[English] 日本語
Yorodumi
- PDB-1n6x: RIP-phasing on Bovine Trypsin -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1n6x
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 / 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
BENZYLAMINE / Serine protease 1
Similarity search - Component
Biological speciesBos taurus (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 1.3Oct 11, 2017Group: Refinement description / Category: software

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
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)54.209, 56.658, 66.126
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

-
Components

-
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 (cattle) / Organ: pancreas / References: UniProt: P00760, trypsin

-
Non-polymers , 5 types, 293 molecules

#2: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


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 / 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 / Glycerol


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


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

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
Sample preparation

CrystalDensity Matthews: 2.18 Å3/Da / Density % sol: 43.48 %
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

-
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: 40997 / % possible obs: 99.89 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 13.4 % / Biso Wilson estimate: 12.45 Å2 / Rmerge(I) obs: 0.047 / Net I/σ(I): 11.3
Reflection shellResolution: 1.4→1.47 Å / Redundancy: 12.5 % / Rmerge(I) obs: 0.227 / Mean I/σ(I) obs: 3.6 / Rsym value: 0.227 / % possible all: 98.3
Reflection
*PLUS
Lowest resolution: 45 Å / % possible obs: 99.7 %
Reflection shell
*PLUS
% possible obs: 98.3 %

-
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→41.89 Å / Cor.coef. Fo:Fc: 0.973 / Cor.coef. Fo:Fc free: 0.963 / SU B: 0.654 / SU ML: 0.027
Isotropic thermal model: Anisotropic for protein and ligands. Water molecules are refined isotropic
Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.057 / ESU R Free: 0.053 / Details: Structure was phased using X-ray damage alone
RfactorNum. reflection% reflectionSelection details
Rfree0.16464 2061 5 %RANDOM
Rwork0.13785 ---
all0.13919 40997 --
obs0.13919 40997 99.89 %-
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: 14.343 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→41.89 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1629 0 25 288 1942
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.0211698
X-RAY DIFFRACTIONr_angle_refined_deg1.6261.9592304
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.3865222
X-RAY DIFFRACTIONr_chiral_restr0.1230.2257
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.021248
X-RAY DIFFRACTIONr_nbd_refined0.1980.2752
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1230.2177
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1650.243
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1470.225
X-RAY DIFFRACTIONr_mcbond_it1.6081.51102
X-RAY DIFFRACTIONr_mcangle_it2.56621771
X-RAY DIFFRACTIONr_scbond_it3.3883596
X-RAY DIFFRACTIONr_scangle_it4.54.5533
X-RAY DIFFRACTIONr_rigid_bond_restr1.26321653
X-RAY DIFFRACTIONr_sphericity_free1.262401
X-RAY DIFFRACTIONr_sphericity_bonded7.071401620
LS refinement shellResolution: 1.4→1.436 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.232 150
Rwork0.185 2812
Refinement
*PLUS
Highest resolution: 1.4 Å / Lowest resolution: 45 Å / Num. reflection obs: 40998 / Rfactor Rfree: 0.167 / Rfactor Rwork: 0.138
Solvent computation
*PLUS
Displacement parameters
*PLUS

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more