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- PDB-7fag: Room temperature structure of elastase with high-strength agarose... -

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Basic information

Entry
Database: PDB / ID: 7fag
TitleRoom temperature structure of elastase with high-strength agarose hydrogel
ComponentsChymotrypsin-like elastase family member 1
KeywordsISOMERASE / elastase / high-strength hydrogel-grown crystal / / room temperature structure serine protease / hydrolase
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 / Serine proteases, trypsin family, histidine active site. / Peptidase S1A, chymotrypsin family / Serine proteases, trypsin family, serine active site. / Serine proteases, trypsin domain profile. / Trypsin-like serine protease / Serine proteases, trypsin domain / Trypsin ...: / Serine proteases, trypsin family, histidine active site / Serine proteases, trypsin family, serine active site / Serine proteases, trypsin family, histidine active site. / Peptidase S1A, chymotrypsin family / Serine proteases, trypsin family, serine active site. / Serine proteases, trypsin domain profile. / 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
SULFITE ION / Chymotrypsin-like elastase family member 1
Similarity search - Component
Biological speciesSus scrofa (pig)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.3 Å
AuthorsSugiyama, S. / Kakinouchi, K. / Adachi, H. / Murata, M. / Mori, Y.
Funding support Japan, 3items
OrganizationGrant numberCountry
Japan Science and TechnologyJPMJTM19DC Japan
Japan Society for the Promotion of Science (JSPS)19K06588 Japan
Japan Science and TechnologyJPMJER1005 Japan
CitationJournal: To Be Published
Title: Room temperature structure of elastase with high-strength agarose hydrogel
Authors: Sugiyama, S. / Kakinouchi, K. / Adachi, H. / Murata, M. / Mori, Y.
History
DepositionJul 6, 2021Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jul 6, 2022Provider: repository / Type: Initial release
Revision 1.1Nov 29, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.2Nov 13, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Chymotrypsin-like elastase family member 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,1454
Polymers25,9291
Non-polymers2163
Water3,351186
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area230 Å2
ΔGint-22 kcal/mol
Surface area10640 Å2
MethodPISA
Unit cell
Length a, b, c (Å)51.209, 58.116, 75.338
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 Chymotrypsin-like elastase family member 1 / Elastase-1


Mass: 25929.016 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Sus scrofa (pig) / Gene: CELA1, ELA1 / Production host: Sus scrofa (pig) / References: UniProt: P00772, pancreatic elastase
#2: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4 / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-SO3 / SULFITE ION


Mass: 80.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO3 / Feature type: SUBJECT OF INVESTIGATION
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 186 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
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: 2.16 Å3/Da / Density % sol: 43.1 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 5.5 / Details: 0.1M Na acetate (pH8.5), 0.03M ammonium sulfate

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Data collection

DiffractionMean temperature: 298 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL38B1 / Wavelength: 0.9 Å
DetectorType: RAYONIX MX225HE / Detector: CCD / Date: Nov 19, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9 Å / Relative weight: 1
ReflectionResolution: 1.3→50 Å / Num. obs: 54930 / % possible obs: 98.2 % / Redundancy: 4.7 % / Rpim(I) all: 0.044 / Net I/σ(I): 9.5
Reflection shellResolution: 1.3→1.32 Å / Num. unique obs: 2663 / Rpim(I) all: 0.314

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Processing

Software
NameVersionClassification
REFMAC5.8.0238refinement
HKL-2000data reduction
HKL-2000data scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5AVD

5avd


Resolution: 1.3→26.91 Å / Cor.coef. Fo:Fc: 0.987 / Cor.coef. Fo:Fc free: 0.98 / SU B: 1.725 / SU ML: 0.031 / Cross valid method: THROUGHOUT / ESU R: 0.039 / ESU R Free: 0.041 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.15288 2803 5.1 %RANDOM
Rwork0.11509 ---
obs0.11701 52091 98.18 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 15.944 Å2
Baniso -1Baniso -2Baniso -3
1-0.35 Å20 Å2-0 Å2
2---0.38 Å20 Å2
3---0.03 Å2
Refinement stepCycle: 1 / Resolution: 1.3→26.91 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1822 0 10 186 2018
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.0131967
X-RAY DIFFRACTIONr_bond_other_d0.0190.0171719
X-RAY DIFFRACTIONr_angle_refined_deg1.9441.6282708
X-RAY DIFFRACTIONr_angle_other_deg1.8441.5643984
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.4765261
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.90422.18896
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.74915290
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.9291512
X-RAY DIFFRACTIONr_chiral_restr0.1080.2257
X-RAY DIFFRACTIONr_gen_planes_refined0.0120.022310
X-RAY DIFFRACTIONr_gen_planes_other0.0090.02426
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.8351.3481017
X-RAY DIFFRACTIONr_mcbond_other1.8171.3451016
X-RAY DIFFRACTIONr_mcangle_it2.2732.0381287
X-RAY DIFFRACTIONr_mcangle_other2.2872.0411288
X-RAY DIFFRACTIONr_scbond_it3.3181.837950
X-RAY DIFFRACTIONr_scbond_other3.2881.822940
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other3.9792.5831411
X-RAY DIFFRACTIONr_long_range_B_refined3.60917.6252185
X-RAY DIFFRACTIONr_long_range_B_other3.52617.2282153
X-RAY DIFFRACTIONr_rigid_bond_restr6.48933686
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.301→1.335 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.285 187 -
Rwork0.249 3716 -
obs--95.43 %

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