[English] 日本語
Yorodumi
- PDB-3bw3: Crystal structures and site-directed mutagenesis study of nitroal... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 3bw3
TitleCrystal structures and site-directed mutagenesis study of nitroalkane oxidase from Streptomyces ansochromogenes
Components2-nitropropane dioxygenase
KeywordsOXIDOREDUCTASE / TIM barrel / Dioxygenase
Function / homology
Function and homology information


nitronate monooxygenase activity / dioxygenase activity / response to toxic substance / nucleotide binding
Similarity search - Function
Nitronate monooxygenase / Nitronate monooxygenase / Aldolase class I / Aldolase-type TIM barrel / TIM Barrel / Alpha-Beta Barrel / Alpha Beta
Similarity search - Domain/homology
FLAVIN MONONUCLEOTIDE / nitroethane / Propionate 3-nitronate monooxygenase
Similarity search - Component
Biological speciesStreptomyces ansochromogenes (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 Å
AuthorsLi, Y.H. / Gao, Z.Q. / Hou, H.F.
CitationJournal: Biochem.Biophys.Res.Commun. / Year: 2011
Title: Crystal structure and site-directed mutagenesis of a nitroalkane oxidase from Streptomyces ansochromogenes
Authors: Li, Y.H. / Gao, Z.Q. / Hou, H.F. / Li, L. / Zhang, J.H. / Yang, H.H. / Dong, Y.H. / Tan, H.R.
History
DepositionJan 8, 2008Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Jan 13, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Aug 10, 2011Group: Database references
Revision 1.3Nov 1, 2023Group: 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_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_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: 2-nitropropane dioxygenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,2895
Polymers38,5211
Non-polymers7684
Water2,864159
1
A: 2-nitropropane dioxygenase
hetero molecules

A: 2-nitropropane dioxygenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)78,57810
Polymers77,0432
Non-polymers1,5368
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation6_564x,-y+3/2,-z-3/41
Buried area5940 Å2
ΔGint-60.3 kcal/mol
Surface area24460 Å2
MethodPISA
Unit cell
Length a, b, c (Å)113.465, 113.465, 115.585
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number98
Space group name H-MI4122

-
Components

#1: Protein 2-nitropropane dioxygenase


Mass: 38521.305 Da / Num. of mol.: 1 / Mutation: H179D
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptomyces ansochromogenes (bacteria)
Strain: 7100 / Gene: 2-npdl / Plasmid: pET23b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q9FDD4, nitroalkane oxidase
#2: Chemical ChemComp-FMN / FLAVIN MONONUCLEOTIDE / RIBOFLAVIN MONOPHOSPHATE


Mass: 456.344 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C17H21N4O9P
#3: Chemical ChemComp-NIE / nitroethane


Mass: 75.067 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H5NO2
#4: Chemical ChemComp-MPD / (4S)-2-METHYL-2,4-PENTANEDIOL


Mass: 118.174 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H14O2 / Comment: precipitant*YM
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 159 / 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: 2.41 Å3/Da / Density % sol: 49.05 %
Crystal growTemperature: 289 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: 0.2M ammonium dihydrogen phosphate, 0.1M Tris-Cl, 50% MPD, pH8.5, VAPOR DIFFUSION, HANGING DROP, temperature 289K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: BSRF / Beamline: 1W2B / Wavelength: 1 Å
DetectorType: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: Jun 10, 2007
RadiationMonochromator: Si 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.8→10 Å / Num. all: 34891 / Num. obs: 30092 / % possible obs: 86.2 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Redundancy: 10.5 % / Rmerge(I) obs: 0.08
Reflection shellResolution: 1.8→1.86 Å / Redundancy: 10.4 % / Rmerge(I) obs: 0.489 / Num. unique all: 3436 / % possible all: 100

-
Processing

Software
NameClassification
HKL-2000data collection
MOLREPphasing
CNSrefinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3BW2

3bw2


Resolution: 2.2→10 Å / σ(F): 1 / Stereochemistry target values: maximum likelihood
RfactorNum. reflection% reflectionSelection details
Rfree0.207 888 4.6 %RANDOM
Rwork0.185 ---
obs0.185 18777 97.7 %-
all-19215 --
Displacement parametersBiso mean: 18.67 Å2
Baniso -1Baniso -2Baniso -3
1--1.128 Å20 Å20 Å2
2---1.128 Å20 Å2
3---2.255 Å2
Refinement stepCycle: LAST / Resolution: 2.2→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2524 0 52 159 2735
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.007
X-RAY DIFFRACTIONc_angle_deg1.36
X-RAY DIFFRACTIONc_dihedral_angle_d22.2
X-RAY DIFFRACTIONc_improper_angle_d1.18
Xplor file
Refine-IDSerial noParam file
X-RAY DIFFRACTION1protein_rep.param
X-RAY DIFFRACTION2water_rep.param
X-RAY DIFFRACTION3FMN.param
X-RAY DIFFRACTION4MPD.param
X-RAY DIFFRACTION5NIE.param

+
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