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- PDB-3mu0: Comparison of the character and the speed of X-ray-induced struct... -

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Basic information

Entry
Database: PDB / ID: 3mu0
TitleComparison of the character and the speed of X-ray-induced structural changes of porcine pancreatic elastase at two temperatures, 100 and 15K. The data set was collected from region A of the crystal. Third step 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: 1.401 Å
AuthorsPetrova, T. / Ginell, S. / Mitschler, A. / Cousido-Siah, A. / Hazemann, I. / Podjarny, A. / 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
DepositionMay 1, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 12, 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

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)26,1434
Polymers25,9281
Non-polymers2153
Water9,440524
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)50.161, 57.826, 74.726
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.: 524 / 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: 41.15 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: The initial concentration of the protein was 20 mg/ml in 10% glycerol solution. The reservoir contained a 250 mM Na2SO4. For cryo-protection, it was supplemented with 25% glycerol, pH 7.5, ...Details: The initial concentration of the protein was 20 mg/ml in 10% glycerol solution. The reservoir contained a 250 mM Na2SO4. For cryo-protection, it was supplemented with 25% glycerol, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 291K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.97895 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Mar 20, 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: 0.97895 Å / Relative weight: 1
ReflectionResolution: 1.4→50 Å / Num. obs: 43068 / % possible obs: 99.3 % / Observed criterion σ(I): 2 / Redundancy: 4.4 % / Biso Wilson estimate: 12.58 Å2 / Rmerge(I) obs: 0.021 / Net I/σ(I): 34.66
Reflection shellResolution: 1.4→1.45 Å / Redundancy: 4.5 % / Rmerge(I) obs: 0.464 / Mean I/σ(I) obs: 2.81 / Num. unique all: 4223 / % possible all: 98.7

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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: PDB entry 1GVK

1gvk


Resolution: 1.401→45.732 Å / SU ML: 0.14 / Isotropic thermal model: Anisotropic / σ(F): 0.1 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.1421 2095 5.06 %Random
Rwork0.1076 ---
obs0.1093 41376 95.28 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 98.913 Å2 / ksol: 0.452 e/Å3
Displacement parametersBiso mean: 18.17 Å2
Baniso -1Baniso -2Baniso -3
1-2.0959 Å2-0 Å2-0 Å2
2---1.9951 Å2-0 Å2
3----0.8077 Å2
Refine analyzeLuzzati coordinate error obs: 0.14 Å
Refinement stepCycle: LAST / Resolution: 1.401→45.732 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1822 0 11 524 2357
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0113849
X-RAY DIFFRACTIONf_angle_d1.1036818
X-RAY DIFFRACTIONf_dihedral_angle_d17.101990
X-RAY DIFFRACTIONf_chiral_restr0.106322
X-RAY DIFFRACTIONf_plane_restr0.007651
LS refinement shell

Refine-ID: X-RAY DIFFRACTION

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection obs% reflection obs (%)
1.401-1.43380.24241210.15742303230385
1.4338-1.46970.18941110.14262411241189
1.4697-1.50940.20421340.13942367236788
1.5094-1.55390.17761210.11022504250492
1.5539-1.6040.14171310.08692536253693
1.604-1.66130.11991540.07852583258395
1.6613-1.72790.13691410.07962614261496
1.7279-1.80650.11281380.08192659265998
1.8065-1.90170.13261360.07972685268598
1.9017-2.02090.13371470.08292730273099
2.0209-2.17690.11751430.08182729272999
2.1769-2.3960.11851440.08582719271999
2.396-2.74270.1171640.09662741274199
2.7427-3.45530.1221500.097527932793100
3.4553-45.75660.17171600.15042907290799

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