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- PDB-1n6y: RIP-phasing on Bovine Trypsin -

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Basic information

Entry
Database: PDB / ID: 1n6y
TitleRIP-phasing on Bovine Trypsin
ComponentsTrypsinogen, cationic
KeywordsHYDROLASE
Function / homology
Function and homology information


trypsin / serpin family protein binding / serine protease inhibitor complex / digestion / endopeptidase activity / 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
BENZYLAMINE / Serine protease 1
Similarity search - Component
Biological speciesBos taurus (domestic cattle)
MethodX-RAY DIFFRACTION / SYNCHROTRON / RIP - Radiation-Damage Induced Phasing / Resolution: 1.4 Å
AuthorsRavelli, R.B.G. / Leiros, H.-K.S. / Pan, B. / Caffrey, M. / McSweeney, S.
CitationJournal: Structure / Year: 2003
Title: Specific Radiation-Damage Can Be Used To Solve Macromolecular Crystal Structures
Authors: Ravelli, R.B.G. / Leiros, H.-K.S. / Pan, B. / Caffrey, M. / McSweeney, S.
History
DepositionNov 12, 2002Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 4, 2003Provider: repository / Type: Initial release
Revision 1.1Apr 28, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Non-polymer description / Version format compliance
Revision 1.3Feb 1, 2017Group: Structure summary
Revision 1.4Oct 11, 2017Group: Refinement description / Category: software
Revision 1.5Nov 13, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / 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_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_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.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_conn.ptnr2_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

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Assembly

Deposited unit
A: Trypsinogen, cationic
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,7566
Polymers23,3241
Non-polymers4315
Water5,188288
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)54.241, 56.752, 66.204
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

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Protein , 1 types, 1 molecules A

#1: Protein Trypsinogen, cationic / Beta-trypsin


Mass: 23324.287 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Bos taurus (domestic cattle) / Organ: pancreas / References: UniProt: P00760, trypsin

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Non-polymers , 5 types, 293 molecules

#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca
#4: Chemical ChemComp-ABN / BENZYLAMINE


Mass: 107.153 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C7H9N
#5: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 288 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 2.18 Å3/Da / Density % sol: 43.67 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 8
Details: 25% polyethylene glycol (PEG) 8000, 0.2 M ammonium sulphate, 0.1 M Tris buffer, pH 8, and 100 mM benzylamine, VAPOR DIFFUSION, SITTING DROP, temperature 298K
Crystal grow
*PLUS
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
125 %PEG80001reservoir
20.2 Mammonium sulfate1reservoir
30.1 MTris1reservoirpH8.
4100 mMbenzylamine1reservoir
515 mg/mlprotein1drop

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-4 / Wavelength: 0.9763 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Jun 13, 2001
RadiationMonochromator: Si111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9763 Å / Relative weight: 1
ReflectionResolution: 1.4→42 Å / Num. all: 41043 / Num. obs: 40971 / % possible obs: 99.83 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 13.1 % / Biso Wilson estimate: 12.31 Å2 / Rmerge(I) obs: 0.05 / Net I/σ(I): 11.2
Reflection shellResolution: 1.4→1.47 Å / Redundancy: 11.7 % / Rmerge(I) obs: 0.312 / Mean I/σ(I) obs: 2.7 / % possible all: 97.4
Reflection
*PLUS
Lowest resolution: 45 Å / % possible obs: 99.6 % / Rmerge(I) obs: 0.05
Reflection shell
*PLUS
% possible obs: 97.4 %

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Processing

Software
NameVersionClassification
ProDCdata collection
SCALAdata scaling
SHELXDphasing
SHARPphasing
REFMAC5.1.24refinement
CCP4(SCALA)data scaling
RefinementMethod to determine structure: RIP - Radiation-Damage Induced Phasing
Resolution: 1.4→42 Å / Cor.coef. Fo:Fc: 0.972 / Cor.coef. Fo:Fc free: 0.96 / SU B: 0.695 / SU ML: 0.029
Isotropic thermal model: Anisotropic for protein and ligands. Water molecules are refined isotropic
Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.058 / ESU R Free: 0.054
Details: Model 1n6x was refined against data collected before the "X-ray burn" and used for some additional cycles of refinement against the data after the "X-ray burn". The resulting difference Fo- ...Details: Model 1n6x was refined against data collected before the "X-ray burn" and used for some additional cycles of refinement against the data after the "X-ray burn". The resulting difference Fo-Fc map shows features characteristic for radiation damage, such as negative density for the disulphides. This model has not been manually adjusted to these features! Structure was phased using X-ray damage alone
RfactorNum. reflection% reflectionSelection details
Rfree0.17021 2061 5 %RANDOM
Rwork0.14051 ---
all0.142 40971 --
obs0.142 40971 99.83 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 14.552 Å2
Baniso -1Baniso -2Baniso -3
1--0.1 Å20 Å20 Å2
2--0.02 Å20 Å2
3---0.08 Å2
Refinement stepCycle: LAST / Resolution: 1.4→42 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1629 0 25 288 1942
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0170.0211698
X-RAY DIFFRACTIONr_angle_refined_deg1.6331.9592304
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.2855222
X-RAY DIFFRACTIONr_chiral_restr0.1250.2257
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.021248
X-RAY DIFFRACTIONr_nbd_refined0.1990.2740
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1250.2185
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1790.240
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1560.226
X-RAY DIFFRACTIONr_mcbond_it1.7581.51102
X-RAY DIFFRACTIONr_mcangle_it2.79921771
X-RAY DIFFRACTIONr_scbond_it3.6563596
X-RAY DIFFRACTIONr_scangle_it4.8764.5533
X-RAY DIFFRACTIONr_rigid_bond_restr1.41921653
X-RAY DIFFRACTIONr_sphericity_free1.774401
X-RAY DIFFRACTIONr_sphericity_bonded7.18401620
LS refinement shellResolution: 1.4→1.436 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.239 150
Rwork0.194 2804
Refinement
*PLUS
Highest resolution: 1.4 Å / Lowest resolution: 45 Å / Num. reflection obs: 40972 / Rfactor Rfree: 0.173 / Rfactor Rwork: 0.143
Solvent computation
*PLUS
Displacement parameters
*PLUS
LS refinement shell
*PLUS
Highest resolution: 1.4 Å / Lowest resolution: 1.47 Å

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