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Basic information

Entry
Database: PDB / ID: 3mnb
TitleInvestigation of global and local effects of radiation damage on porcine pancreatic elastase. First 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: 1.198 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
Revision 1.3Oct 30, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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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
Water9,674537
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)50.003, 57.688, 74.337
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.: 537 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 40.51 %
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: 1.2→50 Å / Num. all: 68113 / Num. obs: 68040 / % possible obs: 100 % / Observed criterion σ(I): 2 / Redundancy: 7 % / Biso Wilson estimate: 9.89 Å2 / Rmerge(I) obs: 0.039 / Net I/σ(I): 33.7
Reflection shellResolution: 1.2→1.22 Å / Redundancy: 5 % / Rmerge(I) obs: 0.623 / Mean I/σ(I) obs: 2.3 / Num. unique all: 3340 / % possible all: 99.9

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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: 1.198→45.575 Å / Isotropic thermal model: Anisotropic / σ(I): 0.14 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.138 3309 -random
Rwork0.113 ---
obs0.138 68040 95.88 %-
all-65402 --
Displacement parametersBiso mean: 15.8 Å2
Baniso -1Baniso -2Baniso -3
1--1.7383 Å2-0 Å2-0 Å2
2---2.1202 Å2-0 Å2
3----3.0418 Å2
Refine analyzeLuzzati coordinate error obs: 0.09 Å
Refinement stepCycle: LAST / Resolution: 1.198→45.575 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1822 0 11 537 2370
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONf_bond_d0.01
X-RAY DIFFRACTIONf_angle_deg1.168
X-RAY DIFFRACTIONf_dihedral_angle_d18.181
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkRefine-IDNum. reflection obs% reflection obs (%)
1.1981-1.21520.24371150.2031X-RAY DIFFRACTION213781
1.2152-1.23330.21381260.1664X-RAY DIFFRACTION234288
1.2333-1.25260.17891330.1546X-RAY DIFFRACTION240390
1.2526-1.27320.16471230.1317X-RAY DIFFRACTION244591
1.2732-1.29510.16181230.1257X-RAY DIFFRACTION244792
1.2951-1.31870.1541290.1167X-RAY DIFFRACTION249093
1.3187-1.3440.14271510.108X-RAY DIFFRACTION247994
1.344-1.37150.13241200.1036X-RAY DIFFRACTION252594
1.3715-1.40130.14651290.1034X-RAY DIFFRACTION254895
1.4013-1.43390.12921520.0936X-RAY DIFFRACTION254096
1.4339-1.46970.14531420.0826X-RAY DIFFRACTION261497
1.4697-1.50950.12151580.079X-RAY DIFFRACTION255797
1.5095-1.55390.12771320.0813X-RAY DIFFRACTION265698
1.5539-1.60410.1141540.0753X-RAY DIFFRACTION262098
1.6041-1.66140.10791540.0742X-RAY DIFFRACTION265999
1.6614-1.72790.12581370.0789X-RAY DIFFRACTION266799
1.7279-1.80660.12251430.0848X-RAY DIFFRACTION270099
1.8066-1.90180.12931360.0875X-RAY DIFFRACTION2677100
1.9018-2.0210.11161290.0901X-RAY DIFFRACTION2709100
2.021-2.1770.11371400.0936X-RAY DIFFRACTION2735100
2.177-2.39610.11371360.0946X-RAY DIFFRACTION2732100
2.3961-2.74280.14011410.1039X-RAY DIFFRACTION2756100
2.7428-3.45540.11221550.1014X-RAY DIFFRACTION2753100
3.4554-45.60760.14431510.1411X-RAY DIFFRACTION290299

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