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- PDB-1okx: Binding Structure of Elastase Inhibitor Scyptolin A -

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Basic information

Entry
Database: PDB / ID: 1okx
TitleBinding Structure of Elastase Inhibitor Scyptolin A
Components
  • ELASTASE 1
  • SCYPTOLIN A
KeywordsHYDROLASE/HYDROLASE INHIBITOR / PROTEASE / ELASTASE / INHIBITOR / HYDROLASE / HYDROLASE-HYDROLASE INHIBITOR COMPLEX
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
SCYPTOLIN A / Chymotrypsin-like elastase family member 1
Similarity search - Component
Biological speciesSUS SCROFA (pig)
SCYTONEMA HOFMANNI (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.8 Å
AuthorsMatern, U. / Schleberger, C. / Jelakovic, S. / Weckesser, J. / Schulz, G.E.
CitationJournal: Chem.Biol. / Year: 2003
Title: Binding Structure of Elastase Inhibitor Scyptolin A
Authors: Matern, U. / Schleberger, C. / Jelakovic, S. / Weckesser, J. / Schulz, G.E.
History
DepositionJul 31, 2003Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 24, 2003Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Atomic model / Database references ...Atomic model / Database references / Derived calculations / Non-polymer description / Structure summary / Version format compliance
Revision 1.2Nov 30, 2012Group: Other
Revision 1.3Jun 13, 2018Group: Data collection / Structure summary / Category: struct / Item: _struct.title
Revision 1.4Jul 31, 2019Group: Advisory / Data collection / Derived calculations / Category: pdbx_validate_close_contact / struct_conn
Revision 1.5Dec 13, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _struct_conn.pdbx_leaving_atom_flag
Remark 700 SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "AB" IN EACH CHAIN ON SHEET RECORDS BELOW ... SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "AB" IN EACH CHAIN ON SHEET RECORDS BELOW IS ACTUALLY AN 6-STRANDED BARREL THIS IS REPRESENTED BY A 7-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL. THE SHEETS PRESENTED AS "BB" IN EACH CHAIN ON SHEET RECORDS BELOW IS ACTUALLY AN 6-STRANDED BARREL THIS IS REPRESENTED BY A 7-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL. THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN THE SHEET RECORDS BELOW, TWO SHEETS ARE DEFINED.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: ELASTASE 1
B: ELASTASE 1
C: SCYPTOLIN A
D: SCYPTOLIN A


Theoretical massNumber of molelcules
Total (without water)53,8274
Polymers53,8274
Non-polymers00
Water1,892105
1
A: ELASTASE 1
C: SCYPTOLIN A


Theoretical massNumber of molelcules
Total (without water)26,9142
Polymers26,9142
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
2
B: ELASTASE 1
D: SCYPTOLIN A


Theoretical massNumber of molelcules
Total (without water)26,9142
Polymers26,9142
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)155.890, 155.890, 91.030
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number177
Space group name H-MP622
Noncrystallographic symmetry (NCS)NCS oper: (Code: given
Matrix: (0.914185, -0.335757, 0.227008), (-0.328652, -0.941884, -0.069582), (0.237178, -0.010996, -0.971404)
Vector: -1.795, 6.464, 20.247)

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Components

#1: Protein ELASTASE 1 / ELA1


Mass: 25928.031 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) SUS SCROFA (pig) / Organ: PANCREAS / References: UniProt: P00772, pancreatic elastase
#2: Protein/peptide SCYPTOLIN A


Type: Polypeptide / Class: Inhibitor / Mass: 985.560 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) SCYTONEMA HOFMANNI (bacteria) / Strain: PCC7110 / References: SCYPTOLIN A
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 105 / Source method: isolated from a natural source / Formula: H2O
Compound detailsCATALYTIC ACTIVITY: HYDROLYSIS OF PROTEINS, INCLUDING . ELASTIN PREFERENTIAL CLEAVAGE: ALA-|-XAA.

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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: 3.18 Å3/Da / Density % sol: 61 %
Crystal growpH: 5 / Details: PH 5.00
Crystal grow
*PLUS
pH: 5 / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
110 mMsodium acetate1droppH5.0
218 mg/mlprotein1drop
30.42 Msodium sulfate1reservoir

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU200B / Wavelength: 1.5418
DetectorType: MARRESEARCH / Detector: IMAGE PLATE
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.8→19.29 Å / Num. obs: 16453 / % possible obs: 99.6 % / Observed criterion σ(I): 0 / Redundancy: 8.3 % / Biso Wilson estimate: 6.2 Å2 / Rmerge(I) obs: 0.13 / Net I/σ(I): 13.6
Reflection shellResolution: 2.8→2.86 Å / Redundancy: 8.4 % / Rmerge(I) obs: 0.39 / Mean I/σ(I) obs: 5.5 / % possible all: 100
Reflection
*PLUS
Highest resolution: 2.8 Å / Lowest resolution: 30 Å / % possible obs: 99 % / Redundancy: 8.3 % / Rmerge(I) obs: 0.133
Reflection shell
*PLUS
% possible obs: 100 % / Redundancy: 8.4 % / Num. unique obs: 999 / Rmerge(I) obs: 0.39 / Mean I/σ(I) obs: 5.5

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Processing

Software
NameVersionClassification
CNS1.1refinement
XDSdata reduction
XSCALEdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1ELB

1elb


Resolution: 2.8→19.29 Å / Rfactor Rfree error: 0.006 / Data cutoff high absF: 5269536.9 / Isotropic thermal model: GROUP / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.26 1645 10 %RANDOM
Rwork0.21 ---
obs0.21 16451 99.6 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 28.37 Å2 / ksol: 0.39 e/Å3
Displacement parametersBiso mean: 26.7 Å2
Baniso -1Baniso -2Baniso -3
1-0.45 Å24.18 Å20 Å2
2--0.45 Å20 Å2
3----0.9 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.41 Å0.31 Å
Luzzati d res low-5 Å
Luzzati sigma a0.48 Å0.35 Å
Refinement stepCycle: LAST / Resolution: 2.8→19.29 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3780 0 0 105 3885
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.006
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_deg1.3
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d25.3
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.74
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it
X-RAY DIFFRACTIONc_mcangle_it
X-RAY DIFFRACTIONc_scbond_it
X-RAY DIFFRACTIONc_scangle_it
LS refinement shellResolution: 2.8→2.98 Å / Rfactor Rfree error: 0.02 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.322 269 10 %
Rwork0.264 2424 -
obs--100 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2WATER_REP.PARAMWATER.TOP
X-RAY DIFFRACTION3DRGCNS.PARDRGCNS.TOP
X-RAY DIFFRACTION4ION.PARAMION.TOP
Refinement
*PLUS
% reflection Rfree: 10 % / Rfactor Rfree: 0.258 / Rfactor Rwork: 0.209
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.007
X-RAY DIFFRACTIONc_angle_deg1.35
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg25.3
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg0.74

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