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

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Basic information

Entry
Database: PDB / ID: 3odf
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. Second 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: 1.1 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
DepositionAug 11, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 25, 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_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_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
Water9,476526
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)50.034, 57.742, 74.449
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.: 526 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsTHIS SEQUENCE IS FROM REFERENCE 3 OF UNIPROT ENTRY P00772 (BIOCHEM. J. 131:643-675(1973) SHOTTON D. ...THIS SEQUENCE IS FROM REFERENCE 3 OF UNIPROT ENTRY P00772 (BIOCHEM. J. 131:643-675(1973) SHOTTON D.M., HARTLEY B.S. EVIDENCE FOR THE AMINO ACID SEQUENCE OF PORCINE PANCREATIC ELASTASE).

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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: 2.07 Å3/Da / Density % sol: 40.69 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop
Details: The initial concentration of the protein was 20 mg/ml in 10% glycerol solution. The reservoir contained a 250 mM Na2SO4, solution at pH 7.5 (adjusted with NaOH). For cryo-protection, the 250 ...Details: The initial concentration of the protein was 20 mg/ml in 10% glycerol solution. The reservoir contained a 250 mM Na2SO4, solution at pH 7.5 (adjusted with NaOH). For cryo-protection, the 250 mM Na2SO4 was supplemented with 25% glycerol, 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: 1.1→50 Å / Num. obs: 82126 / % possible obs: 93.1 % / Observed criterion σ(I): 2 / Redundancy: 3.6 % / Biso Wilson estimate: 9.94 Å2 / Rmerge(I) obs: 0.041 / Net I/σ(I): 22.1
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique all% possible all
1.1-1.143.10.2454.9804692.5
2.37-503.10.03425.6552759.8
1.88-2.373.60.0425.5854595.5
1.64-1.883.80.05224.9875199
1.49-1.643.80.06721870898.8
1.39-1.493.80.07722.8861498.3
1.3-1.393.80.08617.9865998.2
1.24-1.33.70.1413.6849197.5
1.18-1.243.40.1956.7845196.5
1.14-1.183.40.2465.5838496

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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: 1.1→9.813 Å / SU ML: 0.09 / Isotropic thermal model: Anisotropic / σ(F): 0.04 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.1467 4022 5.01 %Random
Rwork0.1224 ---
obs0.1237 80357 91.22 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 79.875 Å2 / ksol: 0.402 e/Å3
Displacement parametersBiso mean: 7.18 Å2
Baniso -1Baniso -2Baniso -3
1-1.029 Å2-0 Å2-0 Å2
2---1.8314 Å2-0 Å2
3----0.9942 Å2
Refine analyzeLuzzati coordinate error obs: 0.09 Å
Refinement stepCycle: LAST / Resolution: 1.1→9.813 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1822 0 11 526 2359
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0113845
X-RAY DIFFRACTIONf_angle_d1.176814
X-RAY DIFFRACTIONf_dihedral_angle_d18.199986
X-RAY DIFFRACTIONf_chiral_restr0.113322
X-RAY DIFFRACTIONf_plane_restr0.006651
LS refinement shell

Refine-ID: X-RAY DIFFRACTION

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection obs% reflection obs (%)
1.1-1.11230.1471430.13042433243386
1.1123-1.12590.14361500.12322503250389
1.1259-1.14010.14831320.12782604260491
1.1401-1.15510.17221380.14562635263592
1.1551-1.17090.17741350.18462613261393
1.1709-1.18760.20331410.18832657265792
1.1876-1.20530.21091230.15882648264892
1.2053-1.22410.1591420.14982625262592
1.2241-1.24410.1311260.11232640264093
1.2441-1.26550.12391410.10082757275796
1.2655-1.28850.13961400.10082705270594
1.2885-1.31320.13731440.09552732273295
1.3132-1.340.13411310.09072796279697
1.34-1.3690.10191470.08732788278898
1.369-1.40080.11881480.08772786278697
1.4008-1.43570.10571550.09092797279798
1.4357-1.47440.13061390.08712816281697
1.4744-1.51760.12361410.10972677267793
1.5176-1.56640.13291330.10262789278996
1.5664-1.62220.11421470.09132818281898
1.6222-1.68680.11661680.09652828282899
1.6868-1.76320.11871500.09942869286999
1.7632-1.85550.11481490.10222883288399
1.8555-1.97090.12231480.09892857285799
1.9709-2.12170.12361720.10362841284198
2.1217-2.33260.12111220.11342667266790
2.3326-2.66420.16141440.12962673267391
2.6642-3.33460.17811250.15682082208270
3.3346-9.81330.3391480.301881681627

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