[English] 日本語
Yorodumi
- PDB-8ppp: Amide bond synthetase from Streptomyces hindustanus K492H mutant ... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 8ppp
TitleAmide bond synthetase from Streptomyces hindustanus K492H mutant in complex with AMP-CPP
ComponentsFatty-acyl-CoA synthase
KeywordsLIGASE / Amide / Amide Bond Synthetase / ATP
Function / homology
Function and homology information


ligase activity, forming carbon-sulfur bonds
Similarity search - Function
: / 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
DIPHOSPHOMETHYLPHOSPHONIC ACID ADENOSYL ESTER / Fatty-acyl-CoA synthase
Similarity search - Component
Biological speciesStreptoalloteichus hindustanus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.57 Å
AuthorsTang, Q. / Grogan, G.
Funding support United Kingdom, 1items
OrganizationGrant numberCountry
Engineering and Physical Sciences Research CouncilEP/T01430X/1 United Kingdom
CitationJournal: Acs Catalysis / Year: 2024
Title: Broad Spectrum Enantioselective Amide Bond Synthetase from Streptoalloteichus hindustanus.
Authors: Tang, Q. / Petchey, M. / Rowlinson, B. / Burden, T.J. / Fairlamb, I.J.S. / Grogan, G.
History
DepositionJul 7, 2023Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 7, 2024Provider: repository / Type: Initial release

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Fatty-acyl-CoA synthase
B: Fatty-acyl-CoA synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)109,0564
Polymers108,0462
Non-polymers1,0102
Water6,179343
1
A: Fatty-acyl-CoA synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)54,5282
Polymers54,0231
Non-polymers5051
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Fatty-acyl-CoA synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)54,5282
Polymers54,0231
Non-polymers5051
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)82.700, 95.700, 87.200
Angle α, β, γ (deg.)90.00, 117.80, 90.00
Int Tables number4
Space group name H-MP1211

-
Components

#1: Protein Fatty-acyl-CoA synthase


Mass: 54022.930 Da / Num. of mol.: 2 / Mutation: K492H
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptoalloteichus hindustanus (bacteria)
Gene: SAMN05444320_10350 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0A1M5ABR5
#2: Chemical ChemComp-APC / DIPHOSPHOMETHYLPHOSPHONIC ACID ADENOSYL ESTER / ALPHA,BETA-METHYLENEADENOSINE-5'-TRIPHOSPHATE


Mass: 505.208 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C11H18N5O12P3 / Feature type: SUBJECT OF INVESTIGATION / Comment: AMP-CPP, energy-carrying molecule analogue*YM
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 343 / 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: 2.83 Å3/Da / Density % sol: 56.46 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 0.2 M lithium sulfate; 0.1 M HEPES pH 7.5; 25% PEG (w/v) 3350; 4 deg C.

-
Data collection

DiffractionMean temperature: 120 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.95881 Å
DetectorType: DECTRIS EIGER2 XE 16M / Detector: PIXEL / Date: Sep 16, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.95881 Å / Relative weight: 1
ReflectionResolution: 2.57→58.19 Å / Num. obs: 38357 / % possible obs: 99.8 % / Redundancy: 6.9 % / CC1/2: 1 / Rmerge(I) obs: 0.17 / Rpim(I) all: 0.1 / Net I/σ(I): 8.5
Reflection shellResolution: 2.57→2.68 Å / Rmerge(I) obs: 1.11 / Mean I/σ(I) obs: 1.7 / Num. unique obs: 4648 / CC1/2: 0.83 / Rpim(I) all: 0.67

-
Processing

Software
NameVersionClassification
REFMAC5.8.0411refinement
XDSdata reduction
SCALAdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.57→58.19 Å / Cor.coef. Fo:Fc: 0.954 / Cor.coef. Fo:Fc free: 0.92 / SU B: 13.669 / SU ML: 0.279 / Cross valid method: THROUGHOUT / ESU R: 0.69 / ESU R Free: 0.335 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.27554 1994 5.2 %RANDOM
Rwork0.2112 ---
obs0.21455 36345 99.79 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 37.599 Å2
Baniso -1Baniso -2Baniso -3
1--0.4 Å20 Å2-1.18 Å2
2--4.05 Å2-0 Å2
3----1.55 Å2
Refinement stepCycle: 1 / Resolution: 2.57→58.19 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7392 0 62 359 7813
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0127630
X-RAY DIFFRACTIONr_bond_other_d0.0010.0167143
X-RAY DIFFRACTIONr_angle_refined_deg1.4771.65310456
X-RAY DIFFRACTIONr_angle_other_deg0.4761.56516367
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.5265998
X-RAY DIFFRACTIONr_dihedral_angle_2_deg7.595563
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.452101089
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.0620.21223
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.029095
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021671
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it3.5833.9163992
X-RAY DIFFRACTIONr_mcbond_other3.5793.9173992
X-RAY DIFFRACTIONr_mcangle_it5.5587.0234984
X-RAY DIFFRACTIONr_mcangle_other5.5587.0244985
X-RAY DIFFRACTIONr_scbond_it4.0874.2583638
X-RAY DIFFRACTIONr_scbond_other4.0864.2593639
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other6.4217.6915471
X-RAY DIFFRACTIONr_long_range_B_refined8.7638.848623
X-RAY DIFFRACTIONr_long_range_B_other8.76238.688590
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.57→2.637 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.381 168 -
Rwork0.322 2653 -
obs--99.86 %

+
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