[English] 日本語
Yorodumi
- PDB-7v4f: Unique non-heme hydroxylase in biosynthesis of nucleoside antibio... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 7v4f
TitleUnique non-heme hydroxylase in biosynthesis of nucleoside antibiotic pathway uncover mechanism of reaction
ComponentsBeta-hydroxylase
KeywordsANTIBIOTIC / caprazamycin / MraY / beta-hydroxylase
Function / homology
Function and homology information


B-lactam Antibiotic, Isopenicillin N Synthase; Chain / Isopenicillin N synthase-like superfamily / Jelly Rolls / Sandwich / Mainly Beta
Similarity search - Domain/homology
Chem-5KC / CARBON DIOXIDE / : / SUCCINIC ACID / Beta-hydroxylase
Similarity search - Component
Biological speciesStreptomyces sp. MK730-62F2 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.98 Å
AuthorsLi, T.L. / Saeid, M.Z.
Funding support Taiwan, 1items
OrganizationGrant numberCountry
Academia Sinica (Taiwan) Taiwan
CitationJournal: Commun Chem / Year: 2022
Title: beta-Hydroxylation of alpha-amino-beta-hydroxylbutanoyl-glycyluridine catalyzed by a nonheme hydroxylase ensures the maturation of caprazamycin
Authors: Zadeh, S.M. / Chen, M.H. / Wang, Z.C. / Astani, E.K. / Lo, I.W. / Lin, K.H. / Hsu, N.S. / Adhikari, K. / Lyu, S.Y. / Tsai, H.Y. / Terasawa, Y. / Yabe, M. / Yamamoto, K. / Ichikawa, S. / Li, T.L.
History
DepositionAug 13, 2021Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Feb 23, 2022Provider: repository / Type: Initial release
Revision 1.1Aug 10, 2022Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Nov 29, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
B: Beta-hydroxylase
A: Beta-hydroxylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)42,87710
Polymers42,1822
Non-polymers6968
Water3,081171
1
B: Beta-hydroxylase
hetero molecules

B: Beta-hydroxylase
hetero molecules

A: Beta-hydroxylase
hetero molecules

A: Beta-hydroxylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)85,75520
Polymers84,3634
Non-polymers1,39116
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_555y,x,-z1
crystal symmetry operation2_555-x,-y,z+1/21
crystal symmetry operation8_554-y,-x,-z-1/21
Buried area6210 Å2
ΔGint-89 kcal/mol
Surface area29560 Å2
MethodPISA
Unit cell
Length a, b, c (Å)82.049, 82.049, 103.893
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212
Components on special symmetry positions
IDModelComponents
11B-205-

FE

21B-343-

HOH

31A-349-

HOH

41A-355-

HOH

-
Components

-
Protein , 1 types, 2 molecules BA

#1: Protein Beta-hydroxylase


Mass: 21090.766 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptomyces sp. MK730-62F2 (bacteria) / Gene: cpz10
Production host: Escherichia coli-Pichia pastoris shuttle vector pPpGUT1 (others)
References: UniProt: C4NCJ7

-
Non-polymers , 5 types, 179 molecules

#2: Chemical ChemComp-5KC / (2S,3S)-2-azanyl-4-(2-hydroxy-2-oxoethylamino)-3-oxidanyl-butanoic acid


Mass: 192.170 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H12N2O5 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-SIN / SUCCINIC ACID


Mass: 118.088 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C4H6O4
#4: Chemical ChemComp-CO2 / CARBON DIOXIDE


Mass: 44.010 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: CO2
#5: Chemical
ChemComp-FE / FE (III) ION


Mass: 55.845 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Fe
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 171 / 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: 2.07 Å3/Da / Density % sol: 40.65 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / Details: 0.2M ammonium sulfate 12% V/V PEG 8K 10 mg

-
Data collection

DiffractionMean temperature: 80 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: NSRRC / Beamline: BL15A1 / Wavelength: 0.99 Å
DetectorType: RAYONIX MX300HE / Detector: CCD / Date: Nov 13, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.99 Å / Relative weight: 1
ReflectionResolution: 1.97→26.48 Å / Num. obs: 25823 / % possible obs: 100 % / Redundancy: 9.8 % / CC1/2: 0.905 / Net I/σ(I): 33.5
Reflection shellResolution: 1.97→2.04 Å / Num. unique obs: 2497 / CC1/2: 0.907

-
Processing

Software
NameVersionClassification
PHENIX(1.18.2_3874: ???)refinement
PDB_EXTRACT3.27data extraction
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4P7X

4p7x


Resolution: 1.98→26.46 Å / SU ML: 0.24 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 25.65 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.251 3041 7.89 %
Rwork0.1911 --
obs0.1959 25285 81.69 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.98→26.46 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2772 0 4 171 2947
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0082852
X-RAY DIFFRACTIONf_angle_d1.133869
X-RAY DIFFRACTIONf_dihedral_angle_d26.342391
X-RAY DIFFRACTIONf_chiral_restr0.065419
X-RAY DIFFRACTIONf_plane_restr0.007511
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.98-2.010.3263880.26231024X-RAY DIFFRACTION51
2.01-2.040.2832880.25181019X-RAY DIFFRACTION52
2.04-2.080.3445890.25041044X-RAY DIFFRACTION53
2.08-2.120.2888890.23931048X-RAY DIFFRACTION53
2.12-2.160.3223950.22981066X-RAY DIFFRACTION54
2.16-2.20.2584910.23191080X-RAY DIFFRACTION55
2.2-2.250.2859970.22881128X-RAY DIFFRACTION57
2.25-2.30.26971040.22151272X-RAY DIFFRACTION64
2.3-2.360.3341240.20871505X-RAY DIFFRACTION75
2.36-2.420.28961540.21981720X-RAY DIFFRACTION88
2.42-2.490.30751630.21981918X-RAY DIFFRACTION97
2.49-2.580.28181650.21811955X-RAY DIFFRACTION99
2.58-2.670.30941740.22511976X-RAY DIFFRACTION100
2.67-2.770.30861660.19881975X-RAY DIFFRACTION100
2.77-2.90.30731710.21631975X-RAY DIFFRACTION100
2.9-3.050.29071720.20891987X-RAY DIFFRACTION100
3.05-3.240.29961700.21011964X-RAY DIFFRACTION100
3.24-3.490.21341660.17951954X-RAY DIFFRACTION100
3.49-3.840.25081720.16521967X-RAY DIFFRACTION100
3.84-4.40.18371710.14721983X-RAY DIFFRACTION100
4.4-5.530.16931700.15091988X-RAY DIFFRACTION100
5.53-26.460.21841620.181948X-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