[English] 日本語
Yorodumi
- PDB-8yyq: Structure of the HitB F328L mutant -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 8yyq
TitleStructure of the HitB F328L mutant
ComponentsPutative ATP-dependent b-aminoacyl-ACP synthetase
KeywordsLIGASE / Hitachimycin / polyketide biosynthesis / ATP binding / adenylation
Function / homology
Function and homology information


amino acid activation for nonribosomal peptide biosynthetic process / secondary metabolite biosynthetic process / phosphopantetheine binding / nucleotide binding / metal ion binding / cytoplasm
Similarity search - Function
AMP-binding / ANL, N-terminal domain / AMP-binding enzyme C-terminal domain / AMP-binding enzyme, C-terminal domain / AMP-binding, conserved site / Putative AMP-binding domain signature. / AMP-dependent synthetase/ligase / AMP-binding enzyme / AMP-binding enzyme, C-terminal domain superfamily
Similarity search - Domain/homology
: / Putative ATP-dependent b-aminoacyl-ACP synthetase
Similarity search - Component
Biological speciesEmbleya scabrispora (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.95 Å
AuthorsWang, D. / Miyanaga, A. / Chisuga, T. / Kudo, F. / Eguchi, T.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: Chembiochem / Year: 2024
Title: Engineering the Substrate Specificity of (S)-beta-Phenylalanine Adenylation Enzyme HitB.
Authors: Wang, D. / Miyanaga, A. / Chisuga, T. / Kudo, F. / Eguchi, T.
History
DepositionApr 4, 2024Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jun 5, 2024Provider: repository / Type: Initial release
Revision 1.1Aug 14, 2024Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation_author.identifier_ORCID

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Putative ATP-dependent b-aminoacyl-ACP synthetase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)60,1602
Polymers59,6421
Non-polymers5191
Water4,017223
1
A: Putative ATP-dependent b-aminoacyl-ACP synthetase
hetero molecules

A: Putative ATP-dependent b-aminoacyl-ACP synthetase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)120,3204
Polymers119,2832
Non-polymers1,0372
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_645y+1,x-1,-z1
Buried area3520 Å2
ΔGint-3 kcal/mol
Surface area38460 Å2
MethodPISA
Unit cell
Length a, b, c (Å)67.574, 67.574, 196.846
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number152
Space group name H-MP3121

-
Components

#1: Protein Putative ATP-dependent b-aminoacyl-ACP synthetase


Mass: 59641.625 Da / Num. of mol.: 1 / Mutation: F328L
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Embleya scabrispora (bacteria) / Gene: hitB / Plasmid: pColdI / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0A0F7R6G7
#2: Chemical ChemComp-A1L0G / [(2~{R},3~{S},4~{R},5~{R})-5-(6-aminopurin-9-yl)-3,4-bis(oxidanyl)oxolan-2-yl]methyl ~{N}-[(3~{S})-3-azanyl-3-(3-cyanophenyl)propanoyl]sulfamate


Mass: 518.503 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C20H22N8O7S / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 223 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.18 Å3/Da / Density % sol: 43.46 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.6 / Details: PEG 400, calcium acetate, sodium acetate

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-5A / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Jul 4, 2022
RadiationMonochromator: Numerical link type Si(111) double crystal monochromator
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.95→50 Å / Num. obs: 39053 / % possible obs: 100 % / Redundancy: 8.8 % / CC1/2: 0.999 / Rmerge(I) obs: 0.078 / Net I/σ(I): 20.3
Reflection shellResolution: 1.95→2 Å / Redundancy: 4.5 % / Rmerge(I) obs: 0.636 / Mean I/σ(I) obs: 1.9 / Num. unique obs: 2699 / CC1/2: 0.776 / % possible all: 99.9

-
Processing

Software
NameVersionClassification
REFMAC5.8.0238refinement
PDB_EXTRACT3.27data extraction
XDSdata reduction
Aimlessdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.95→43.71 Å / Cor.coef. Fo:Fc: 0.957 / Cor.coef. Fo:Fc free: 0.929 / SU B: 8.767 / SU ML: 0.123 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.162 / ESU R Free: 0.159 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: U VALUES : WITH TLS ADDED HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.2445 1979 5.1 %RANDOM
Rwork0.1886 ---
obs0.1915 37009 99.96 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 100.31 Å2 / Biso mean: 38.115 Å2 / Biso min: 19.22 Å2
Baniso -1Baniso -2Baniso -3
1-0.89 Å20.44 Å20 Å2
2--0.89 Å20 Å2
3----2.88 Å2
Refinement stepCycle: final / Resolution: 1.95→43.71 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3706 0 36 223 3965
Biso mean--27.02 39.11 -
Num. residues----484
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0133832
X-RAY DIFFRACTIONr_bond_other_d0.0010.0173652
X-RAY DIFFRACTIONr_angle_refined_deg1.8481.6635222
X-RAY DIFFRACTIONr_angle_other_deg1.4091.5798385
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.0825480
X-RAY DIFFRACTIONr_dihedral_angle_2_deg28.47319.171217
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.0415582
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.4881548
X-RAY DIFFRACTIONr_chiral_restr0.0870.2497
X-RAY DIFFRACTIONr_gen_planes_refined0.010.024337
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02879
LS refinement shellResolution: 1.95→2.001 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.307 123 -
Rwork0.299 2696 -
all-2819 -
obs--99.79 %
Refinement TLS params.Method: refined / Origin x: 37.609 Å / Origin y: -31.152 Å / Origin z: -19.081 Å
111213212223313233
T0.0303 Å2-0.0054 Å20.0063 Å2-0.1015 Å20.0048 Å2--0.002 Å2
L0.2514 °2-0.1666 °20.3033 °2-0.114 °2-0.2449 °2--0.9467 °2
S-0.0014 Å °0.0382 Å °0.011 Å °-0.0029 Å °-0.0099 Å °-0.0075 Å °0.0194 Å °-0.1273 Å °0.0112 Å °

+
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