47330.1681380.15692601X-RAY DIFFRACTION95
1.4733-1.51310.16681500.15132618X-RAY DIFFRACTION96
1.5131-1.55770.1751590.15212593X-RAY DIFFRACTION96
1.5577-1.60790.14141470.14622629X-RAY DIFFRACTION96
1.6079-1.66540.16731450.14022640X-RAY DIFFRACTION97
1.6654-1.73210.16291360.14452653X-RAY DIFFRACTION97
1.7321-1.81090.16761370.13972698X-RAY DIFFRACTION97
1.8109-1.90640.14561350.13522698X-RAY DIFFRACTION98
1.9064-2.02590.13921470.12932707X-RAY DIFFRACTION98
2.0259-2.18230.14211580.13322692X-RAY DIFFRACTION98
2.1823-2.40190.16311330.13162769X-RAY DIFFRACTION98
2.4019-2.74940.18111290.14322762X-RAY DIFFRACTION98
2.7494-3.46380.1481580.1492780X-RAY DIFFRACTION99
3.4638-45.68780.13241510.13412880X-RAY DIFFRACTION97

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