[English] 日本語
Yorodumi
- PDB-1cb5: HUMAN BLEOMYCIN HYDROLASE. -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1cb5
TitleHUMAN BLEOMYCIN HYDROLASE.
ComponentsBLEOMYCIN HYDROLASE
KeywordsHYDROLASE / AMINOPEPTIDASE / CYSTEINE PROTEASE / SELF-COMPARTMENTALIZING / BLEOMYCIN
Function / homology
Function and homology information


bleomycin hydrolase / cysteine-type aminopeptidase activity / homocysteine catabolic process / aminopeptidase activity / carboxypeptidase activity / cysteine-type peptidase activity / response to toxic substance / protein polyubiquitination / Antigen processing: Ubiquitination & Proteasome degradation / response to xenobiotic stimulus ...bleomycin hydrolase / cysteine-type aminopeptidase activity / homocysteine catabolic process / aminopeptidase activity / carboxypeptidase activity / cysteine-type peptidase activity / response to toxic substance / protein polyubiquitination / Antigen processing: Ubiquitination & Proteasome degradation / response to xenobiotic stimulus / cysteine-type endopeptidase activity / proteolysis / extracellular exosome / identical protein binding / nucleus / cytosol / cytoplasm
Similarity search - Function
Peptidase C1B, bleomycin hydrolase / Peptidase C1-like family / Cysteine proteinases / Cysteine peptidase, cysteine active site / Eukaryotic thiol (cysteine) proteases cysteine active site. / Cathepsin B; Chain A / Papain-like cysteine peptidase superfamily / Alpha-Beta Complex / Alpha Beta
Similarity search - Domain/homology
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.59 Å
AuthorsO'Farrell, P.A. / Gonzalez, F. / Zheng, W. / Johnston, S.A. / Joshua-Tor, L.
CitationJournal: Structure Fold.Des. / Year: 1999
Title: Crystal structure of human bleomycin hydrolase, a self-compartmentalizing cysteine protease.
Authors: O'Farrell, P.A. / Gonzalez, F. / Zheng, W. / Johnston, S.A. / Joshua-Tor, L.
History
DepositionMar 1, 1999Deposition site: BNL / Processing site: RCSB
Revision 1.0Mar 1, 2000Provider: repository / Type: Initial release
Revision 1.1Apr 26, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Aug 9, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: BLEOMYCIN HYDROLASE
B: BLEOMYCIN HYDROLASE
C: BLEOMYCIN HYDROLASE


Theoretical massNumber of molelcules
Total (without water)157,0283
Polymers157,0283
Non-polymers00
Water0
1
A: BLEOMYCIN HYDROLASE
B: BLEOMYCIN HYDROLASE
C: BLEOMYCIN HYDROLASE

A: BLEOMYCIN HYDROLASE
B: BLEOMYCIN HYDROLASE
C: BLEOMYCIN HYDROLASE


Theoretical massNumber of molelcules
Total (without water)314,0576
Polymers314,0576
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_555-x,y,-z+1/21
Buried area33060 Å2
ΔGint-133 kcal/mol
Surface area98690 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)133.304, 171.494, 145.707
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221
Noncrystallographic symmetry (NCS)NCS oper:
IDCodeMatrixVector
1given(0.513106, 0.485919, -0.707535), (-0.500181, -0.500615, -0.706543), (-0.697525, 0.716427, -0.013821)6.01965, 86.07539, 8.37166
2given(0.510626, -0.494729, -0.70321), (0.500027, -0.494472, 0.710964), (-0.699452, -0.714661, -0.005113)45.38722, 34.23413, 65.37015

-
Components

#1: Protein BLEOMYCIN HYDROLASE /


Mass: 52342.754 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Cellular location: CYTOPLASM / Plasmid: PKH260HUBH / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)/PLYSS
References: UniProt: Q13867, Hydrolases; Acting on peptide bonds (peptidases); Cysteine endopeptidases

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.65 Å3/Da / Density % sol: 53.59 %
Crystal growpH: 8 / Details: pH 8.00
Crystal grow
*PLUS
Temperature: 17 ℃ / pH: 8 / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
116-20 %PEG100001reservoir
212 mg/mlprotein1drop
325 mMTris1drop
45 %glycerol1drop
5140 mM1dropKCl
61 mMdithiothreitol1drop

