[English] 日本語
Yorodumi
- PDB-8r2j: X-ray crystallographic structure of SwaQ2 in complex with NADP+ a... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 8r2j
TitleX-ray crystallographic structure of SwaQ2 in complex with NADP+ and doxorubicin
ComponentsNmrA family transcriptional regulator
KeywordsBIOSYNTHETIC PROTEIN / Polyketide / antibiotic / biosynthesis
Function / homologyDOXORUBICIN / NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE
Function and homology information
Biological speciesStreptomyces swartbergensis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.4 Å
AuthorsSchnell, R. / Schneider, G.
Funding support Sweden, 1items
OrganizationGrant numberCountry
Swedish Research Council2018-03999 Sweden
CitationJournal: Acs Catalysis / Year: 2024
Title: Mechanism of Two-Component Mono-Oxygenases Involved in Anthracycline 1-Hydroxylation
Authors: Wandi, B.N. / Dinis, P. / Siitonen, V. / Schneider, G. / Schnell, R. / Metsa-Ketele, M.
History
DepositionNov 6, 2023Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 7, 2024Provider: repository / Type: Initial release

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: NmrA family transcriptional regulator
B: NmrA family transcriptional regulator
hetero molecules


Theoretical massNumber of molelcules
Total (without water)66,5378
Polymers62,8762
Non-polymers3,6616
Water5,062281
1
A: NmrA family transcriptional regulator
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,2694
Polymers31,4381
Non-polymers1,8303
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: NmrA family transcriptional regulator
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,2694
Polymers31,4381
Non-polymers1,8303
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)87.313, 87.313, 174.382
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number170
Space group name H-MP65

-
Components

#1: Protein NmrA family transcriptional regulator


Mass: 31438.068 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: The N-terminal His6-tag used for purification was removed, the first residue, Ser1, is a remnant of the expression tag.
Source: (gene. exp.) Streptomyces swartbergensis (bacteria) / Gene: CA983_01310 / Plasmid: pBAD
Details (production host): N-terminal His6-tag, removable by TEV protease
Production host: Escherichia coli BL21(DE3) (bacteria)
#2: Chemical
ChemComp-DM2 / DOXORUBICIN / ADRIAMYCIN


Mass: 543.519 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C27H29NO11 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-NAP / NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE / 2'-MONOPHOSPHOADENOSINE 5'-DIPHOSPHORIBOSE


Mass: 743.405 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C21H28N7O17P3 / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 281 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 3.05 Å3/Da / Density % sol: 59.5 % / Description: needle
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 6.67 / Details: 0.1 M NaCacodylate pH6.67, 1M Na3-CITRATE

-
Data collection

DiffractionMean temperature: 110 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: MAX IV / Beamline: BioMAX / Wavelength: 0.976254 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Nov 19, 2022 / Details: MIRRORS
RadiationMonochromator: 0.976254 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.976254 Å / Relative weight: 1
ReflectionResolution: 2.4→29.08 Å / Num. obs: 27570 / % possible obs: 94.2 % / Redundancy: 4.1 % / Biso Wilson estimate: 39.5 Å2 / CC1/2: 0.992 / Rmerge(I) obs: 0.173 / Rpim(I) all: 0.087 / Net I/σ(I): 6.9
Reflection shellResolution: 2.4→2.49 Å / Redundancy: 4.1 % / Rmerge(I) obs: 0.774 / Mean I/σ(I) obs: 2 / Num. unique obs: 2894 / CC1/2: 0.722 / Rpim(I) all: 0.523 / % possible all: 93.8

-
Processing

Software
NameVersionClassification
REFMAC5.8.0257refinement
Aimlessdata scaling
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.4→29.08 Å / Cor.coef. Fo:Fc: 0.965 / Cor.coef. Fo:Fc free: 0.945 / SU B: 14.709 / SU ML: 0.179 / Cross valid method: THROUGHOUT / ESU R: 0.333 / ESU R Free: 0.217 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.20344 1444 5.3 %RANDOM
Rwork0.16127 ---
obs0.16353 26051 93.59 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 41.083 Å2
Baniso -1Baniso -2Baniso -3
1-0.79 Å20.4 Å20 Å2
2--0.79 Å2-0 Å2
3----2.58 Å2
Refinement stepCycle: 1 / Resolution: 2.4→29.08 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4182 0 252 281 4715
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0134603
X-RAY DIFFRACTIONr_bond_other_d0.0010.0174186
X-RAY DIFFRACTIONr_angle_refined_deg1.8141.6886326
X-RAY DIFFRACTIONr_angle_other_deg1.3821.5899635
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.8535558
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.0820.345261
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.52915664
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.7521550
X-RAY DIFFRACTIONr_chiral_restr0.0760.2591
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.025214
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021022
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.3392.2542206
X-RAY DIFFRACTIONr_mcbond_other1.3382.2532205
X-RAY DIFFRACTIONr_mcangle_it2.3353.3672754
X-RAY DIFFRACTIONr_mcangle_other2.3353.3682755
X-RAY DIFFRACTIONr_scbond_it1.7892.6582397
X-RAY DIFFRACTIONr_scbond_other1.7892.6582398
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other3.0333.9173566
X-RAY DIFFRACTIONr_long_range_B_refined6.34244.37919200
X-RAY DIFFRACTIONr_long_range_B_other6.28744.10818998
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.4→2.462 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.264 103 -
Rwork0.239 1920 -
obs--93.44 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
11.37710.3064-0.20721.2248-0.26282.01920.03210.10440.059-0.0887-0.05220.2093-0.1338-0.48760.02010.17960.0709-0.03560.2218-0.03110.0427-24.8863.29-8.846
20.9058-0.06210.01611.47150.17551.9987-0.0158-0.0496-0.13360.1047-0.0196-0.01950.4410.25850.03540.2060.0960.01250.19190.03670.02487.187-23.82-6.774
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 410
2X-RAY DIFFRACTION2B1 - 410

+
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