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- PDB-5avd: The 0.86 angstrom structure of elastase crystallized in high-stre... -

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Basic information

Entry
Database: PDB / ID: 5avd
TitleThe 0.86 angstrom structure of elastase crystallized in high-strength agarose hydrogel
ComponentsChymotrypsin-like elastase family member 1
KeywordsISOMERASE / elastase / high-strength agarose / hydrogel
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
Chymotrypsin-like elastase family member 1
Similarity search - Component
Biological speciesSus scrofa (pig)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 0.86 Å
AuthorsSugiyama, S. / Shimizu, N. / Maruyama, M. / Sazaki, G. / Adachi, H. / Takano, K. / Murakami, S. / Inoue, T. / Mori, Y. / Matsumura, H.
Funding support Japan, 3items
OrganizationGrant numberCountry
JSPS KAKENHI23860028 Japan
JSPS KAKENHI25650051 Japan
JSPS KAKENHI25286051 Japan
CitationJournal: J.Am.Chem.Soc. / Year: 2012
Title: Growth of protein crystals in hydrogels prevents osmotic shock
Authors: Sugiyama, S. / Maruyama, M. / Sazaki, G. / Hirose, M. / Adachi, H. / Takano, K. / Murakami, S. / Inoue, T. / Mori, Y. / Matsumura, H.
History
DepositionJun 15, 2015Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jul 8, 2015Provider: repository / Type: Initial release
Revision 1.1Feb 19, 2020Group: Advisory / Data collection ...Advisory / Data collection / Derived calculations / Source and taxonomy
Category: diffrn_source / entity_src_gen ...diffrn_source / entity_src_gen / pdbx_prerelease_seq / pdbx_struct_oper_list / pdbx_validate_close_contact
Item: _diffrn_source.pdbx_synchrotron_site / _entity_src_gen.pdbx_alt_source_flag / _pdbx_struct_oper_list.symmetry_operation
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 1.3Nov 6, 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

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)26,1203
Polymers25,9281
Non-polymers1922
Water4,936274
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area190 Å2
ΔGint-14 kcal/mol
Surface area10460 Å2
MethodPISA
Unit cell
Length a, b, c (Å)49.992, 58.210, 74.425
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: 25928.031 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Sus scrofa (pig) / Gene: CELA1, ELA1 / Production host: Escherichia coli (E. coli) / References: UniProt: P00772, pancreatic elastase
#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 274 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY
Sequence detailsTHE SEQUENCE CONFLICT D92N IS BASED ON REFERENCE PUBMED IS 4578945 ACCORDING TO DATABASE P00772 (CELA1_PIG)

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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: 2.09 Å3/Da / Density % sol: 41.1 %
Crystal growTemperature: 293 K / Method: microbatch / pH: 5 / Details: 0.1 M Na acetate (pH 5.0), 0.03 M (NH4)2SO4

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: AR-NW12A / Wavelength: 0.9 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Jan 20, 2009
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9 Å / Relative weight: 1
ReflectionResolution: 0.86→50 Å / Num. obs: 174535 / % possible obs: 94.7 % / Redundancy: 10.8 % / Rmerge(I) obs: 0.088 / Net I/σ(I): 10.3
Reflection shellResolution: 0.86→0.87 Å / Redundancy: 5.5 % / Rmerge(I) obs: 0.612 / Mean I/σ(I) obs: 2.2 / % possible all: 77.1

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Processing

Software
NameVersionClassification
REFMAC5.8.0049refinement
DENZOdata reduction
HKL-2000data scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1GVK

1gvk


Resolution: 0.86→45.85 Å / Cor.coef. Fo:Fc: 0.977 / Cor.coef. Fo:Fc free: 0.974 / SU B: 0.34 / SU ML: 0.01 / Cross valid method: THROUGHOUT / ESU R: 0.015 / ESU R Free: 0.015 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.13988 8775 5 %RANDOM
Rwork0.12799 ---
obs0.1286 165717 94.67 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 10.282 Å2
Baniso -1Baniso -2Baniso -3
1--0.01 Å20 Å20 Å2
2---0.03 Å20 Å2
3---0.04 Å2
Refinement stepCycle: LAST / Resolution: 0.86→45.85 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1822 0 10 274 2106
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0470.0192127
X-RAY DIFFRACTIONr_bond_other_d0.0010.021938
X-RAY DIFFRACTIONr_angle_refined_deg2.381.922942
X-RAY DIFFRACTIONr_angle_other_deg1.34534436
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.5055291
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.91323.78995
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.23815320
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.861516
X-RAY DIFFRACTIONr_chiral_restr0.1440.2326
X-RAY DIFFRACTIONr_gen_planes_refined0.0130.022628
X-RAY DIFFRACTIONr_gen_planes_other0.0050.02548
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_it1.3910.8211101
X-RAY DIFFRACTIONr_mcbond_other1.3930.821100
X-RAY DIFFRACTIONr_mcangle_it1.881.2451413
X-RAY DIFFRACTIONr_mcangle_other1.881.2451414
X-RAY DIFFRACTIONr_scbond_it2.2821.0591026
X-RAY DIFFRACTIONr_scbond_other2.2311.0371018
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other2.2991.4731517
X-RAY DIFFRACTIONr_long_range_B_refined2.648.0492599
X-RAY DIFFRACTIONr_long_range_B_other2.4017.462424
X-RAY DIFFRACTIONr_rigid_bond_restr9.57334065
X-RAY DIFFRACTIONr_sphericity_free16.935107
X-RAY DIFFRACTIONr_sphericity_bonded5.70854218
LS refinement shellResolution: 0.86→0.882 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.287 542 -
Rwork0.257 10127 -
obs--78.88 %

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