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- PDB-3mu4: Comparison of the character and the speed of X-ray-induced struct... -

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Basic information

Entry
Database: PDB / ID: 3mu4
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 B of the crystal. First 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 / Peptidase S1A, chymotrypsin family / Serine proteases, trypsin family, histidine active site. / 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 / Peptidase S1A, chymotrypsin family / Serine proteases, trypsin family, histidine active site. / 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: 1.101 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
Revision 1.3Nov 6, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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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
Water9,656536
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)50.003, 57.794, 74.505
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.: 536 / 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: 2.08 Å3/Da / Density % sol: 40.75 %
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: 1.1→50 Å / Num. obs: 85749 / % possible obs: 97.3 % / Observed criterion σ(I): 2 / Redundancy: 4.3 % / Biso Wilson estimate: 7.78 Å2 / Rmerge(I) obs: 0.031 / Net I/σ(I): 26.46
Reflection shellResolution: 1.1→1.14 Å / Redundancy: 3.5 % / Mean I/σ(I) obs: 2.98 / Num. unique all: 7852 / % possible all: 90.3

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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: 1.101→45.666 Å / SU ML: 0.07 / Isotropic thermal model: Anisotropic / σ(F): 0.09 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.1271 4167 5.01 %Random
Rwork0.1142 ---
obs0.1149 83253 94.53 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 64.127 Å2 / ksol: 0.394 e/Å3
Displacement parametersBiso mean: 12.88 Å2
Baniso -1Baniso -2Baniso -3
1--0.8151 Å2-0 Å2-0 Å2
2---2.4706 Å2-0 Å2
3----0.2575 Å2
Refine analyzeLuzzati coordinate error obs: 0.07 Å
Refinement stepCycle: LAST / Resolution: 1.101→45.666 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1822 0 11 536 2369
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.013827
X-RAY DIFFRACTIONf_angle_d1.166789
X-RAY DIFFRACTIONf_dihedral_angle_d19.275973
X-RAY DIFFRACTIONf_chiral_restr0.1318
X-RAY DIFFRACTIONf_plane_restr0.006643
LS refinement shell

Refine-ID: X-RAY DIFFRACTION

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection obs% reflection obs (%)
1.101-1.11310.18981160.17032135213578
1.1131-1.12610.1871160.15552320232084
1.1261-1.13990.14981180.14932347234785
1.1399-1.15430.1771300.14992451245188
1.1543-1.16950.17191210.15782428242889
1.1695-1.18550.14071440.15582462246290
1.1855-1.20250.18441350.14562473247390
1.2025-1.22040.14251220.13342552255292
1.2204-1.23950.1371290.11852569256993
1.2395-1.25980.13731270.10732592259293
1.2598-1.28150.12711530.09222590259095
1.2815-1.30480.13041290.08762638263895
1.3048-1.32990.08931220.08482664266496
1.3299-1.35710.10961600.08712656265696
1.3571-1.38660.11321570.0842669266996
1.3866-1.41890.11511380.08192684268497
1.4189-1.45430.09831280.07792676267697
1.4543-1.49370.11271410.08012724272497
1.4937-1.53760.10581480.07812693269398
1.5376-1.58720.10511380.07952726272698
1.5872-1.6440.091580.07782755275599
1.644-1.70980.10321590.08372748274899
1.7098-1.78760.11911360.09282796279699
1.7876-1.88190.09581300.09252760276099
1.8819-1.99980.10731460.08982795279599
1.9998-2.15420.10571580.09562772277299
2.1542-2.3710.11321330.09762807280799
2.371-2.7140.12471590.11262814281499
2.714-3.41920.10121650.11042852285299
3.4192-45.7050.161510.14492938293897

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