[English] 日本語
Yorodumi
- PDB-1xds: Crystal structure of Aclacinomycin-10-hydroxylase (RdmB) in compl... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1xds
TitleCrystal structure of Aclacinomycin-10-hydroxylase (RdmB) in complex with S-adenosyl-L-methionine (SAM) and 11-deoxy-beta-rhodomycin (DbrA)
ComponentsProtein RdmB
KeywordsTRANSFERASE / Anthracycline / hydroxylase / S-adenosyl-L-methionine / streptomyces / polyketide antibiotics / divergent evolution / Structural Proteomics in Europe / SPINE / Structural Genomics
Function / homology
Function and homology information


Lyases; Carbon-carbon lyases; Carboxy-lyases / O-methyltransferase activity / carboxy-lyase activity / S-adenosylmethionine-dependent methyltransferase activity / antibiotic biosynthetic process
Similarity search - Function
Helix Hairpins - #1350 / O-methyltransferase domain / O-methyltransferase domain / SAM-dependent O-methyltransferase class II-type profile. / O-methyltransferase COMT-type / Vaccinia Virus protein VP39 / Winged helix-like DNA-binding domain superfamily/Winged helix DNA-binding domain / Helix Hairpins / Arc Repressor Mutant, subunit A / Winged helix DNA-binding domain superfamily ...Helix Hairpins - #1350 / O-methyltransferase domain / O-methyltransferase domain / SAM-dependent O-methyltransferase class II-type profile. / O-methyltransferase COMT-type / Vaccinia Virus protein VP39 / Winged helix-like DNA-binding domain superfamily/Winged helix DNA-binding domain / Helix Hairpins / Arc Repressor Mutant, subunit A / Winged helix DNA-binding domain superfamily / Winged helix-like DNA-binding domain superfamily / S-adenosyl-L-methionine-dependent methyltransferase superfamily / Rossmann fold / Orthogonal Bundle / 3-Layer(aba) Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
11-DEOXY-BETA-RHODOMYCIN / S-ADENOSYLMETHIONINE / Aclacinomycin 10-hydroxylase RdmB
Similarity search - Component
Biological speciesStreptomyces purpurascens (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
AuthorsJansson, A. / Koskiniemi, H. / Erola, A. / Wang, J. / Mantsala, P. / Schneider, G. / Niemi, J. / Structural Proteomics in Europe (SPINE)
CitationJournal: J.Biol.Chem. / Year: 2005
Title: Aclacinomycin 10-Hydroxylase Is a Novel Substrate-assisted Hydroxylase Requiring S-Adenosyl-L-methionine as Cofactor
Authors: Jansson, A. / Koskiniemi, H. / Erola, A. / Wang, J. / Schneider, G. / Niemi, J.
History
DepositionSep 8, 2004Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 23, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Apr 3, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details / _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: Protein RdmB
B: Protein RdmB
hetero molecules


Theoretical massNumber of molelcules
Total (without water)82,6696
Polymers80,3322
Non-polymers2,3374
Water2,126118
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area10090 Å2
ΔGint-71 kcal/mol
Surface area27790 Å2
MethodPISA
Unit cell
Length a, b, c (Å)79.890, 79.890, 232.598
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Cell settingtrigonal
Space group name H-MP3221

-
Components

#1: Protein Protein RdmB


Mass: 40166.207 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptomyces purpurascens (bacteria) / Gene: rdmb / Plasmid: pRDM16 from pGEX4T-3 / Production host: Escherichia coli (E. coli) / References: UniProt: Q54527
#2: Chemical ChemComp-SAM / S-ADENOSYLMETHIONINE / S-Adenosyl methionine


Mass: 398.437 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C15H22N6O5S
#3: Chemical ChemComp-DRA / 11-DEOXY-BETA-RHODOMYCIN


Mass: 769.831 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C40H51NO14
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 118 / 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: 2.88 Å3/Da / Density % sol: 56.9 %
Crystal growTemperature: 294 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: cobalt chloride, ammonium sulphate, MES-buffer, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 294K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-1 / Wavelength: 0.934 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Jan 31, 2003
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.934 Å / Relative weight: 1
ReflectionResolution: 2.29→76 Å / Num. all: 38051 / Num. obs: 38051 / % possible obs: 99.4 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 11.4 % / Biso Wilson estimate: 45 Å2 / Rsym value: 0.06 / Net I/σ(I): 14.4
Reflection shellResolution: 2.29→2.41 Å / Mean I/σ(I) obs: 5.3 / Rsym value: 0.187 / % possible all: 73.7

-
Processing

Software
NameVersionClassification
MOSFLMdata reduction
SCALAdata scaling
PHASERphasing
REFMAC5.1.24refinement
CCP4(SCALA)data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: RdmB+SAM complex

Resolution: 2.3→76 Å / Isotropic thermal model: Isotropic B-factors for each atom / Cross valid method: THROUGHOUT / Details: Hydrogens have been added in the riding position
RfactorNum. reflection% reflectionSelection details
Rfree0.29613 1910 -RANDOM
Rwork0.25102 ---
obs0.25324 36141 95.83 %-
all-37903 --
Displacement parametersBiso mean: 38.043 Å2
Baniso -1Baniso -2Baniso -3
1-2.43 Å22.43 Å2-3.65 Å2
2--1.22 Å20 Å2
3---0 Å2
Refinement stepCycle: LAST / Resolution: 2.3→76 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5035 0 164 118 5317
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONr_bond_refined_d0.013
X-RAY DIFFRACTIONr_angle_refined_deg1.496
LS refinement shellResolution: 2.3→2.38 Å /
RfactorNum. reflection
Rfree0.34 145
Rwork0.3 -
obs-2383

+
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