[English] 日本語
Yorodumi
- PDB-1qto: 1.5 A CRYSTAL STRUCTURE OF A BLEOMYCIN RESISTANCE DETERMINANT FRO... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1qto
Title1.5 A CRYSTAL STRUCTURE OF A BLEOMYCIN RESISTANCE DETERMINANT FROM BLEOMYCIN-PRODUCING STREPTOMYCES VERTICILLUS
ComponentsBLEOMYCIN-BINDING PROTEIN
KeywordsANTIBIOTIC INHIBITOR / ARM-EXCHANGE
Function / homology
Function and homology information


response to antibiotic
Similarity search - Function
Bleomycin resistance protein / 2,3-Dihydroxybiphenyl 1,2-Dioxygenase, domain 1 / 2,3-Dihydroxybiphenyl 1,2-Dioxygenase; domain 1 / Vicinal oxygen chelate (VOC) domain / Vicinal oxygen chelate (VOC) domain profile. / Glyoxalase/Bleomycin resistance protein/Dihydroxybiphenyl dioxygenase / Roll / Alpha Beta
Similarity search - Domain/homology
Bleomycin resistance protein
Similarity search - Component
Biological speciesStreptomyces verticillus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SIRAS / Resolution: 1.5 Å
AuthorsKawano, Y. / Kumagai, T. / Muta, K. / Matoba, Y. / Davies, J. / Sugiyama, M.
Citation
Journal: J.Mol.Biol. / Year: 2000
Title: The 1.5 A crystal structure of a bleomycin resistance determinant from bleomycin-producing Streptomyces verticillus.
Authors: Kawano, Y. / Kumagai, T. / Muta, K. / Matoba, Y. / Davies, J. / Sugiyama, M.
#1: Journal: Gene / Year: 1994
Title: Characterisation by molecular cloning of two genes from Streptomyces verticillus encoding resistance to bleomycin
Authors: Sugiyama, M. / Thompson, C.J. / Kumagai, T. / Suzuki, K. / Deblaere, R. / Villarroel, R. / Davies, J.
#2: Journal: FEBS Lett. / Year: 1995
Title: Overproduction of the bleomycin-binding proteins from bleomycin-producing Streptomyces verticillus and a methicillin-resistant Staphylococcus aureus in Escherichia coli and their immunological characterisation
Authors: Sugiyama, M. / Kumagai, T. / Matsuo, H. / Bhuiyan, M.Z.A. / Ueda, K. / Mochizuki, H. / Nakamura, N. / Davies, J.
#3: Journal: Acta Crystallogr.,Sect.D / Year: 1998
Title: Crystallization and preliminary X-ray diffraction studies of bleomycin-binding protein from bleomycin-producing Streptomyces verticillus
Authors: Kumagai, T. / Muta, K. / Matoba, Y. / Kawano, Y. / Kamiya, N. / Davies, J. / Sugiyama, M.
#4: Journal: FEBS Lett. / Year: 1999
Title: Characterization of the bleomycin resistance determinant encoded on the transposon Tn5
Authors: Kumagai, T. / Nakano, T. / Maruyama, M. / Mochizuki, H. / Sugiyama, M.
#5: Journal: FEBS Lett. / Year: 1999
Title: Mutation of the N-terminal proline 9 of BLMA from Streptomyces verticillus abolishes the binding affinity for bleomycin
Authors: Kumagai, T. / Hibino, R. / Kawano, Y. / Sugiyama, M.
History
DepositionJun 28, 1999Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 28, 2000Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Nov 16, 2011Group: Atomic model
Revision 1.4Oct 4, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 1.5Feb 14, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: BLEOMYCIN-BINDING PROTEIN


Theoretical massNumber of molelcules
Total (without water)13,2441
Polymers13,2441
Non-polymers00
Water1,63991
1
A: BLEOMYCIN-BINDING PROTEIN

A: BLEOMYCIN-BINDING PROTEIN


Theoretical massNumber of molelcules
Total (without water)26,4872
Polymers26,4872
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,-y,z1
Buried area3120 Å2
ΔGint-25 kcal/mol
Surface area11450 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)54.94, 67.88, 35.61
Angle α, β, γ (deg.)90.0, 90.0, 90.0
Int Tables number18
Space group name H-MP21212
Components on special symmetry positions
IDModelComponents
11A-209-

HOH

21A-226-

HOH

DetailsThe biological assembly is a homodimer.

