[English] 日本語
Yorodumi
- PDB-5z9i: Identification of the functions of unusual cytochrome p450-like m... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 5z9i
TitleIdentification of the functions of unusual cytochrome p450-like monooxygenases involved in microbial secondary metablism
ComponentsPutative P450-like enzyme
KeywordsOXIDOREDUCTASE / cytochrome p450 / monooxygenase
Function / homology
Function and homology information


oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen / monooxygenase activity / iron ion binding / heme binding
Similarity search - Function
Cytochrome P450, B-class / Cytochrome p450 / Cytochrome P450 / Cytochrome P450 / Cytochrome P450 superfamily / Cytochrome P450 / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
PROTOPORPHYRIN IX CONTAINING FE / Putative P450-like enzyme
Similarity search - Component
Biological speciesStreptomyces himastatinicus ATCC 53653 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.199 Å
AuthorsLu, M. / Lin, L. / Zhang, C. / Chen, Y.
CitationJournal: Chembiochem / Year: 2020
Title: Riboflavin Is Directly Involved in the N-Dealkylation Catalyzed by Bacterial Cytochrome P450 Monooxygenases.
Authors: Zhang, C. / Lu, M. / Lin, L. / Huang, Z. / Zhang, R. / Wu, X. / Chen, Y.
History
DepositionFeb 3, 2018Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Feb 6, 2019Provider: repository / Type: Initial release
Revision 1.1May 6, 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.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Mar 27, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Putative P450-like enzyme
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,3862
Polymers44,7701
Non-polymers6161
Water2,036113
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1230 Å2
ΔGint-24 kcal/mol
Surface area16780 Å2
MethodPISA
Unit cell
Length a, b, c (Å)57.987, 72.492, 98.829
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

-
Components

#1: Protein Putative P450-like enzyme


Mass: 44769.738 Da / Num. of mol.: 1 / Mutation: L340F
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptomyces himastatinicus ATCC 53653 (bacteria)
Gene: hmtS / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: G0LWB2
#2: Chemical ChemComp-HEM / PROTOPORPHYRIN IX CONTAINING FE / HEME


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


Mass: 18.015 Da / Num. of mol.: 113 / 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: 2.32 Å3/Da / Density % sol: 46.98 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / Details: PEG 3350, Bis-Tris hydrochloride, ammonium acetate

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL18U1 / Wavelength: 0.97791 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Apr 14, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97791 Å / Relative weight: 1
ReflectionResolution: 2.2→45.282 Å / Num. obs: 40569 / % possible obs: 99.1 % / Redundancy: 3.442 % / Biso Wilson estimate: 36.63 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.065 / Rrim(I) all: 0.077 / Χ2: 1.03 / Net I/σ(I): 13.17 / Num. measured all: 139630
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. possibleNum. unique obsCC1/2Rrim(I) all% possible all
2.2-2.333.2140.442.8820699663564400.8260.52697.1
2.33-2.493.5120.3314.1921659618461680.9080.3999.7
2.49-2.693.530.2086.2620297576957500.9570.24599.7
2.69-2.953.3910.1338.9218046533553210.980.15799.7
2.95-3.293.580.08513.917238483348150.9910.199.6
3.29-3.83.3840.05121.414263424342150.9960.0699.3
3.8-4.653.5730.03830.3812756358035700.9970.04599.7
4.65-6.543.4110.03630.369408278127580.9970.04399.2
6.54-45.2823.4360.02837.345264155715320.9980.03498.4

-
Processing

Software
NameVersionClassification
PHENIX1.8.4_1496refinement
XSCALEdata scaling
PDB_EXTRACT3.24data extraction
DENZOdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.199→45.282 Å / FOM work R set: 0.8494 / SU ML: 0.26 / Cross valid method: THROUGHOUT / σ(F): 1.36 / Phase error: 22.72 / Stereochemistry target values: ML
Details: THE STRUCTURE FACTOR FILE CONTAINS FRIEDEL PAIRS IN I_PLUS/MINUS COLUMNS
RfactorNum. reflection% reflection
Rfree0.2336 3715 9.16 %
Rwork0.1831 36853 -
obs0.1877 40568 99.15 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 121.67 Å2 / Biso mean: 47.32 Å2 / Biso min: 19.77 Å2
Refinement stepCycle: final / Resolution: 2.199→45.282 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2911 0 43 113 3067
Biso mean--20 43.76 -
Num. residues----386
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0093041
X-RAY DIFFRACTIONf_angle_d1.4714159
X-RAY DIFFRACTIONf_chiral_restr0.046464
X-RAY DIFFRACTIONf_plane_restr0.006544
X-RAY DIFFRACTIONf_dihedral_angle_d13.4541083
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 27

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.1989-2.22680.28541250.23971240136590
2.2268-2.25610.31391360.23651352148899
2.2561-2.2870.30651390.24071365150499
2.287-2.31960.2791380.234513751513100
2.3196-2.35430.28791410.231213661507100
2.3543-2.39110.28991370.22441362149999
2.3911-2.43030.28961450.220113801525100
2.4303-2.47220.29011360.218813631499100
2.4722-2.51710.30971330.204814021535100
2.5171-2.56550.27191410.20713591500100
2.5655-2.61790.2341370.200113691506100
2.6179-2.67480.23411410.206813791520100
2.6748-2.7370.26851420.201313881530100
2.737-2.80540.25121290.18871345147499
2.8054-2.88130.21271370.181913901527100
2.8813-2.96610.24421380.189513731511100
2.9661-3.06180.2641410.184613751516100
3.0618-3.17120.28321340.198113751509100
3.1712-3.29810.23761380.182813741512100
3.2981-3.44820.21431380.177513691507100
3.4482-3.62990.24361400.1641372151299
3.6299-3.85720.20651360.16351355149199
3.8572-4.15480.1471380.15613531491100
4.1548-4.57260.20541360.151214001536100
4.5726-5.23340.23521370.16491368150599
5.2334-6.59030.26231400.21061350149099
6.5903-45.29180.19981420.1631354149698
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)
11.2760.9785-0.10082.86570.5983.00390.3502-0.45330.19351.0344-0.414-0.0073-0.0206-0.41060.06720.6467-0.0827-0.01540.476-0.01460.2866-20.6587-12.729932.1109
21.5260.23880.08882.53770.64742.3211-0.02080.15660.0402-0.09250.0727-0.0598-0.1628-0.1092-0.05770.15150.034-0.00870.27350.00410.2403-11.3356-8.74267.6354
35.21330.2565-0.45624.0359-0.19982.7066-0.2266-0.13730.63650.19770.25260.0431-0.035-0.2178-0.03760.24510.0408-0.08230.4072-0.03910.3449-23.6385-13.67665.1513
41.75991.21360.44253.37020.53050.84760.153-0.2910.07040.6751-0.1583-0.385-0.0949-0.06130.03570.35640.0188-0.10610.3085-0.02020.3314-9.1451-5.217323.661
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 7 through 67 )A7 - 67
2X-RAY DIFFRACTION2chain 'A' and (resid 68 through 149 )A68 - 149
3X-RAY DIFFRACTION3chain 'A' and (resid 150 through 223 )A150 - 223
4X-RAY DIFFRACTION4chain 'A' and (resid 224 through 398 )A224 - 398

+
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