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- PDB-3mo3: Investigation of global and local effects of radiation damage on ... -

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Basic information

Entry
Database: PDB / ID: 3mo3
TitleInvestigation of global and local effects of radiation damage on porcine pancreatic elastase. Fifth stage of radiation damage
ComponentsChymotrypsin-like elastase family member 1
KeywordsHYDROLASE / radiation damage / disulfide bridge / atomic resolution
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: 1.805 Å
AuthorsPetrova, T. / Ginell, S. / Kim, Y. / Joachimiak, G. / Joachimiak, A.
CitationJournal: Acta Crystallogr.,Sect.D / Year: 2010
Title: X-ray-induced deterioration of disulfide bridges at atomic resolution.
Authors: Petrova, T. / Ginell, S. / Mitschler, A. / Kim, Y. / Lunin, V.Y. / Joachimiak, G. / Cousido-Siah, A. / Hazemann, I. / Podjarny, A. / Lazarski, K. / Joachimiak, A.
History
DepositionApr 22, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 5, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Sep 6, 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 / pdbx_struct_conn_angle / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_ref_seq_dif.details / _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

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)26,1434
Polymers25,9281
Non-polymers2153
Water9,296516
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)50.229, 57.821, 74.684
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 natural source / Source: (natural) Sus scrofa (pig) / References: UniProt: P00772, pancreatic elastase
#2: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#3: Chemical ChemComp-SO4 / SULFATE ION


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


Mass: 18.015 Da / Num. of mol.: 516 / Source method: isolated from a natural source / Formula: H2O

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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: 41.19 %
Crystal growTemperature: 297 K / Method: vapor diffusion, hanging drop / pH: 8.2
Details: The initial concentration of the protein was 10 mg/ml in water. The reservoir contained 25 mM Na2SO4. The cryo-solution contained 25 mM Na2SO4 and 25% glycerol, pH 8.2, VAPOR DIFFUSION, ...Details: The initial concentration of the protein was 10 mg/ml in water. The reservoir contained 25 mM Na2SO4. The cryo-solution contained 25 mM Na2SO4 and 25% glycerol, pH 8.2, VAPOR DIFFUSION, HANGING DROP, temperature 297K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.97918 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Nov 26, 2008
Details: 1.02-M FLAT MIRROR MADE OF ZERODUR PROVIDING VERTICAL FOCUSING AND REJECTION OF HARMONIC CONTAMINATION
RadiationMonochromator: DOUBLE CRYSTAL MONOCHROMATOR UTILIZING A SI-111 AND SAGITAL HORIZONTAL FOCUSING
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97918 Å / Relative weight: 1
ReflectionResolution: 1.8→50 Å / Num. obs: 20478 / % possible obs: 99.9 % / Observed criterion σ(I): 2 / Redundancy: 7 % / Biso Wilson estimate: 20.89 Å2 / Rmerge(I) obs: 0.047 / Net I/σ(I): 26.49
Reflection shellResolution: 1.8→1.83 Å / Redundancy: 7.1 % / Rmerge(I) obs: 0.702 / Mean I/σ(I) obs: 2.98 / Num. unique all: 1002 / % possible all: 100

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Processing

Software
NameVersionClassification
HKL-3000data collection
AMoREphasing
PHENIX(phenix.refine)refinement
HKL-3000data reduction
HKL-3000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1GVK

1gvk


Resolution: 1.805→33.811 Å / SU ML: 0.18 / Isotropic thermal model: Isotropic / σ(F): 0.12 / Phase error: 18.2 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2108 1024 5.15 %RANDOM
Rwork0.1434 ---
obs0.1468 19893 96.56 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 96.526 Å2 / ksol: 0.331 e/Å3
Displacement parametersBiso mean: 30.1 Å2
Baniso -1Baniso -2Baniso -3
1--1.3599 Å20 Å20 Å2
2--1.0086 Å20 Å2
3---0.3513 Å2
Refine analyzeLuzzati coordinate error obs: 0.18 Å
Refinement stepCycle: LAST / Resolution: 1.805→33.811 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1822 0 11 516 2349
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.012104
X-RAY DIFFRACTIONf_angle_d1.3032907
X-RAY DIFFRACTIONf_dihedral_angle_d17.168730
X-RAY DIFFRACTIONf_chiral_restr0.103322
X-RAY DIFFRACTIONf_plane_restr0.006388
LS refinement shell

Refine-ID: X-RAY DIFFRACTION

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection obs% reflection obs (%)
1.8053-1.90040.23631290.15912332233286
1.9004-2.01950.24681350.14462637263795
2.0195-2.17540.19491410.14062679267997
2.1754-2.39420.20951630.12882712271299
2.3942-2.74060.21661560.13872766276699
2.7406-3.45230.21021530.121327932793100
3.4523-33.81680.18651470.148629502950100

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