-
Components

#1: Protein BLEOMYCIN-BINDING PROTEIN


Mass: 13243.607 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptomyces verticillus (bacteria) / Production host: Escherichia coli (E. coli) / References: UniProt: Q53793
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 91 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 2

-
Sample preparation

CrystalDensity Matthews: 2.51 Å3/Da / Density % sol: 51 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 5.7
Details: NH4-acetate, Na-acetate, PEG4000, pH 5.7, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal grow
*PLUS
Temperature: 20 ℃
Details: drop consists of equal volume of protein and reservoir solutions
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
120 mg/mlprotein1drop
20.2 Mammonium acetate1reservoir
30.1 Msodium acetate1reservoir
430 %PEG40001reservoir

-
Data collection

Diffraction
IDMean temperature (K)Crystal-ID
12981
22981
Diffraction source
SourceSiteBeamlineIDWavelength
SYNCHROTRONPhoton Factory BL-6B11
SYNCHROTRONPhoton Factory BL-6A21
Detector
TypeIDDetectorDate
WEISSENBERG1DIFFRACTOMETERMay 8, 1996
WEISSENBERG2DIFFRACTOMETERNov 14, 1996
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.5→67.42 Å / Num. all: 75281 / Num. obs: 74090 / % possible obs: 94.3 % / Observed criterion σ(F): 16.24 / Observed criterion σ(I): 263.62 / Redundancy: 3.6 % / Biso Wilson estimate: 16.4 Å2 / Rmerge(I) obs: 0.054 / Net I/σ(I): 7.95
Reflection shellResolution: 1.5→1.58 Å / Redundancy: 2.7 % / Rmerge(I) obs: 0.139 / Num. unique all: 2671 / % possible all: 85.7
Reflection
*PLUS
Num. obs: 19723 / Num. measured all: 74090
Reflection shell
*PLUS
% possible obs: 85.7 %

-
Processing

Software
NameVersionClassification
DMmodel building
X-PLOR3.851refinement
WEISdata reduction
CCP4(AGROVATAdata scaling
ROTAVATAdata scaling
DMphasing
RefinementMethod to determine structure: SIRAS / Resolution: 1.5→10 Å / Rfactor Rfree error: 0.005 / SU B: 18.1 / Data cutoff high absF: 1000000 / Data cutoff low absF: 0.001 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 2 / σ(I): 4 / Stereochemistry target values: X-PLOR 3.851
RfactorNum. reflection% reflectionSelection details
Rfree0.221 2021 9.8 %RANDOM
Rwork0.19 ---
all-20570 --
obs-20570 93.9 %-
Refine analyze
FreeObs
Luzzati coordinate error0.18 Å0.17 Å
Luzzati d res low-5 Å
Luzzati sigma a0.1 Å0.13 Å
Refinement stepCycle: LAST / Resolution: 1.5→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms934 0 0 91 1025
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONx_dihedral_angle_d26.9
X-RAY DIFFRACTIONx_angle_deg1.24
X-RAY DIFFRACTIONx_bond_d0.005
X-RAY DIFFRACTIONx_improper_angle_d0.65
X-RAY DIFFRACTIONx_mcbond_it1.451.5
X-RAY DIFFRACTIONx_mcangle_it2.52
X-RAY DIFFRACTIONx_scbond_it2.462
X-RAY DIFFRACTIONx_scangle_it4.052.5
LS refinement shellResolution: 1.5→1.55 Å / Rfactor Rfree error: 0.02 / Total num. of bins used: 10
RfactorNum. reflection% reflection
Rfree0.263 178 9.7 %
Rwork0.283 1651 -
obs--84.9 %
Xplor fileSerial no: 1 / Param file: protein_rep.param / Topol file: tophcsdx.pro
Software
*PLUS
Name: X-PLOR / Version: 3.851 / Classification: refinement
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_deg26.9
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg0.65

+
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