[English] 日本語
Yorodumi
- PDB-1ewj: CRYSTAL STRUCTURE OF BLEOMYCIN-BINDING PROTEIN COMPLEXED WITH BLE... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1ewj
TitleCRYSTAL STRUCTURE OF BLEOMYCIN-BINDING PROTEIN COMPLEXED WITH BLEOMYCIN
ComponentsBLEOMYCIN RESISTANCE DETERMINANT
KeywordsANTIBIOTIC INHIBITOR / bleomycin-binding protein / bleomycin / antibiotics resistance / homodimer
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 / Glyoxalase/fosfomycin resistance/dioxygenase domain / Glyoxalase/Bleomycin resistance protein/Dioxygenase superfamily / 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 A2 / Bleomycin resistance protein
Similarity search - Component
Biological speciesKlebsiella pneumoniae (bacteria)
MethodX-RAY DIFFRACTION / Resolution: 2.5 Å
AuthorsMaruyama, M. / Kumagai, T. / Matoba, Y. / Hata, Y. / Sugiyama, M.
Citation
Journal: J.Biol.Chem. / Year: 2001
Title: Crystal structures of the transposon Tn5-carried bleomycin resistance determinant uncomplexed and complexed with bleomycin.
Authors: Maruyama, M. / Kumagai, T. / Matoba, Y. / Hayashida, M. / Fujii, T. / Hata, Y. / Sugiyama, M.
#1: Journal: To be Published
Title: The 1.7 A Crystal structure of a bleomycin resistance protein encoded on the transposon Tn5
Authors: Maruyama, M. / Matoba, Y. / Kumagai, T. / Sugiyama, M.
#2: Journal: Acta Crystallogr.,Sect.D / Year: 1999
Title: Crystallization and preliminary X-ray diffraction studies of bleomycin-binding protein encoded on the transposon Tn5
Authors: Kumagai, T. / Maruyama, M. / Matoba, Y. / Kawano, Y. / Sugiyama, M.
#3: 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. / Sugiyama, M.
History
DepositionApr 26, 2000Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 26, 2001Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 4, 2017Group: Refinement description / Category: software
Revision 1.4Feb 7, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: BLEOMYCIN RESISTANCE DETERMINANT
B: BLEOMYCIN RESISTANCE DETERMINANT
C: BLEOMYCIN RESISTANCE DETERMINANT
D: BLEOMYCIN RESISTANCE DETERMINANT
E: BLEOMYCIN RESISTANCE DETERMINANT
F: BLEOMYCIN RESISTANCE DETERMINANT
G: BLEOMYCIN RESISTANCE DETERMINANT
H: BLEOMYCIN RESISTANCE DETERMINANT
hetero molecules


Theoretical massNumber of molelcules
Total (without water)124,01216
Polymers112,6798
Non-polymers11,3328
Water86548
1
A: BLEOMYCIN RESISTANCE DETERMINANT
B: BLEOMYCIN RESISTANCE DETERMINANT
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,0034
Polymers28,1702
Non-polymers2,8332
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6250 Å2
ΔGint-28 kcal/mol
Surface area10590 Å2
MethodPISA
2
C: BLEOMYCIN RESISTANCE DETERMINANT
D: BLEOMYCIN RESISTANCE DETERMINANT
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,0034
Polymers28,1702
Non-polymers2,8332
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6120 Å2
ΔGint-28 kcal/mol
Surface area10640 Å2
MethodPISA
3
E: BLEOMYCIN RESISTANCE DETERMINANT
F: BLEOMYCIN RESISTANCE DETERMINANT
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,0034
Polymers28,1702
Non-polymers2,8332
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6160 Å2
ΔGint-28 kcal/mol
Surface area10580 Å2
MethodPISA
4
G: BLEOMYCIN RESISTANCE DETERMINANT
H: BLEOMYCIN RESISTANCE DETERMINANT
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,0034
Polymers28,1702
Non-polymers2,8332
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6160 Å2
ΔGint-28 kcal/mol
Surface area10520 Å2
MethodPISA
Unit cell
Length a, b, c (Å)115.270, 117.000, 79.860
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
DetailsThe biological assembly is a homodimer

-
Components

#1: Protein
BLEOMYCIN RESISTANCE DETERMINANT


Mass: 14084.935 Da / Num. of mol.: 8 / Fragment: CORE DOMAIN
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Klebsiella pneumoniae (bacteria) / Description: CULTURE BROTH / Gene: TRANSPOSON TN5 / Plasmid: PKKTRP / Production host: Streptomyces verticillus (bacteria) / References: UniProt: P13081
#2: Chemical
ChemComp-BLM / BLEOMYCIN A2 / N1-[3-(DIMETHYLSULFONIO)-PROPYL]BLEOMYCINAMIDE


Mass: 1416.560 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C55H85N17O21S3 / Comment: medication*YM
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 48 / 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: 2.39 Å3/Da / Density % sol: 48.5 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 5
Details: PEG 8000, ammonium sulfate, magnesium chloride, 2-(N-morpholino)-etanesulfonic acid, pH 5.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal grow
*PLUS
Temperature: 25 ℃
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
114 mg/mlprotein1drop
215 %PEG60001reservoir
30.1 Mammonium sulfate1reservoir
40.02 Mmagnesium chloride1reservoir
50.05 MMES-NaOH1reservoir

-
Data collection

DiffractionMean temperature: 293 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU300 / Wavelength: 1.5418
DetectorType: RIGAKU RAXIS IIC / Detector: IMAGE PLATE / Date: Mar 20, 1999
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.5→100 Å / Num. all: 31016 / Num. obs: 27188 / % possible obs: 70 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 2.03 % / Biso Wilson estimate: 16.1 Å2 / Rmerge(I) obs: 0.125 / Net I/σ(I): 4.06
Reflection shellResolution: 2.5→2.75 Å / Rmerge(I) obs: 0.372 / Num. unique all: 7014 / % possible all: 56.9
Reflection
*PLUS
% possible obs: 70.1 % / Num. measured all: 62934
Reflection shell
*PLUS
% possible obs: 56.9 %

-
Processing

Software
NameVersionClassification
X-PLORmodel building
X-PLOR3.851refinement
X-PLORphasing
RefinementResolution: 2.5→30 Å / Rfactor Rfree error: 0.008 / Data cutoff high absF: 10000000 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.302 1313 4.9 %RANDOM
Rwork0.218 ---
all0.225 27188 --
obs0.218 27018 71 %-
Displacement parametersBiso mean: 29.5 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.47 Å0.32 Å
Luzzati d res low-5 Å
Luzzati sigma a0.72 Å0.48 Å
Refinement stepCycle: LAST / Resolution: 2.5→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7536 0 768 48 8352
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONx_bond_d0.007
X-RAY DIFFRACTIONx_angle_deg1.3
X-RAY DIFFRACTIONx_dihedral_angle_d28.6
X-RAY DIFFRACTIONx_improper_angle_d0.67
X-RAY DIFFRACTIONx_mcbond_it3.551.5
X-RAY DIFFRACTIONx_mcangle_it5.382
X-RAY DIFFRACTIONx_scbond_it5.762
X-RAY DIFFRACTIONx_scangle_it7.822.5
LS refinement shellResolution: 2.5→2.66 Å / Rfactor Rfree error: 0.032 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.431 184 5.1 %
Rwork0.333 3448 -
obs--58.3 %
Software
*PLUS
Name: X-PLOR / Version: 3.851 / Classification: refinement
Refinement
*PLUS
Rfactor Rwork: 0.221
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_angle_deg1.2
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_deg28.6
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg0.57

+
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