[English] 日本語
Yorodumi
- PDB-2blv: Trypsin before a high dose x-ray "burn" -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 2blv
TitleTrypsin before a high dose x-ray "burn"
ComponentsTRYPSIN
KeywordsHYDROLASE / RADIATION DAMAGE / SYNCHROTRON / PHASING / RIP / CALCIUM-BINDING / DIGESTION / PANCREAS / PROTEASE / SERINE PROTEASE / ZYMOGEN
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
BENZAMIDINE / Serine protease 1
Similarity search - Component
Biological speciesBOS TAURUS (domestic cattle)
MethodX-RAY DIFFRACTION / SYNCHROTRON / OTHER / Resolution: 1.2 Å
AuthorsNanao, M.H. / Ravelli, R.B.
CitationJournal: Acta Crystallogr.,Sect.D / Year: 2005
Title: Improving Radiation-Damage Substructures for Rip.
Authors: Nanao, M.H. / Sheldrick, G.M. / Ravelli, R.B.
History
DepositionMar 8, 2005Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 7, 2005Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 9, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_entry_details / pdbx_modification_feature / pdbx_struct_conn_angle / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _pdbx_entry_details.has_protein_modification / _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
Remark 700 SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "AB" IN EACH CHAIN ON SHEET RECORDS BELOW ... SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "AB" IN EACH CHAIN ON SHEET RECORDS BELOW IS ACTUALLY AN 6-STRANDED BARREL THIS IS REPRESENTED BY A 7-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL.

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: TRYPSIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,9618
Polymers23,3241
Non-polymers6377
Water5,657314
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)54.162, 58.253, 66.582
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 TRYPSIN / 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

-
Non-polymers , 5 types, 321 molecules

#2: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca
#3: Chemical ChemComp-BEN / BENZAMIDINE


Mass: 120.152 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C7H8N2
#4: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: SO4
#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.: 314 / Source method: isolated from a natural source / Formula: H2O

-
Details

Compound detailsCATALYTIC ACTIVITY
Has protein modificationY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 1.77 Å3/Da / Density % sol: 30.04 %

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-4 / Wavelength: 0.9392
DetectorType: ADSC CCD / Detector: CCD / Date: Dec 18, 2004 / Details: BENT MIRROR
RadiationMonochromator: SI(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9392 Å / Relative weight: 1
ReflectionResolution: 1.2→50 Å / Num. obs: 122171 / % possible obs: 96 % / Observed criterion σ(I): -3 / Redundancy: 2.1 % / Rmerge(I) obs: 0.05 / Net I/σ(I): 12.46
Reflection shellResolution: 1.2→1.3 Å / Redundancy: 2.1 % / Rmerge(I) obs: 0.12 / Mean I/σ(I) obs: 6.47 / % possible all: 93.5

-
Processing

Software
NameVersionClassification
XDSdata reduction
XSCALEdata scaling
SHELXDphasing
SHELXEphasing
REFMAC5.2.0005refinement
RefinementMethod to determine structure: OTHER / Resolution: 1.2→10 Å / Cor.coef. Fo:Fc: 0.978 / Cor.coef. Fo:Fc free: 0.972 / SU B: 0.643 / SU ML: 0.014 / Cross valid method: THROUGHOUT / ESU R: 0.03 / ESU R Free: 0.03 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. SIDECHAIN OCCUPANCIES HAVE BEEN REDUCED BECAUSE OF STRONG NEGATIVE PEAKS IN DIFFERENCE FOURIER MAPS IN RESIDUES VAL 53, LYS 109, ASN 115, ...Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. SIDECHAIN OCCUPANCIES HAVE BEEN REDUCED BECAUSE OF STRONG NEGATIVE PEAKS IN DIFFERENCE FOURIER MAPS IN RESIDUES VAL 53, LYS 109, ASN 115, SER 116, LYS 145, LYS 169, SER 178, GLU 186, GLN 240
RfactorNum. reflection% reflectionSelection details
Rfree0.128 3234 5.1 %RANDOM
Rwork0.106 ---
obs0.107 60646 96.3 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 6.47 Å2
Baniso -1Baniso -2Baniso -3
1-0.14 Å20 Å20 Å2
2---0.12 Å20 Å2
3----0.02 Å2
Refinement stepCycle: LAST / Resolution: 1.2→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1629 0 36 314 1979
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0221853
X-RAY DIFFRACTIONr_bond_other_d0.0010.021585
X-RAY DIFFRACTIONr_angle_refined_deg1.6251.9622545
X-RAY DIFFRACTIONr_angle_other_deg0.90633748
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.8235258
X-RAY DIFFRACTIONr_dihedral_angle_2_deg40.56225.80662
X-RAY DIFFRACTIONr_dihedral_angle_3_deg10.99415301
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.934153
X-RAY DIFFRACTIONr_chiral_restr0.1040.2278
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.022160
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02342
X-RAY DIFFRACTIONr_nbd_refined0.2090.2372
X-RAY DIFFRACTIONr_nbd_other0.1860.21646
X-RAY DIFFRACTIONr_nbtor_refined0.1770.2930
X-RAY DIFFRACTIONr_nbtor_other0.0890.21095
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2440.2188
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.3080.25
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2260.236
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2730.235
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.371.51241
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.9521969
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it2.6233711
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it3.3244.5576
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.2→1.26 Å / Total num. of bins used: 10 /
RfactorNum. reflection
Rfree0.119 437
Rwork0.093 8493

+
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