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

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Basic information

Entry
Database: PDB / ID: 3mnc
TitleInvestigation of global and local effects of radiation damage on porcine pancreatic elastase. Second 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 / Peptidase S1A, chymotrypsin family / Serine proteases, trypsin family, histidine active site. / Serine proteases, trypsin domain profile. / Serine proteases, trypsin family, serine active site. / Trypsin-like serine protease / Serine proteases, trypsin domain / Trypsin / Trypsin-like serine proteases ...Serine proteases, trypsin family, histidine active site / Serine proteases, trypsin family, serine active site / Peptidase S1A, chymotrypsin family / Serine proteases, trypsin family, histidine active site. / Serine proteases, trypsin domain profile. / Serine proteases, trypsin family, serine active site. / 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: 1.119 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 21, 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_alt_id / _pdbx_struct_conn_angle.ptnr1_label_asym_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_alt_id / _pdbx_struct_conn_angle.ptnr3_label_asym_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.pdbx_ptnr2_label_alt_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_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
Water9,656536
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)50.139, 57.723, 74.468
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 / Sulfate


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


Mass: 18.015 Da / Num. of mol.: 536 / 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: 2.08 Å3/Da / Density % sol: 40.81 %
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: 1.12→50 Å / Num. obs: 80647 / % possible obs: 96.1 % / Observed criterion σ(I): 2 / Redundancy: 4.2 % / Biso Wilson estimate: 10.65 Å2 / Rmerge(I) obs: 0.071 / Net I/σ(I): 20.63
Reflection shellResolution: 1.12→1.14 Å / Redundancy: 1.8 % / Rmerge(I) obs: 0.42 / Mean I/σ(I) obs: 2.01 / Num. unique all: 3405 / % possible all: 82.4

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Processing

Software
NameClassification
HKL-3000data collection
AMoREphasing
PHENIXrefinement
HKL-3000data reduction
HKL-3000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1GVK

1gvk


Resolution: 1.119→9.819 Å / Isotropic thermal model: Anisotropic / σ(I): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.1411 3858 -Random
Rwork0.116 ---
obs0.1172 77321 92.21 %-
Displacement parametersBiso mean: 16.2 Å2
Baniso -1Baniso -2Baniso -3
1--0.2624 Å2-0 Å2-0 Å2
2---0.3379 Å2-0 Å2
3----0.5992 Å2
Refine analyzeLuzzati coordinate error obs: 0.07 Å
Refinement stepCycle: LAST / Resolution: 1.119→9.819 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1822 0 11 536 2369
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONf_bond_d0.011
X-RAY DIFFRACTIONf_angle_deg1.5
X-RAY DIFFRACTIONf_dihedral_angle_d18.161
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkRefine-IDNum. reflection obs% reflection obs (%)
1.1187-1.13230.231800.2138X-RAY DIFFRACTION180664
1.1323-1.14660.2172990.1881X-RAY DIFFRACTION212775
1.1466-1.16170.17371030.1631X-RAY DIFFRACTION221479
1.1617-1.17760.1831380.1537X-RAY DIFFRACTION236284
1.1776-1.19430.14261190.1366X-RAY DIFFRACTION249788
1.1943-1.21210.15881410.1218X-RAY DIFFRACTION254791
1.2121-1.2310.13021410.1108X-RAY DIFFRACTION261093
1.231-1.25120.14081210.0999X-RAY DIFFRACTION268494
1.2512-1.27270.13611370.0965X-RAY DIFFRACTION267795
1.2727-1.29580.12181570.0942X-RAY DIFFRACTION267296
1.2958-1.32070.13091530.0936X-RAY DIFFRACTION271696
1.3207-1.34760.13491400.0869X-RAY DIFFRACTION270897
1.3476-1.37680.10991340.0837X-RAY DIFFRACTION272896
1.3768-1.40870.1041620.0843X-RAY DIFFRACTION275097
1.4087-1.44390.13131390.0832X-RAY DIFFRACTION275797
1.4439-1.48280.11831290.0809X-RAY DIFFRACTION275797
1.4828-1.52620.11431540.0784X-RAY DIFFRACTION277397
1.5262-1.57530.11291500.0856X-RAY DIFFRACTION275298
1.5753-1.63140.11091340.0832X-RAY DIFFRACTION279398
1.6314-1.69640.11391400.0896X-RAY DIFFRACTION282898
1.6964-1.77320.12741500.095X-RAY DIFFRACTION279999
1.7732-1.8660.11221680.0979X-RAY DIFFRACTION281799
1.866-1.98210.12771450.0984X-RAY DIFFRACTION283399
1.9821-2.13360.12571620.105X-RAY DIFFRACTION2859100
2.1336-2.34570.12831640.1067X-RAY DIFFRACTION283999
2.3457-2.67910.15471520.1159X-RAY DIFFRACTION287999
2.6791-3.35290.12871360.119X-RAY DIFFRACTION277894
3.3529-9.8190.20621100.187X-RAY DIFFRACTION190163

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