[English] 日本語
Yorodumi
- PDB-7v5l: Crystal structure of human bleomycin hydrolase -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 7v5l
TitleCrystal structure of human bleomycin hydrolase
ComponentsBleomycin hydrolase
KeywordsHYDROLASE / cysteine protease
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 peptidase, cysteine active site / Eukaryotic thiol (cysteine) proteases cysteine active site. / Papain-like cysteine peptidase superfamily
Similarity search - Domain/homology
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.74 Å
AuthorsChang, C.Y. / Zheng, Y.Z. / Huang, S.J. / Wang, Y.L. / Toh, S.I. / Lin, E.C.
Funding support Taiwan, 1items
OrganizationGrant numberCountry
Ministry of Science and Technology (MoST, Taiwan)110-2113-M-A49 -026 -MY3 Taiwan
CitationJournal: Chembiochem / Year: 2022
Title: The Structure-Function Relationship of Human Bleomycin Hydrolase: Mutation of a Cysteine Protease into a Serine Protease.
Authors: Zheng, Y.Z. / Cui, J. / Wang, Y.L. / Huang, S.J. / Lin, E.C. / Huang, S.C. / Rudolf, J.D. / Yan, X. / Chang, C.Y.
History
DepositionAug 17, 2021Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jun 29, 2022Provider: repository / Type: Initial release
Revision 1.1Jul 6, 2022Group: Database references / Category: citation / Item: _citation.journal_volume
Revision 1.2Nov 29, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Bleomycin hydrolase
B: Bleomycin hydrolase
C: Bleomycin hydrolase
D: Bleomycin hydrolase


Theoretical massNumber of molelcules
Total (without water)219,1984
Polymers219,1984
Non-polymers00
Water26,5001471
1
A: Bleomycin hydrolase
B: Bleomycin hydrolase

A: Bleomycin hydrolase
B: Bleomycin hydrolase

A: Bleomycin hydrolase
B: Bleomycin hydrolase


Theoretical massNumber of molelcules
Total (without water)328,7976
Polymers328,7976
Non-polymers00
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-y,x-y,z1
crystal symmetry operation3_555-x+y,-x,z1
Buried area33870 Å2
ΔGint-147 kcal/mol
Surface area96730 Å2
MethodPISA
2
C: Bleomycin hydrolase
D: Bleomycin hydrolase

C: Bleomycin hydrolase
D: Bleomycin hydrolase

C: Bleomycin hydrolase
D: Bleomycin hydrolase


Theoretical massNumber of molelcules
Total (without water)328,7976
Polymers328,7976
Non-polymers00
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-y,x-y,z1
crystal symmetry operation3_555-x+y,-x,z1
Buried area33730 Å2
ΔGint-137 kcal/mol
Surface area96360 Å2
MethodPISA
Unit cell
Length a, b, c (Å)181.944, 181.944, 166.307
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number146
Space group name H-MH3

-
Components

#1: Protein
Bleomycin hydrolase / / BH / BLM hydrolase / BMH


Mass: 54799.453 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: BLMH / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q13867, bleomycin hydrolase
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 1471 / 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: 2.53 Å3/Da / Density % sol: 51.45 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: 0.2M sodium chloride, 10% (w/v) PEG 8000, 0.1mM CHES, pH 9.5

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: NSRRC / Beamline: TPS 05A / Wavelength: 1 Å
DetectorType: RAYONIX MX300-HS / Detector: CCD / Date: Aug 10, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.74→30 Å / Num. obs: 209843 / % possible obs: 99.7 % / Redundancy: 4.7 % / CC1/2: 0.99 / Net I/σ(I): 22.9
Reflection shellResolution: 1.74→1.8 Å / Mean I/σ(I) obs: 2.7 / Num. unique obs: 21057 / CC1/2: 0.78

-
Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
SCALAdata scaling
PDB_EXTRACT3.27data extraction
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1CB5

1cb5


Resolution: 1.74→29.47 Å / Cor.coef. Fo:Fc: 0.964 / Cor.coef. Fo:Fc free: 0.947 / SU B: 2.106 / SU ML: 0.068 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.102 / ESU R Free: 0.101 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2002 10468 5 %RANDOM
Rwork0.1654 ---
obs0.1671 198839 99.35 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 97.49 Å2 / Biso mean: 20.264 Å2 / Biso min: 10.71 Å2
Baniso -1Baniso -2Baniso -3
1--0 Å2-0 Å20 Å2
2---0 Å20 Å2
3---0 Å2
Refinement stepCycle: final / Resolution: 1.74→29.47 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms14680 0 0 1479 16159
Biso mean---28.52 -
Num. residues----1808
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.01315056
X-RAY DIFFRACTIONr_bond_other_d0.0010.01714073
X-RAY DIFFRACTIONr_angle_refined_deg1.4711.64220357
X-RAY DIFFRACTIONr_angle_other_deg1.4111.58132469
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.22851806
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.5523.06830
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.937152675
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.4481581
X-RAY DIFFRACTIONr_chiral_restr0.0790.21869
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.0217047
X-RAY DIFFRACTIONr_gen_planes_other0.0010.023555
LS refinement shellResolution: 1.74→1.785 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.246 744 -
Rwork0.223 14212 -
all-14956 -
obs--96.3 %

+
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