[English] 日本語
Yorodumi
- PDB-8z16: Crystal structure of DiatB mutant N57A -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 8z16
TitleCrystal structure of DiatB mutant N57A
ComponentsFlavin-dependent monooxygenase
KeywordsOXIDOREDUCTASE / FAD-dependent oxidoreductase
Function / homology
Function and homology information


N,N-dimethylaniline monooxygenase activity / NADP binding / flavin adenine dinucleotide binding
Similarity search - Function
: / Flavin monooxygenase FMO / Flavin monooxygenase-like / Flavin-binding monooxygenase-like / FAD/NAD(P)-binding domain superfamily
Similarity search - Domain/homology
: / FLAVIN-ADENINE DINUCLEOTIDE / NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE / Flavin-dependent monooxygenase
Similarity search - Component
Biological speciesStreptomyces ardesiacus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.419 Å
AuthorsPeng, M. / Wu, Q.L.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC) China
CitationJournal: Acs Catalysis / Year: 2024
Title: Bacterial Biosynthesis of Nitrile-Containing Natural Products: Basis for Recognition of Diversified Substrates
Authors: Peng, M. / Wu, Q. / Ma, L. / Teng, Z.J. / Hou, X. / Zhu, H. / Ju, J.
History
DepositionApr 10, 2024Deposition site: PDBJ / Processing site: PDBC
Revision 1.0Feb 19, 2025Provider: repository / Type: Initial release

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Flavin-dependent monooxygenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,6174
Polymers46,8161
Non-polymers1,8013
Water77543
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1490 Å2
ΔGint-10 kcal/mol
Surface area19520 Å2
MethodPISA
Unit cell
Length a, b, c (Å)67.928, 67.928, 381.657
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number178
Space group name H-MP6122

-
Components

#1: Protein Flavin-dependent monooxygenase


Mass: 46815.859 Da / Num. of mol.: 1 / Mutation: N57A
Source method: isolated from a genetically manipulated source
Details: Sequence reference for Streptomyces ardesiacus (285564) is not available in UniProt at the time of biocuration. Current sequence reference is from UniProt ID A0A7T1BYC5. GenBank Accession ...Details: Sequence reference for Streptomyces ardesiacus (285564) is not available in UniProt at the time of biocuration. Current sequence reference is from UniProt ID A0A7T1BYC5. GenBank Accession Number: PP691700 protein_id="WZN32524.1"
Source: (gene. exp.) Streptomyces ardesiacus (bacteria) / Production host: Escherichia coli (E. coli) / References: UniProt: A0A7T1BYC5
#2: Chemical ChemComp-FAD / FLAVIN-ADENINE DINUCLEOTIDE


Mass: 785.550 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C27H33N9O15P2 / Comment: FAD*YM
#3: Chemical ChemComp-NAP / NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE / 2'-MONOPHOSPHOADENOSINE 5'-DIPHOSPHORIBOSE


Mass: 743.405 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C21H28N7O17P3
#4: Chemical ChemComp-A1D7R / (2~{S})-2-azanyl-3-[6-(3-methylbut-2-enyl)-1~{H}-indol-3-yl]propanoic acid / 6-dimethylallyl-L-tryptophan


Type: L-peptide linking / Mass: 272.342 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C16H20N2O2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 43 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN
Has protein modificationN

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.57 Å3/Da / Density % sol: 52.21 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop
Details: 0.2 M Sodium citrate tribasic dihydrate and 18% w/v Polyethylene glycol 3,350

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL18U1 / Wavelength: 0.97946 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Jul 1, 2024
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97946 Å / Relative weight: 1
ReflectionResolution: 2.419→46.595 Å / Num. obs: 21263 / % possible obs: 100 % / Redundancy: 34.39 % / CC1/2: 0.9975 / Rmerge(I) obs: 0.5528 / Rpim(I) all: 0.0941 / Rrim(I) all: 0.561 / Net I/σ(I): 10
Reflection shellResolution: 2.419→2.506 Å / Redundancy: 32.79 % / Rmerge(I) obs: 3.3094 / Mean I/σ(I) obs: 1.09 / Num. unique obs: 1500 / CC1/2: 0.3618 / Rpim(I) all: 0.5768 / Rrim(I) all: 3.3605 / % possible all: 99.9

-
Processing

Software
NameVersionClassification
PHENIX(1.16_3549: ???)refinement
autoPXdata reduction
autoPXdata processing
PHASERphasing
Aimlessdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.419→46.595 Å / SU ML: 0.62 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 41.27 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.3453 1029 4.88 %
Rwork0.26 --
obs0.264 21084 99.38 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.419→46.595 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3252 0 121 43 3416
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0083464
X-RAY DIFFRACTIONf_angle_d1.0554741
X-RAY DIFFRACTIONf_dihedral_angle_d11.6591980
X-RAY DIFFRACTIONf_chiral_restr0.054513
X-RAY DIFFRACTIONf_plane_restr0.009612
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.419-2.54640.47291620.42972678X-RAY DIFFRACTION97
2.5464-2.7060.42931530.39272794X-RAY DIFFRACTION100
2.706-2.91490.48931330.35442807X-RAY DIFFRACTION100
2.9149-3.20810.38871360.32412840X-RAY DIFFRACTION100
3.2081-3.67220.34551380.27082868X-RAY DIFFRACTION100
3.6722-4.62590.32881500.21952909X-RAY DIFFRACTION100
4.6259-46.5950.28631570.20323159X-RAY DIFFRACTION99

+
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