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X26C / Wavelength: 1.126
DetectorType: MARRESEARCH / Detector: IMAGE PLATE
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.126 Å / Relative weight: 1
ReflectionResolution: 2.6→100 Å / Num. obs: 47154 / Observed criterion σ(I): 0 / Redundancy: 5.1 % / Biso Wilson estimate: 39.1 Å2 / Rsym value: 7.2 / Net I/σ(I): 18.8
Reflection shellResolution: 2.59→2.68 Å / Mean I/σ(I) obs: 3.5 / Rsym value: 43.1 / % possible all: 94
Reflection
*PLUS
Highest resolution: 2.59 Å / Lowest resolution: 25 Å / % possible obs: 91.6 % / Observed criterion σ(I): 0 / Redundancy: 5.1 % / Num. measured all: 242494 / Rmerge(I) obs: 0.072 / Biso Wilson estimate: 39.1 Å2
Reflection shell
*PLUS
Highest resolution: 2.59 Å / Lowest resolution: 2.68 Å / % possible obs: 94 % / Rmerge(I) obs: 0.431 / Mean I/σ(I) obs: 3.5

-
Processing

Software
NameVersionClassification
AMoREphasing
CNS0.4refinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1GCB

1gcb


Resolution: 2.59→100 Å / Rfactor Rfree error: 0.005 / Data cutoff high absF: 274249.39 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT
Details: RESIDUES 384-387 LIE IN A LOOP REGION FOR WHICH THE DENSITY IS DIFFICULT TO INTERPRET. THEY HAVE BEEN MODELED, BUT OCCUPANCY HAS BEEN SET TO ZERO FOR NON-MAINCHAIN ATOMS. OCCUPANCY HAS ALSO ...Details: RESIDUES 384-387 LIE IN A LOOP REGION FOR WHICH THE DENSITY IS DIFFICULT TO INTERPRET. THEY HAVE BEEN MODELED, BUT OCCUPANCY HAS BEEN SET TO ZERO FOR NON-MAINCHAIN ATOMS. OCCUPANCY HAS ALSO BEEN SET TO ZERO FOR SOME SIDE-CHAIN ATOMS ON THE PROTEIN SURFACE.
RfactorNum. reflection% reflectionSelection details
Rfree0.26 2409 5.1 %RANDOM
Rwork0.237 ---
obs-47632 91.3 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 23.49 Å2 / ksol: 0.322 e/Å3
Displacement parametersBiso mean: 40 Å2
Baniso -1Baniso -2Baniso -3
1-7.31 Å20 Å20 Å2
2---1.98 Å20 Å2
3----5.33 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.41 Å0.36 Å
Luzzati d res low-5 Å
Luzzati sigma a0.42 Å0.39 Å
Refinement stepCycle: LAST / Resolution: 2.59→100 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11022 0 0 0 11022
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.007
X-RAY DIFFRACTIONx_bond_d_na
X-RAY DIFFRACTIONx_bond_d_prot
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_angle_d_na
X-RAY DIFFRACTIONx_angle_d_prot
X-RAY DIFFRACTIONx_angle_deg1.3
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d21.2
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d0.81
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it
X-RAY DIFFRACTIONx_mcangle_it
X-RAY DIFFRACTIONx_scbond_it
X-RAY DIFFRACTIONx_scangle_it
Refine LS restraints NCSNCS model details: CONSTR
LS refinement shellResolution: 2.59→2.75 Å / Rfactor Rfree error: 0.02 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.323 411 5.1 %
Rwork0.303 7595 -
obs--93.4 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PAPROTEIN.TOP
X-RAY DIFFRACTION2PROTEIN_REP.PARAMPROTEIN.TOP
Software
*PLUS
Name: CNS / Version: 0.4 / Classification: refinement
Refinement
*PLUS
Highest resolution: 2.59 Å / Lowest resolution: 25 Å / Rfactor obs: 0.238 / Rfactor Rfree: 0.26
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_deg
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg21.2
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg0.81
X-RAY DIFFRACTIONc_mcbond_it
X-RAY DIFFRACTIONc_scbond_it
X-RAY DIFFRACTIONc_mcangle_it
X-RAY DIFFRACTIONc_scangle_it
LS refinement shell
*PLUS
Rfactor Rfree: 0.323 / Rfactor Rwork: 0.303 / Rfactor obs: 0.304

+
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