[English] 日本語
Yorodumi
- PDB-5l1s: X-ray Structure of F232L mutant of Cytochrome P450 PntM with pent... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 5l1s
TitleX-ray Structure of F232L mutant of Cytochrome P450 PntM with pentalenolactone F
ComponentsPentalenolactone synthase
KeywordsOXIDOREDUCTASE / PntM / cytochrome P450 / pentalenolactone F / mutant / F232L
Function / homology
Function and homology information


pentalenolactone synthase / pentalenolactone biosynthetic process / oxidoreductase activity, acting on the CH-CH group of donors, iron-sulfur protein as acceptor / oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen / antibiotic biosynthetic process / monooxygenase activity / iron ion binding / heme binding
Similarity search - Function
: / Cytochrome P450, B-class / Cytochrome p450 / Cytochrome P450 / Cytochrome P450, conserved site / Cytochrome P450 cysteine heme-iron ligand signature. / Cytochrome P450 / Cytochrome P450 superfamily / Cytochrome P450 / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
pentalenolactone F / PROTOPORPHYRIN IX CONTAINING FE / Pentalenolactone synthase
Similarity search - Component
Biological speciesStreptomyces arenae (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.08 Å
AuthorsDuan, L. / Jogl, G. / Cane, D.E.
CitationJournal: J.Am.Chem.Soc. / Year: 2016
Title: The Cytochrome P450-Catalyzed Oxidative Rearrangement in the Final Step of Pentalenolactone Biosynthesis: Substrate Structure Determines Mechanism.
Authors: Duan, L. / Jogl, G. / Cane, D.E.
History
DepositionJul 29, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 14, 2016Provider: repository / Type: Initial release
Revision 1.1Oct 12, 2016Group: Database references
Revision 1.2Oct 4, 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 / pdbx_struct_oper_list
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_oper_list.symmetry_operation

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Pentalenolactone synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,3663
Polymers44,4711
Non-polymers8952
Water8,701483
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)44.595, 164.145, 82.535
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP21212
Components on special symmetry positions
IDModelComponents
11A-504-

HOH

21A-664-

HOH

-
Components

#1: Protein Pentalenolactone synthase / Pentalenolactone biosynthesis protein M


Mass: 44470.793 Da / Num. of mol.: 1 / Mutation: F232L
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptomyces arenae (bacteria) / Strain: Tu469 / Gene: pntM / Plasmid: pET28a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: E3VWI3, pentalenolactone synthase
#2: Chemical ChemComp-7PF / pentalenolactone F / (2R,4a'R,7a'S,9a'R)-6',6'-dimethyl-3'-oxo-1',5',6',7',7a',9a'-hexahydro-3'H-spiro[oxirane-2,4'-pentaleno[1,6a-c]pyran]-9'-carboxylic acid


Mass: 278.300 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C15H18O5
#3: Chemical ChemComp-HEM / PROTOPORPHYRIN IX CONTAINING FE / HEME


Mass: 616.487 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C34H32FeN4O4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 483 / 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: 3.43 Å3/Da / Density % sol: 64.12 % / Mosaicity: 0.22 °
Crystal growTemperature: 288 K / Method: evaporation / pH: 9 / Details: Bicine, sodium citrate, glycerol

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU FR-E SUPERBRIGHT / Wavelength: 1.5418 Å
DetectorType: RIGAKU SATURN 944+ / Detector: CCD / Date: Oct 31, 2014 / Details: mirrors
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.08→45.6 Å / Num. obs: 37071 / % possible obs: 98.6 % / Redundancy: 7.1 % / Biso Wilson estimate: 16.19 Å2 / CC1/2: 0.993 / Rmerge(I) obs: 0.153 / Rpim(I) all: 0.062 / Rrim(I) all: 0.166 / Net I/σ(I): 11 / Num. measured all: 262065 / Scaling rejects: 294
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsCC1/2Diffraction-ID% possible all
2.08-2.134.80.550.724192.1
9.05-45.66.20.0450.998199.6

-
Processing

Software
NameVersionClassification
Aimless0.5.15data scaling
PHENIX1.10pre_2131refinement
PDB_EXTRACT3.2data extraction
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2x9p

2x9p


Resolution: 2.08→45.6 Å / SU ML: 0.19 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 18.35
RfactorNum. reflection% reflection
Rfree0.1931 1910 5.16 %
Rwork0.154 --
obs0.1561 37025 98.45 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 91.41 Å2 / Biso mean: 21.1409 Å2 / Biso min: 6.71 Å2
Refinement stepCycle: final / Resolution: 2.08→45.6 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3098 0 63 483 3644
Biso mean--12.05 31.13 -
Num. residues----397
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0083282
X-RAY DIFFRACTIONf_angle_d0.9764485
X-RAY DIFFRACTIONf_chiral_restr0.052498
X-RAY DIFFRACTIONf_plane_restr0.006593
X-RAY DIFFRACTIONf_dihedral_angle_d17.3762035
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 14

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.0756-2.12750.29011270.22612302242991
2.1275-2.1850.24711310.181924582589100
2.185-2.24930.18811230.16992441256497
2.2493-2.32190.25371260.16272475260199
2.3219-2.40490.211260.16092471259798
2.4049-2.50120.20391260.15762483260998
2.5012-2.6150.22171570.15782496265399
2.615-2.75280.19011410.163925002641100
2.7528-2.92530.20271360.16192494263099
2.9253-3.15110.19741470.16112527267499
3.1511-3.46810.21561190.14352566268599
3.4681-3.96970.17721530.134425382691100
3.9697-5.00040.11711410.121926192760100
5.0004-45.61510.18361570.154927452902100
Refinement TLS params.Method: refined / Origin x: 21.1166 Å / Origin y: 26.8118 Å / Origin z: 20.411 Å
111213212223313233
T0.0793 Å2-0.0073 Å2-0.0131 Å2-0.0867 Å2-0.0013 Å2--0.0913 Å2
L0.6573 °20.0572 °2-0.082 °2-0.7215 °2-0.1046 °2--0.7594 °2
S-0.0041 Å °-0.0275 Å °-0.0533 Å °-0.0011 Å °-0.0117 Å °-0.0294 Å °0.0224 Å °-0.0098 Å °0.0174 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1allX1
2X-RAY DIFFRACTION1allY501
3X-RAY DIFFRACTION1allA2 - 398
4X-RAY DIFFRACTION1allS1 - 483

+
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