[English] 日本語
Yorodumi
- PDB-6vxv: Crystal structure of cyclo-L-Trp-L-Pro-bound cytochrome P450 NasF... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6vxv
TitleCrystal structure of cyclo-L-Trp-L-Pro-bound cytochrome P450 NasF5053 from Streptomyces sp. NRRL F-5053
Componentscytochrome P450 NasF5053
KeywordsOXIDOREDUCTASE / biosynthetic protein / cytochrome P450 / cyclodipeptide / regio-selecitivty / stereo-selectivity / pyrroloindoline alkaloids / radical mediated reaction / F5053 / Streptomyces
Function / homologyPROTOPORPHYRIN IX CONTAINING FE / Chem-QRP
Function and homology information
Biological speciesStreptomyces sp. NRRL F-5053 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.6 Å
AuthorsLuo, Z. / Jia, X. / Sun, C. / Qu, X. / Kobe, B.
Funding support Australia, China, 2items
OrganizationGrant numberCountry
National Health and Medical Research Council (NHMRC, Australia)1071659 Australia
National Natural Science Foundation of China (NSFC)31770063 China
CitationJournal: Nat Commun / Year: 2020
Title: Molecular basis of regio- and stereo-specificity in biosynthesis of bacterial heterodimeric diketopiperazines.
Authors: Sun, C. / Luo, Z. / Zhang, W. / Tian, W. / Peng, H. / Lin, Z. / Deng, Z. / Kobe, B. / Jia, X. / Qu, X.
History
DepositionFeb 24, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 11, 2020Provider: repository / Type: Initial release
Revision 1.1Dec 23, 2020Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Oct 11, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: cytochrome P450 NasF5053
hetero molecules


Theoretical massNumber of molelcules
Total (without water)44,7056
Polymers43,4591
Non-polymers1,2465
Water6,323351
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1550 Å2
ΔGint-42 kcal/mol
Surface area16220 Å2
MethodPISA
Unit cell
Length a, b, c (Å)42.314, 91.836, 93.604
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP22121
Space group name HallP22ab(z,x,y)
Symmetry operation#1: x,y,z
#2: x,-y,-z
#3: -x,y+1/2,-z+1/2
#4: -x,-y+1/2,z+1/2
Components on special symmetry positions
IDModelComponents
11A-832-

HOH

-
Components

-
Protein , 1 types, 1 molecules A

#1: Protein cytochrome P450 NasF5053


Mass: 43459.074 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptomyces sp. NRRL F-5053 (bacteria)
Production host: Escherichia coli BL21(DE3) (bacteria)
References: Oxidoreductases; Acting on paired donors, with incorporation or reduction of molecular oxygen

-
Non-polymers , 5 types, 356 molecules

#2: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#3: Chemical ChemComp-QRP / (3S,8aS)-3-(1H-indol-3-ylmethyl)hexahydropyrrolo[1,2-a]pyrazine-1,4-dione / Brevianamide F / cyclo-L-Trp-L-Pro


Mass: 283.325 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C16H17N3O2 / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-HEM / PROTOPORPHYRIN IX CONTAINING FE / HEME


Mass: 616.487 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C34H32FeN4O4 / Feature type: SUBJECT OF INVESTIGATION
#5: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Formula: Ca
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 351 / Source method: isolated from a natural source / Formula: H2O

-
Details

Has ligand of interestY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.09 Å3/Da / Density % sol: 41.22 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / Details: 0.2 M calcium chloride, 20% w/v PEG3350

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX2 / Wavelength: 0.954 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Aug 15, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.954 Å / Relative weight: 1
ReflectionResolution: 1.6→46.8 Å / Num. obs: 48951 / % possible obs: 99.9 % / Redundancy: 6.7 % / Biso Wilson estimate: 19.96 Å2 / CC1/2: 0.99 / Rmerge(I) obs: 0.085 / Rpim(I) all: 0.036 / Rrim(I) all: 0.092 / Χ2: 0.96 / Net I/σ(I): 11.8
Reflection shellResolution: 1.6→1.63 Å / Redundancy: 6.9 % / Rmerge(I) obs: 1.177 / Mean I/σ(I) obs: 1.7 / Num. unique obs: 2415 / CC1/2: 0.709 / Rpim(I) all: 0.476 / Rrim(I) all: 1.271 / % possible all: 99.7

-
Processing

Software
NameVersionClassification
PHENIX1.14_3260refinement
Blu-Icedata collection
XDSdata reduction
Aimlessdata scaling
PHASERphasing
PHENIXmodel building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 3ABB

3abb


Resolution: 1.6→46.8 Å / SU ML: 0.1716 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 21.0621 / Stereochemistry target values: CDL v1.2
RfactorNum. reflection% reflectionSelection details
Rfree0.2034 2431 4.97 %Random selection of 5% diffraction data
Rwork0.1696 46446 --
obs0.1712 48877 99.73 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 26.8 Å2
Refinement stepCycle: LAST / Resolution: 1.6→46.8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3038 0 87 351 3476
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00523241
X-RAY DIFFRACTIONf_angle_d0.93114428
X-RAY DIFFRACTIONf_chiral_restr0.0535476
X-RAY DIFFRACTIONf_plane_restr0.0048582
X-RAY DIFFRACTIONf_dihedral_angle_d16.04691913
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.6-1.630.30471510.28662681X-RAY DIFFRACTION99.54
1.63-1.670.30981290.27152667X-RAY DIFFRACTION99.36
1.67-1.710.25581540.2482689X-RAY DIFFRACTION99.41
1.71-1.750.2741600.23742655X-RAY DIFFRACTION99.75
1.75-1.80.29321330.21452722X-RAY DIFFRACTION99.65
1.8-1.850.22361510.19672677X-RAY DIFFRACTION99.68
1.85-1.910.21931580.17762700X-RAY DIFFRACTION99.86
1.91-1.980.25231180.17452721X-RAY DIFFRACTION99.89
1.98-2.060.24341260.17262719X-RAY DIFFRACTION99.58
2.06-2.150.21421420.16652735X-RAY DIFFRACTION99.72
2.15-2.260.20171410.15532717X-RAY DIFFRACTION99.86
2.26-2.410.22271550.16422721X-RAY DIFFRACTION99.83
2.41-2.590.19221340.16782744X-RAY DIFFRACTION99.83
2.59-2.850.20511480.1722766X-RAY DIFFRACTION99.97
2.85-3.270.17551520.16832764X-RAY DIFFRACTION99.9
3.27-4.110.16551380.14032806X-RAY DIFFRACTION99.97
4.11-46.80.18281410.15612962X-RAY DIFFRACTION99.71

+
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